diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000007.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e829ca9b5ba806f32663e2e817689bb1e8dd63b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000007.fa
@@ -0,0 +1,100 @@
+>ACLBLIBL_01214
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_00157
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01034
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01292
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01384
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE
+>MOLHKGIG_02077
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01011
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01104
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01112
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01114
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_02023
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE
+>LFPAFLNI_00588
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>LFPAFLNI_00590
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS
+>LFPAFLNI_01250
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>LFPAFLNI_01339
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH
+>LFPAFLNI_01885
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV
+>LFPAFLNI_02205
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000008.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a656559773c97404ad5212aae190cb72c84f7f02
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000008.fa
@@ -0,0 +1,83 @@
+>MOLHKGIG_00711
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MOLHKGIG_01398
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN
+>MOLHKGIG_01502
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN
+>MOLHKGIG_02225
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN
+>MOLHKGIG_02227
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV
+>MHAAABBN_00092
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_00343
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_01013
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_01394
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_02284
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_00606
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01016
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01158
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01349
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_02164
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000012.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14f264e6db5b58446df91d7eaa980214a84a2d6f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000012.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00720
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
+>ACLBLIBL_00722
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG
+>MOLHKGIG_00156
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL
+>MOLHKGIG_00159
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG
+>MOLHKGIG_01075
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>MOLHKGIG_02063
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>NAFOICDF_02223
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>MHAAABBN_00297
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>MHAAABBN_00338
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>MHAAABBN_00345
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>MHAAABBN_00794
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>LFPAFLNI_01024
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000017.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d29c920a4ebe5b4e2b0ba2745292ae354d25964
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000017.fa
@@ -0,0 +1,57 @@
+>ACLBLIBL_01236
+MRVHRRTVPVEHRSVVHGLTVTSPERTWADLCAVRPRWDEADLVAAGDHLVRHPWAGGGR
+LPPRTTVERLAEVLEALAPFHGVGRARAALGRVRVGADSAMETHARLALIDAGLGEPLLQ
+HKVAPDDPALAESDLYFADLRVALEYDGEHHLGRQQQARDARRDRRLLSYGVTPMRITAA
+DHAEGYRSVIAQLQQRRRAHDSPSEETARGES
+>MOLHKGIG_01559
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRARPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHALPMPTRAWRRRDPATGELEADPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTLVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPVSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGPSAST
+>MOLHKGIG_01658
+MPFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPALQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTGRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>MOLHKGIG_01845
+MPRRPAPLPPALAGRVFTRREALDRLSLSSDRLRSLDLRQVTHGAHRAVVDVPGSWAALG
+YPRPVAALPPEEAAVVVALTRGVASHLTAARLHGLVLPWWAEEDMRVHVSRPHRTGRTGR
+AGVACHGRTVPAEDRVEVHGVPVTSLERTWVDLCSLLRPDQVADAVVAGDALVNRPWVDG
+SRLPPRTTASRLSAALERAGRFKGVRVARAALALIRVGADSPPETRLRLALLDAGLPEPR
+LQAQLVSPAGERTDADMVVERSRVALHYDGGHHRTPEQQRRDARRDRLWQEAGHLSITVM
+GADLAEDFRTVVAAVVRHDRAARATSTISAPAPAAGLSNVKSGEWALSNVG
+>NAFOICDF_01147
+MLERVRVGADSAVVSLARLALVDAGLGEPLLQHRLDPWDPDCPETHMFSPELAVALEYDG
+GGHLTPAQQARDARRDRRLPARGVTPLRNTAEDHAEGYRRLIAQLQDRRRGR
+>MHAAABBN_01269
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPGLQAALEPEDPFSPVADVAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGHSAST
+>MHAAABBN_01363
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>LFPAFLNI_01486
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRITTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRWALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPFSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLSPSAST
+>LFPAFLNI_01588
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAELPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000020.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9af874847fb8e7ca8fc275d46a7519c7d07851ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000020.fa
@@ -0,0 +1,109 @@
+>ACLBLIBL_00405
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVLREGSVIGAVALE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>MOLHKGIG_00633
+MSTPHHHDHPTDQTAEHPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>MOLHKGIG_01289
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>NAFOICDF_00711
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQHTGHQGHAMDHGQHSGHT
+GLDEHGGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGY
+EVPGWAGWVAAALGTVMYVWGGRPFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATL
+GLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAALLPDEAERVEGENVVKV
+APADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATD
+SGLRVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWT
+LIGMPDEAVVRTITVLVIACPHALGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDA
+VLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEHPLAKAIVTAAKDKGFAL
+QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEAWRSEGAIILHVLRGGQ
+VVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPED
+KSAKVSQLQEEGKRVAMVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSV
+LSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGILAPVGLVLPMSIGAILMSASTVVVA
+LNAQLLRRIDLTPEASTRSVLERQK
+>NAFOICDF_02196
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>MHAAABBN_01008
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>LFPAFLNI_00598
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>LFPAFLNI_01247
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000026.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20bf4ff742dce62f5a03b07096b4139cb5607c1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000026.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00124
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR
+>MOLHKGIG_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR
+>NAFOICDF_00093
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR
+>MHAAABBN_00096
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD
+>MHAAABBN_00100
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR
+>MHAAABBN_02257
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR
+>LFPAFLNI_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000027.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af04e743771537b382216b3f972445252a09c21f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000027.fa
@@ -0,0 +1,68 @@
+>ACLBLIBL_00171
+MSALRRWSALAVLVLPVLLISIDMSVLGIAVPALSADLDPTSGQLLWIIDLYSFLLAGLL
+IFMGSLGDRIGRRRILLIGAPLFGAASLAAAFASSAEMLIAARALLGVGGATLMPSTLGL
+IRTIFPDRAERRTAIAVWAMAFSGGAALGPVVGGILLERFWWGSVFLMNVPVMAVFLLVA
+PFLLPESRDPSPGPFDPLSSVLSIAGIVGLVYALKTAAKSPDWTALAGLVVGATALAWFI
+ARQRRLAHPMIDVALFRNVAFTSAVSVNVISVFAFMGLMFFLPQFLMLVQGMGPAEAGLW
+MLPLAAAAVVGTLLAPLLARVVAVRTVILTGLALVIAGFAVGTRLDGAAPLVAFVLLSCL
+FGVGVGLAETLTNDVILTAAPPERAGAAAAISETGYEFGGAMGTAVLGTVGMAVYAARVQ
+EAAGLPGLGPADAEAAAQTLAAAHRIGEGLPDGGARLVEVANGAFTAGMDLVAGIGIGVA
+AVTLLLAWRGLRSEARVERPVED
+>ACLBLIBL_00191
+MVILNETIMSVALPRLMAEFTVTAATAQWLTTGFMLTMAVVIPFTGWLLNRMSLRAVFIL
+AMGTFTAGTAIAGLAPTFGLLLTGRVVQAVGTAIMMPLLMTTVLNVVPLSRRGRVMGLIS
+IVISVAPASGPAVGGVILEHLSWRWLFFTVLPIAAIALAAGAAWVRNVTEPRPVRLDVLS
+GVLSAVGFASLIFGLSSIGEAAAGNAAMPPWIPVAVGVLALALFAVRQLRLKDDALLDLR
+TLSRPTFTVALAVMLTSMLALFGTIVLLPIYLQEVLGWTTQQSGLALLPGGMVMALLGYV
+VGHLYDRVGAPPLIVPGAVLGAAGLWGYTFLSEDSSAFMVVGLHVLISTGLSMLFSPLMT
+TALSALPRSLYAHGSALVSTLQQVAGAAGTALFITLLTVGTASSVAGGLGEVASLMDGVH
+LAFLSGALVFTVNVVAVWFVKRPAPNPL
+>ACLBLIBL_02217
+MLSGTSTTSRGTGPAPVRAWLVLCAMSMLQFFIAVDVTVVNIALPSIGADLGVAGHSLTW
+VVVGYTITGGGLLMLGGRIGDLLGRRRTLLVGTSVFGAASLLAGLAPSFPVLVAARLLQG
+AGEAVALPAAMATIVLLFPEGPRRSRALSVWAAVASCGLVLGFALSGIITAHLGWRWVFL
+VSVPFILVVIVTALLLVPADRPASGGRVRLDLPGSLLLTACPLLFVYAAVEAGEPATGLW
+VSGVALLCAVLAAAGFVRVESRSPNPLVPLTFFADRARLRANLTTMLLSGALSTSFLLFT
+FYLQDRLGIGPLGAGLTMLPLAVALIVASVLVPRLLGRWGARACVLVGLGAAAGAMGVVA
+LVAVLGSGATWLLPAMLLIAAGMGFGLVGLQYIAVSGTTEEDAGIASGVQRASDQLGGAA
+GVAVYVGLGFAPALHADAGDPFVVAAVLAVVGLVVGAVVISRSPSTAAGQPQAG
+>ACLBLIBL_02334
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPSPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAVIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>MOLHKGIG_00169
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAALSPNPAFLIGARALLAVGAAAMMPATLALIRLAFNDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAIIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAASALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>MHAAABBN_00360
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>LFPAFLNI_02010
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAATALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000028.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b393ee5269a53f53c7466e6a4142ed038f0eb54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000028.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00251
+MSTSPSGSRVAEPGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITAYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQAGLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVA
+SGEEAAASHR
+>MOLHKGIG_00134
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>NAFOICDF_00186
+MNASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFYGSAGGIQTAG
+PGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAV
+VIVADTAAVTKYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIV
+AMIFGGLILMFTGASFTDGTPAGLHNLVDHGGFLPHGFGGVLIALTIVTFSFGGIETLGV
+AAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPFVQIFEGLGVP
+FAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLG
+VMVLGAILITVNPDAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFG
+IVGTVLGLAFVATVVITMATIPESRQALLIGLAWVVALTAAWFVTGVRKTAALHDRTGQL
+PVVHRHH
+>NAFOICDF_00187
+MQSTPAPEAPAQAQLQRGLNPRHITFIALGTAVGTGLFYGSAAGIQAAGPGVVLAFMLAG
+AAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVTV
+YMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMF
+SGASFQDGVTPGPHNLVEHGGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASA
+LPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPFVQIFETLGVPFAPHLLNFVVL
+TAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMSV
+KEDTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFV
+AVVAGTMAFDQGGAVLGALGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHD
+RHGTPPPLTWDV
+>NAFOICDF_02180
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGL
+SMRHIQFIALGSAIGTGLFYGSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPV
+PGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFGVYMGFWFPDTPRWIWVTAVI
+LFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMT
+MVVIMSLVPWDRITGEASPFVEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLF
+GMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNAVIPEDVFVVVASIATFATVW
+VWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWFSDTRVAMI
+VGLVWLVLLGAAYRLFLHGHGRSRPDLEEGAASSP
+>MHAAABBN_02148
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>LFPAFLNI_00142
+MSTSPFGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000029.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df569c65005f3bb60e5369a3ed2752bad1cd6b6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000029.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00292
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK
+>MOLHKGIG_00099
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>NAFOICDF_00617
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+>NAFOICDF_00670
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
+>MHAAABBN_02112
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>LFPAFLNI_00094
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>LFPAFLNI_02014
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000032.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b70e87f720accdfc599dbfa16e13a8ab3c56c982
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000032.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00398
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA
+>ACLBLIBL_01066
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
+>ACLBLIBL_02643
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ
+>MOLHKGIG_01808
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>NAFOICDF_01001
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA
+>MHAAABBN_01505
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>LFPAFLNI_01729
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000035.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8930af3014681c4ba99022816347a0af786394be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000035.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00413
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDRA
+ARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ
+>MOLHKGIG_01401
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>NAFOICDF_00326
+MAPSSYYAAKTRTPSARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELATLGW
+VHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK
+>NAFOICDF_00649
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>NAFOICDF_02217
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>MHAAABBN_01131
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQA
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>LFPAFLNI_01351
+MGSFSWPLTHSDAGSQFTSIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVR
+GPARPGPWRTVEDLELATLGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000046.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0403c35bec3fb01196f69c2e8614cc9bd5921583
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000046.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00837
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS
+>MOLHKGIG_02005
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>NAFOICDF_00774
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>MHAAABBN_01715
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>LFPAFLNI_00173
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>LFPAFLNI_00174
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA
+>LFPAFLNI_01943
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000047.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8a18eb3a7bff9f25df48ac06369e797e2c9a73d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000047.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00855
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD
+>ACLBLIBL_01010
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG
+>NAFOICDF_00792
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG
+>NAFOICDF_00870
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED
+>NAFOICDF_00943
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR
+>MHAAABBN_01696
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD
+>LFPAFLNI_00735
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000053.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..958fc3e93aa36620db7887d5584b81810a70dd18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000053.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_02181
+MRAPGVRGAVALGGAAGVVAGSTAMELVGVGGLLALAGRDGGVGLGPVAALAFAALPLAV
+VNVLGSFLLGLLLARSRHAGLDRRPALVAGLGTGFLGSFTTIATAAAVFLLTPLEAGWSA
+IAASSGVGGFLSATAGLLLPPLALLALLAALSTAAAVLGLRLGGAPARGADAEARVDGVA
+SDGTAADGAPA
+>MOLHKGIG_00749
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLAAAVAVLLVLALMAALSTAAAMLGLRAGGAPGSRVVGT
+DRSEEDA
+>NAFOICDF_00685
+MNAALIVVVALGGGAGAAGRFLLDGLINTGREFRLPVGTLTINITGSLLLGIIVGAATHL
+GAVPVAVLGTGVMGGYTTFSTASFETVRLARSGRITAAAINGLGMLVVSVAAATAGILLG
+GTL
+>NAFOICDF_00686
+MTTRTDTPMPDDQLPPDPDVDVSDPATTMRPVHLRWRYVGLVAVGGAGGTALRDVISSVL
+PADGGVSWSIFWINITGALALGVLLEALAHRGPDAGRRRVLRLLLGTGVLGGFTTYSTLA
+ESTAALFLDGHGLAGTGYALLTVLSGAIATACGLVVAGWFRPRTEEA
+>NAFOICDF_02076
+MADARPAAGGAAARRTLPWVALGGAAGALASLGAGALIAQAMGPGDPSISGPLGTASATL
+ASVAAVNVLGSFLLGLLRGASGRPGARWDPRLVAALGTGFLGAFTTFGTVAATLALPVMM
+TAGLAATGDTWWILLAVVVVGLLIAVAVLAALSTAAAALGLHLGGRGAGSGSAGRPDGAA
+A
+>MHAAABBN_00479
+MAARGEPTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLTAAASVLLVLALMAALSTAAAVLGLRAGGAPGSRVVGA
+DRSAEDA
+>LFPAFLNI_00713
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRCRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAASGAGGVLAAAVAVLLVLALMAALSTAAAVLGLRAGGAPGSRAVGT
+DRSAEDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000055.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21fcc22fd35ca9662c8c14d75651315192ef5989
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000055.fa
@@ -0,0 +1,35 @@
+>MOLHKGIG_02246
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>MOLHKGIG_02261
+MDHKQILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+DRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITALGADAHGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPVWGADRWAA
+HVDRLTAIAEGSGGPGRN
+>NAFOICDF_00418
+MDHKQILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIELEYFGGTF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITALGADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLRSPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGVGWN
+>NAFOICDF_00422
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPEDVNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAVADL
+SAPVPVPDAPWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSYELNDLADA
+AAQG
+>MHAAABBN_01948
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELECFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVLDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>LFPAFLNI_02178
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFDEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>LFPAFLNI_02192
+MDHKQILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAALDADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGPGRN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000056.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46ee40470bfbcdef329cfd5a2c83cfbcf2859284
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000056.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00019
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+FDTPPPALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVPDLKASKTV
+LVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>MOLHKGIG_00318
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>NAFOICDF_00015
+MADTFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTSL
+LKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRSF
+DVPPPPLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVPDLKAGKTVM
+VAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRYLDPEAAAAG
+AAAVAAQGDKK
+>NAFOICDF_00687
+MLTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTSTLRRAV
+RTAELVCDALGTQLPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRSRTGTPPP
+MSLHLWEELRSSSALRGLPDGALRRTEALSDVIKRVRPVLHDRLLPMVRSGRSVLVVAHG
+NSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAFLDPVAAQHAAALVA
+AEGGT
+>MHAAABBN_00033
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>LFPAFLNI_00325
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000058.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f494bbde8bf0992d0938a14845ea34f3fd67a79
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000058.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_00038
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF
+>ACLBLIBL_00285
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA
+>MOLHKGIG_00105
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR
+>NAFOICDF_00231
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS
+>MHAAABBN_02118
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR
+>LFPAFLNI_00100
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000061.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b8ad00e75b5bcf1245f387970567ff1c4457af3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000061.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00071
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG
+>MOLHKGIG_00282
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>NAFOICDF_00057
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA
+>NAFOICDF_00450
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA
+>MHAAABBN_02297
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>LFPAFLNI_00281
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000062.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51e5b5771e84078f73f50199ef33748d89c2e3f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000062.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00074
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>MOLHKGIG_00279
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>NAFOICDF_02346
+MPDLFDPLPLGGLTLPNRVTMAPLTRQRAGEDGVPGDLHVEYYRQRASAGLIVSEGVFPT
+VDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGRMCHPDLLRGAEPVAPS
+AIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFASAARRAVDAGADGVEVHGANGYLL
+HEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEIGAERTALRLSPEHDVQGVLEQDR
+ADVLATYGAILDGVADLDLAYLSLLHRDVAGDLVAALRARFGGPVLLNSGFSEVTGAAEA
+RRIVEGGLADAAVVGRALIANPDLVRRWREDRETNAPDPSTFYVGGAHGYTDYPSLEG
+>MHAAABBN_00203
+MPSLFDPLDVGALRLDNRIVMAPLTRQRAGEDGVPTELPAEHYAQRATAGLLVTEGAFPS
+FRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGRMCHPDLLRGAEPEAPS
+AIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFADAARRAVEAGLDGVEVHGANGYLL
+HEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAIGAERTALRISPEHNVQGTIEEDR
+ADVLATYDALLAGLADLDLAYLSVIHQDVAGDLAAHLRESFSGPLVLNSGFGAVTGLEEA
+RRIVEDGLADAVAVGRELIANPDLARRWREGLPLNEPDPTTFYTGGAHGYTDYPFVDGSP
+SS
+>MHAAABBN_02294
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>LFPAFLNI_00278
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000066.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54923a54e724cd959819aae79d3d0b1590966c2e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000066.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00111
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDGSDLTDRERDVLRLLARGQSNPEIAAN
+LHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>MOLHKGIG_00258
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGMEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>NAFOICDF_00079
+MPDSPEDEIRVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLM
+DMQMPRMDGVEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLG
+AVEAVRRGESVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDGSDLTEREHQVLTLLARG
+RSNPEIAAELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>NAFOICDF_00526
+MDAITVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMP
+VLDGVEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAV
+EAGTMALGPSIAREVVDLLLRSGVAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQE
+MAARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIPG
+>MHAAABBN_02272
+MSEELRILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQM
+PLMDGVEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>LFPAFLNI_00257
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGVEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000068.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b5d3f2dcd7a0d96f126ad8a0df383958413f562
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000068.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_00129
+MAEFSAAPTAHPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYGFLAVYVAANFFKSE
+NPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLPTY
+ATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLLLG
+GVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTSKT
+PLRETLRYQRQLFLMGALITLLGSTFYLVLTYLTTYMRTILELTPGAIFWLVLLTGAAAA
+AFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPLVPSLLALGITTGL
+YCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPMYFFLL
+TAAIALVGVAMLRPTDLLGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL
+>ACLBLIBL_00826
+MSHTTVAHGAEHPARTRDRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFAPMG
+EQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLPTYA
+SIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGMLLAT
+GVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDESAP
+LGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKYGQKNLGMAPNDTLIAALVGGFGWF
+IFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTASLPMFAAALFILSIGLGPSY
+GPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVAWYMIIISA
+VSLIAVLFVPKGIQDRNLHDEGVVVAETGTREPVA
+>MOLHKGIG_02014
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGEN
+GSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPT
+>NAFOICDF_00765
+MSHTVASPAVAAARDPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQPMGESG
+AQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLPTYAQIG
+VWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMILATGVL
+FLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDESAPLGE
+LFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFIF
+TLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTASLLLFSLALFVLTMGLGPSYGP
+QSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKSGWPSVAWYIIGISAISL
+IAVLFVPKGIQDRELHDEEVVATRSNPVVPA
+>MHAAABBN_01724
+MSHTVASPAAPAPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAVS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
+>LFPAFLNI_01952
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGGVGWFI
+FTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000072.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1cc6d0f0c80710b67ea695fe93f76bb5f03a06c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000072.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00163
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALLPRQAVFYANHTSHL
+DFVTLWAVLPPALQRRVRPVAAADYWGSGLRRRVAEGLFHAYLVERGKTRRRGPGAASGS
+GVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRGLHALAAAFPQVPVVPVS
+LVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPASGTAATDAPEPGRGEDE
+AARTAWLERARAVLVQDLSASLRG
+>ACLBLIBL_01775
+MATSEPVRRSAAALLRLTCRPEVTGMDQVPAEGPFIMASNHLSFFDSVILQALAPRPVHF
+FAKEEYFTGAGVRGRAQRWFFESVGSVPVRRGEQAASVAALESLVGLLDSGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERLDAYNAAPGARG
+>MOLHKGIG_01118
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>NAFOICDF_01668
+MATSEQLRRAVAGAIRLSCRPHVRGLEHVPPEGPFIVASNHLSFVDSVILQALCPRPVGF
+FAKAEYFEAPGLRGRAQRRFFEAVGSIPVRRGEQAASVAALEDLVALLDGGHGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDF
+GHPGRRHSLPQRREATATIMAAIAALSGQERVDEYNAAPAARG
+>MHAAABBN_00837
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>LFPAFLNI_01068
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000073.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..555fa35ed6a2b4d177b95a218f831ba3a5a4e783
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000073.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00167
+MENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIEDLF
+SPDPPA
+>ACLBLIBL_02206
+MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLRDLLAPLDEALERGTR
+>MOLHKGIG_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>NAFOICDF_00321
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG
+>MHAAABBN_02209
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>LFPAFLNI_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000078.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28253e967d35bd19b16aa4be29b100d873997663
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000078.fa
@@ -0,0 +1,72 @@
+>ACLBLIBL_00193
+MAPARLDPADRTQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVI
+DDALPNQDVPLLIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQP
+LAFFTRTRGGEVQSRLTHDIAGMQSVVTSTATGVASNLTAVVATAAAMVALSPRLSLISL
+VVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLGTTGHDAERF
+TGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTAL
+QGQVFRPVMGLLNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEG
+VDFAYDDGAPALSGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDV
+ARLDPADLAAIVGVVSQETYLIHASVRDNLRLADPEATDERLWAALETASLARTVAALPE
+GLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQAALDELAE
+HRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAP
+AEPALAR
+>ACLBLIBL_02595
+MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASP
+VLAGDVVNAITGGDDGGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVF
+DHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVATSW
+QVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFGRP
+AAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGD
+VVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPLS
+VRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGSTVALVGSSGAGKS
+TIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLLARPD
+ATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVL
+DEATAALDSTNERAIQEALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAE
+LLAAGGRYAELYTTQFADAE
+>MOLHKGIG_00366
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAADGRYAELYTTQFADAE
+>NAFOICDF_02454
+MSMESVARVSMMRLQRGGTAPQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVAS
+PVLAGDVVNAITGGTDRALVVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRV
+FDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANAVSLALTLAVMLATS
+WQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFGE
+PGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAG
+DVVTMALLLTRLYAPLTSLANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL
+AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVLHGVDVDVPAGRTVALVGSSGAGK
+STIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLLARP
+AATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVV
+LDEATAALDSTNERAIQEALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHA
+ALLAAGGRYAELYTTQFAEGA
+>MHAAABBN_00082
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
+>LFPAFLNI_00373
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000079.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2111ba466774c77a56eaca47e9ef97bb982b8997
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000079.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_00197
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAAFDRIPQGVAVTFEVLGPLALSVLANRRWLSVVWAAL
+AFAGIALLGRDGFSAGMDGAGLDPLGVAFALAAAACWAGFILANRHAGTHLPGVQGLALA
+MVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQVLRTMPTGLFSLIT
+CLSPVVAALTAWAVRGQRLAVLDLGGMGLVVLACGAAVWAAERAARPSRRAPRTS
+>MOLHKGIG_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>NAFOICDF_00149
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>MHAAABBN_02026
+MAVAVYPLAFYTSIHWAGVAIGSVVSLASAPLASGLLERIVEYRRLSRWWMLAAALGGTG
+AALLCLSQLDQEAASSTATLAGVLLGLVAGATYATYSWAAHRLIHDGISRAASMGAVFGA
+GGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYGLTRVPASTATTITLTE
+PAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTADRHGRTPTSEAIQPALA
+PSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVRGRFRKPYRLRPVSPDH
+GRATCGERTEIMRPARGLDARSVLAATMET
+>MHAAABBN_02194
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQQLTPLDLAGMLLVIAACAAAVWTSRSPGVSGGARG
+>LFPAFLNI_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQVLRHMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTGRSPGVAGGGRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000085.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f6d72a6e079c26f4dea4d33a0f2bba6b6a245e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000085.fa
@@ -0,0 +1,44 @@
+>ACLBLIBL_00354
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD
+>ACLBLIBL_01608
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR
+>MOLHKGIG_00049
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>NAFOICDF_01503
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR
+>MHAAABBN_02062
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>LFPAFLNI_00044
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000086.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e3e44c9cacd580656e2a2d69551bda0a14b9eaf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000086.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00370
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP
+>ACLBLIBL_00371
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA
+>MOLHKGIG_00025
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
+>NAFOICDF_00353
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA
+>MHAAABBN_02043
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA
+>LFPAFLNI_00025
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000088.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a9b5985518b5f5e67f9d7f2ae32fa9a972def5d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000088.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00399
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMFTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTVWIYQLQNLA
+GTFTTPV
+>ACLBLIBL_02642
+MDVQQLVADGQLLVASVIALAAGLLSFLSPCVLPLVPGYLAYVSASAGAAPGEKPARGRL
+VLGSLLFVAGFTAVLVALLAAAGTVGVWLLEWEQLITRVMGAVVILMGLVFIGAFGFMQR
+TTKLRIKPRTGLLGAPLLGVVFAIGWTPCLGPTLAAIMTLSVQQGSVARSVVLALAYCIG
+LGLPFVLAAFGFGWMTQTMTFFKRHIRTVNLIGGVLLILIGLLMVTGLWSQMMYALQAVI
+GGYVTPL
+>MOLHKGIG_00610
+MSLGGFFAEMVQSGALLVAMPLAAIAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFILGFAAVFTFYGAAFGVIGGWLLQWQDALIRALGVFVVLMGLVLIGWLPFL
+QNTRRMSFQPKTGIVGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGILLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>NAFOICDF_02202
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMLTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTAWIYQLQNLA
+GTFTTPV
+>MHAAABBN_01770
+MSLGGFFAEMVQSGALLVAMPLAVVAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFIMGFAAVFTLYGAAFGVIGGWLLQWQDALIRALGVFVILMGLVLIGWLPFL
+QNTRRMSFQPRTGIAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGVLLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>LFPAFLNI_02004
+MSIGNYFAETVNSGALLIAAPLAMIAGIVSFLSPCILPLVPGYLGYVSGLSNPTHPDNRR
+RVLTGVGLFILGFAAVFTLYGAAFGTIGHWLVRWQDPMIRVLGVLVIVMGLVMVGKFSLF
+QRTLKPTLAPRTGLAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFLLAAAGINWVTTALSYIRRNIRVFNIIGGCLLVLVGVLMVSGLWMLWMYQLQN
+LAGTFTTPV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000090.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afccf71ed682881a355b9a6616eda92388575f8e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000090.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00432
+MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSK
+ETSEAKTPAPRAASASKSSGGAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKA
+NSAAAPAAARKTPDRAAQRPVDVFFSPDPEDAPAARRGTKARPAMPTVKAPTKREAASSS
+GEEAAAGASTAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELVTSIREVGIL
+QPIVVREVDGPTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDALLENLHRSQL
+NALEEAAAYQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGH
+ARALLGLTDPSDMERLAQRIQAEGLSVRATEEAVAQLQGGLRPGRTPRRTADDARHERLD
+HYATALTSRLDTSVKITLGARKGRIAIDFTTVEDLNRIMDVIQGEKGGRGAAS
+>ACLBLIBL_01948
+MVASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQ
+VAAMLQENLHRQDLTAVEEADAFAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEA
+TLASLHDGQVTLERAQALAEFAGSPEEELLEEHLTATATNWDFYLARAKQTRDRRKALSA
+EQKAHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYLVKHA
+EQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRV
+AARHLAATACEETHFRRAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATR
+WTSTARVHAWRDATREDSSPAVWLAMRQELGRELAAPEQVAFDAAKAGEL
+>MOLHKGIG_02305
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>NAFOICDF_00384
+MSTRRGGLGRGLGALIQNTAEIEQPPTREDSSPSAASSNKTTAAPAKRSTRTARTAESSQ
+NGLPASDGATQQDHSSDRAEKTASSGTGSQKTSRSTGSKGAKTPEPTATRSAQEEVPRPA
+DIFFGGGEGTSDEPPESGRHRPTRSARPSMPTVKAPSKPAPKSETEQAAPVRKDEPEGTV
+SADIAVLRELPVGDIHPNPRQPREVFDEDHMAELVASITEVGVLQPIVVREVEGAATPYE
+LIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDALLENLHRSQLNPLEEAAAYQQLMED
+FSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMER
+LAQRIVSEGLSVRATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQV
+KITLGARKGKIAIDFASVEDLNRIMDLIQGGGDSTPVKG
+>MHAAABBN_01998
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>LFPAFLNI_02246
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPYELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000092.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b50c3bc35fa8a367b3f226ad5d0cbc72cc5567d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000092.fa
@@ -0,0 +1,61 @@
+>ACLBLIBL_00464
+MANTPGSGALIVGVSKTAELIGTALDREWLRFRLYELTGRALTVDVQEVQVQGARLLVLY
+PPAAVEPIRVEGRIRWRVDDHCAEVDASTWFTRQMYRRQYDWSAETSNVPAGEARPAAVD
+IARAFLYDSGDERGEELAEAETPQLLRRLNVVAEGGMLTNAGVLAFVGRPEPALDYTHHE
+VAGADSSIRVHRGGRSLLEELADVLQAFEARNTVRHVQSGLTIGQLRDIPRLAAREALVN
+GLAHREWGDPGATRVEHIGRTLRVTSPGGFFGGVDPSNIITHPSVSRNPALTQLLADLRV
+AERQGIGVDRMVREMVRVGHPQPGIEEVAGPYVRTTLVGETLDEPWMAWLSQVQPRPLTR
+DVSAVLILRHLVDRVWIDEMTAAALTQVSRAESRSMLERLHTATVGGGTILEAVSGVPDA
+VPQAWRLGEAAAQLLAALDQETGIQRTVPDRRALAADYARARGRISTTELASLVGGHASN
+MGAPLRALETEGFLEPSNASRRGRGFFYRWVGDEPA
+>MOLHKGIG_00037
+MLDEVLAQLRSTGSETALIEVKSAAGGCPRSVRETLSAFANARGGVVVLGLDDSTFEPTG
+ADAPALRDALAGMAADDMTPPVRGVISIENAEGGHQVVVMEVPEFAPDQKPCYITAAGRY
+QGSYTRSDEGDRRLTAYEIDRLIEGQGQPQHDREPVHGATADDLRPDLVEALTGRLRTVQ
+PRAFGSLTDQECLRRANVLVDADGVLVPTLAGLLACGEYPQGFFPQLSISVVVLPGTTFG
+DTGPHGERFVDNRTCEGPLVDMIADARDVLVRHMSRASVIDGTGRADRLEYPLEVIRELL
+VNAVMHRDYSAGARGTQVQVELYPDRLVVRSPGGFFGPVDPSSFGEPDVSSSRNSVLARL
+LSDLPGSDGRMIAENRGSGIPTVLKVLEAAGMVPPEFHSTLTRVEVDVAHDSLLTAETHE
+WIQGLGQDGLTQWQIQALALARSGRTVRNQTLQGWGAHQADATRELSDLVRRGLTVKLGD
+RRGARYTLNPDYVPPAAETGAGGLSERQQAILRALADGPMKATEVGDAVGTSYRTAMNAL
+NDLIEAGLVEPTAPPRSRRRRYRLTPQEETA
+>MOLHKGIG_00568
+MDVIQLDQTQLMALLSRAEGHFLDYKRTDVAPGKLTRSLAAFCNSDGGDIYVGIAETDGT
+QSWQGAADPEEFNGHLQAFEEVSPFGADWNAEFITAQNESGYVLRINALKSRQVRSDSSG
+KVYKRVGAQNVPVDSEEGLQTLRRLKGLESFEEETLNVDMEEVTNSTHIIKFLVNDPSPT
+DPELYLKRQQLIRGGKPTVASALLFAELPQAMLPKRCGIKIYRYTSSVAHRDQLYSDPVT
+VEGYLYGQIYEAVDQTIDIINQAQFLDVDGLRQVRYPRETLHEVITNAVLHRDYSIQDDI
+HVRIFENRVEVQSPGRLPGHITLKNILEERLSRNGHLVRNINRFVDPPNKDVGEGLNTAF
+ESMRKFNLKEPIIEELENSVMVTIRHQSLASPEQQIMEYLAEHSQIRNQEARNLVGIESE
+SKMKKILQGLVGTGEIEHVPGTAKRGYAYRARAEAAAQEGNR
+>MOLHKGIG_02274
+MNWSSDDLTATLDALRARRGDTTSVEVKRATGGVPSMPETLCAFANMPDGGTVVCGVDEA
+HGEFRVVGVPDVAVLEAGLVAQAREAVTPSPTLLPQVFRLEGKDVLVAHVVPLRLTDRPA
+TVRGQAYLRQSDGDYVMHAHELRMVEVAKLHADERVDYDVKPVTGMSEEDLVPELVTDYV
+AAVRERDRRLRDRTHQEILRQTNVLTAAGEPTLAGLYALGDYPQGRYPGLTVTAAVQVRG
+GEGQARSRNLTDFTGPVPVLLDEVMAWVRQNLGTEHVYRPDGQLERRPELPLAAVRELLG
+NALVHRDLGPDTLGAGKAIQVRLTDRALFIQSPGGLRGVSLTQLESDEHAQAAVNQRLYQ
+IAKKLTTPDGASVIEGEGGGIHEVFRSARQWGLGRPQLIDTGVQFKALLWRPRPEGARPS
+RREPAVEVARTPPVEEVPDVKADAPSSAVPPSSAPTRHEGRVLGALAAGEAVGIRDLEEA
+TMLTARQIRYALRQPLLDGLVEMTGGQGHKDTRYRLVSARGAGD
+>NAFOICDF_00427
+MDLGPLLAAGETLDVEFKRRLGKDDLYQAVVCMANGIGGRILVGVDDDGTVVGTTADHGG
+AVDADLLAGRIQNGIEPPLSVDVEVVPWEGKDVAVITVPQAKSSFVGTRKGLFVKRVVGP
+DGRPACMPMTPMDVLRAGFDGVGLDYARAEARGAEWGHLDPTEFDRFRRLAGQSAGDSGL
+AELTDAELLRTLDLLTPDGGISLGAVLVFGTSEALRRWAPTAEVLFQDSRPHGVEANEDL
+LLPLLNAFEEIETRLALRNSITPVEVGLVRVDVPLLAESVRRESIANALVHRDYAEAGPI
+QVTLTGSTFSVASPGGFPRDVSPANILNRSAPRSPALANVFKRAGLVERRGKGVQDMFAS
+QLRAGRGAPDYSRSTHRSVIVDIPLGDEDRELLIFLARRQNEGQRALTLTELRVVHEIKH
+GGPAGAAEAAERLRLPVADVRAAATALVEAGVLESRGNGRAQRYMLTARFYELAEDRAAY
+LRLRPVDRIQQRRLIADYIREYGSITRGKAAELCQIAPTAARAVLKGMTEEGLLELRGER
+RAAHYVLPDS
+>LFPAFLNI_02208
+MRRGDTTNVEVKRAAGGVPQLAETLCAFANMPEGGTIILGVDEARGAFNVTGVADVALLE
+AGVAAQAREGVTPSPQIIPQTLQLDERQVLLIHVVPLRTADKPATVQGVAYLRQSDGDYR
+MHEHELRMLEVAKLHADERVDYELKVATGLGEQDLVSSLVDEYVAAVRRKNRRLRDRTSE
+EILRQTSVLTSSGEPTLAGLYALGDFPQGRFPGLTVTAAVQLPGGEGQPRNRNLEDFVGP
+LPDLLRDLMAWVSDNIDTVRRYRRDGHMEEVAELPLTAVRELLANALVHRDLGPSTLGMG
+KGVQVRLTPRNLFIQNPGGLQGLSLTQLQSDDHAQAAVNQRLYQFAKKLTTSDGASLIEG
+EGGGIREVFRAAERQGLPRPQLIDTGVQFKAILWRAADRNARAGVEDAKGASAVETAVPR
+AVPASASPTRHEHAVLAALVRMPDGATLRALTSVTGLTDRQVRYALRLPLDEGIVVMDGG
+QGNRQTAYRLMSDSRRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000096.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dcb26689bf2ac3b47aa717b98819e47dc60bcc2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000096.fa
@@ -0,0 +1,66 @@
+>ACLBLIBL_00566
+MDSPASPGAPHPETTRPADVVARLQAALPGRVDVSPPPSRPPARDRSGHRSPAVPLAVVH
+AASVADVQAVCRLAHETRTPLVTRGAGTGLAGGAVAGAGEVVLDVMGMDRILEVSPADRV
+AVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTREAVLG
+LDVVLADGTLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVGATLSLRPAVRGTQVTLGG
+FFPDVVAGAAAAEAVTGAGHVPALMELMDEVTLAAVRADAGPERGAALPESGAFLLVQAD
+GAGAEEDGAAMADLMRAHGGDVTVTADHAEGEALMALRRTAFPALERLGTPLVEDVAVPR
+SRMAEMFARIRDIEARTGIPIPTTAHAGDGNLHPILLFGAAAQVGGAAEDATSIPADVWE
+AAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHALQAKIKAVFDPHGILNPGKV
+FTP
+>MOLHKGIG_02184
+MDFSAPLDPTPAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP
+>NAFOICDF_00491
+MTCIISVSPDDVLHRLRAALGDAVVTDPAALEPLRADRSGHRSPGAPLAAVRARTVEDVQ
+AACRIAHATGTPLVTRGAGTGLAGGAVAGPGQVVLDLSGMDRILEVAPEDRVAVVEPGVL
+NGALNRALEPHGLWWAPDPASKEISTVGGNIAMNAGGLLCAKYGVTREAVLGLAVVLADG
+TLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVEATLALRPLPEGAVHTLGAFFPDVAVG
+ARAAAAITGAGHVPAIMELMDEATLAAVRAHVSADDAARLPETGAFLLVQADGPGADEQA
+AAMAELIRSAGGEVTVTADPAEADRLVSLRRTAFPALEALGTPLVEDVAVPRSRMPEMFA
+RIREIEAETGLRIPTSAHAGDGNLHPVVLFGEPSRVGGEDGAQEAIPAEVWAAAGMLFRA
+GLELGGTLTGEHGVGLLKRAFLKEELGEAQHGLQERIKAVFDPRGILNPGIVFTP
+>MHAAABBN_01898
+MDFSAPLAPAAPLAPAPAADAPPADVVARLQAELPGRVDVSAAALQAARADRSGHRSPAA
+PRAVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEV
+SPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVT
+REAVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGV
+PVTLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAF
+LLVQADGAGAEADGEAMAALMRAHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVE
+DVAVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASI
+PADVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGI
+LNPGKVFTP
+>LFPAFLNI_00166
+MLRSLEDVLTKPGQVSGRALDRHAAAADASHFLLVPEAVVTPTDAAEVGALMRASAAQGV
+SLTFRSGGTSLSGQAVTDSVLVDVRKNFRDIEVLDEGARVRVRPGATVRQVNARLARHGR
+RLGPDPASEAACTIGGVVANNSSGMNCGITENTYQTLESMTLVLPSGTVIDTAAPDADGI
+LRHHEPHLYRGLAQLADRVRSDSASVATVRRQFSMKNTMGYGLNALLDFDTPAQILAHLA
+IGSEGTLGFVAEAVFRTVVRPTHSATALLVFEELQAANEALPALVDSRAATVELLDATSL
+RVGQRLTGTPPIVRDLRVQDHAALLVEYSATTAEQLEELRQHGEALTGRIGLSQPAGFTT
+DADARAALWHLRKGLYASVAGARPQGTTALLEDIVVPVLALGRTCTALTQLFDRYDYRDS
+VIFGHAKDGNVHFMLTDDFADPARLQRYSDFTEDMVDLVLGEGGSLKAEHGTGRVMAPYV
+RRQYGDELYGVMREIKQLCDPGGVLNPGVLLNDDPQAHLRHIKAEPSVAEEVDRCVSCGY
+CEPVCPSRDLTLTPRQRIVTLRAIRSARLAGDEALAQSLEEDYDYAAVQTCAVDGMCQTA
+CPVEINTGDLVKRLRRQETGAVAQAGWNLAAQHWGTASIVAGRALDLAAKLPAAATITAN
+QLVRRIAGADSVPLYSPELPRGGGRRRRPAPVGEPVAVYFPACVSAMFGPAQPGTGAPGA
+AGVQDSVLALAQRAGVELLVPSDIDALCCGTPWSSKGKHTGQETITGRTIAALRRDSDHG
+RLPIVCDASSCTEGLRHALEVEVPPAGQQPLRILDAVEFTAEHLLPRLPEPRRIPSLTLH
+PTCSSTRMGLNPALARVAEAIAEDVQIPDDWGCCAFAGDRGLLHPELTASATARQAEQVQ
+AIDASAHASCNRTCELGMSRATGYPYSHVLELLNQSTIAGG
+>LFPAFLNI_02129
+MDSSAPLDPTRAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000098.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ff74ed36b04c68a5473ca38dca2566de352d306
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000098.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00584
+MSPSPSGSVPSSSSVSAESRGMGAAAPGQAAVPGETGAAAAVETIRVSAVVLARPDRRVL
+TVRKAGTTMFMFPGGKHLPGEDPLDTAVREVAEETGLRLRPDELTRLGAWDTDAANEPGA
+ALHSEVFALWRPVARHETPAPTDEIVELHWMDPAAPAAPAGHQVAPLLVAVLAAVAKNPP
+F
+>MOLHKGIG_02168
+MSPSPSDSARTPTVTAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VALHWMDPAAPAAPGGHGVAPLLHPVLAAVAATPPF
+>NAFOICDF_00510
+MTAPAARSDEPAEIRVSAVVIARPDRRVLTVRKAGTAVFMFPGGKHEPGETPLETAVRET
+REETGLRIRPDELVHLGAWDTPAANEPGMALHSEVFALWRPMARHEVPAADDEIAELHWM
+DPAAPAAPAGAGVAPLLLPVLARVAAQPLF
+>NAFOICDF_01906
+MAAPDFVLSLREHVGHAPLWLSGVKAVALRAGDREVLLVRRADDGRWTLPAGILEPGEEP
+ADAAVREVAEETGVRCAPRRLAGVGTTAGAVYPNGDRARYLDVVLVLDETGGHAHVADDE
+NLEVGWFSVDGLSDLPPLHARALSWALEDGPARFVAGGDVLP
+>MHAAABBN_01882
+MSPSPSDSSRTPTVAAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHVPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF
+>LFPAFLNI_02113
+MSPSPSDSARTPTVAGGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAAVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000100.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1edab05c60865f4625a89a03f98af9bc2ba3b78f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000100.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00640
+MERPAPTAEICPVRPEDTDAVVALWERTLPEYGDPTRPQRAPRPSIRRKLDWGDGLFWLA
+VSDEEVVGTVMAGYDGHRGWIYSLAVHPDHRRGGLGTALVAHAEQELARLGCPKVNLQVL
+ATNADGAEFWAATGYQPDPVLGLGKRLGG
+>ACLBLIBL_02391
+MTETAPTVPTPPARPQVRPLRPEDHEAVAALTVASYVDGGHIAPGSRYVKTLRDVAGRAA
+RAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMAVIE
+ERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGPFLV
+YRLPLA
+>MOLHKGIG_00554
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>NAFOICDF_02275
+MSDVTVRALRPEDHEAVAALTLASYTTGGHFEAESDYLETLADVAGRAAVAEVLVAELDG
+QVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLAEVVRRARATPGVEA
+IALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGPFLVYRLPLT
+>MHAAABBN_00279
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>LFPAFLNI_00557
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000105.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f514e04d93085c8d813a081dc86a7d1350aa5fc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000105.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00736
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT
+>ACLBLIBL_00740
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN
+>ACLBLIBL_00741
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS
+>MOLHKGIG_02072
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST
+>NAFOICDF_00488
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA
+>LFPAFLNI_02000
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000108.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c92adc9989c61bd567b4d507783dedd59e487ec3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000108.fa
@@ -0,0 +1,57 @@
+>ACLBLIBL_00786
+MDLPQITPLAVAVGLAVAVVGWLLGRLLGAGVAWLFARRGRSPSSARVFGKLVAAGITVL
+SLGAAVTVVFPSVKPVDLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDRFRVGDQIQV
+GEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRSSLRVDVETGNDL
+ARTREIAVRAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHA
+VLTAFEKNGVATGDDVRVVDAGPELRRILEGPGAPRGQGGPDYPGGLAGPGEPDRAARPG
+SD
+>ACLBLIBL_00939
+MLLAALSGPASPPVLGSLARLFAGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAF
+AVGATLVYAALQVTRVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMPALRERLTQLLDSTDLWDGRESSMQVTDAIGGTVRIRAVVSARNSGDLWDLRCLV
+REDLVTFLRSEHPEAIVVQRVVERHPAHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAA
+REPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITAVQRNRELHGPGEDAFAE
+RRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED
+>MOLHKGIG_01921
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>NAFOICDF_00874
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAA
+VLGAFLAGGLVVLGVFLVARLALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQ
+PWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQPGVNDRRERKIRTQTMLLRRV
+LNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVV
+EMDVDWRVPMDPLRARLTELLESTDLWDGRENAMQVIDAVGGMVRIRAVVSAKNSGELWD
+LRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPAPEAHDDPAPDAHDDAAPAAAPAAPA
+PSDRGSSTRAEPTPQTRPMPTVTGSVPLARAGENASLYTGSIRAVERNQEMDGPGEEAYA
+ERRARAAEREDRAARDAGRGGAHAARS
+>MHAAABBN_01617
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQETSVEHRRERRIRTQTILIRRILNAVI
+VVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>LFPAFLNI_01841
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVD
+WRVPMDALRARLTQLLESTDLWDGREHALQVTDATGGIVRIRAVVSARNSGDLWDLRCLV
+REDLVSFLRHEHPEGIVVQRMVVRHPAHGDASPASEGSDAEARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000109.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92be2ad5b7ce2bdbfbe585a3badd0c8f3e8f5888
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000109.fa
@@ -0,0 +1,97 @@
+>ACLBLIBL_00789
+MFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTLTVTGRLEPGTEVRPRRN
+SQERFKLNALYEQPPRGAELAPNAVRWQSRSPVDVTEVEEIAPGRFRVSLLQRLSAKYEP
+EPHAEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPEGAVFDILARRAPRTTGRTLA
+AIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVGSRAVKELLDRGWTVGVT
+AQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGLHRWTSLGSSEVHAFLAPGRVLGGTAW
+TFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQQLPQVSRGEHPQPIGDA
+ALTWIAEGAPVLRADRGFFLDTSWRMHSALTRAVSELSYAGRLGAREEVTDARRLDGVEP
+GLHPWPVSHTGNAVSSPEEAAAVVEIIQSLLGRTWSTGPDDPGRPLEPSDVIVVAPYNAQ
+VATVREALDAAGLEGTAVGTVDKFQGREAAVAILTMAASSPQEVPRGLDFLLNRNRLNVS
+ISRGQWAAYLVHSPALADALPTGPEDLPMIGAFLRLVHR
+>MOLHKGIG_02029
+MVTFAPDRASFMLSPSDITVAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRSRLEALLQDHVAAGEPARWGDDRLSVCGACEVCEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+GGVPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAVKPLVVV
+>MOLHKGIG_02031
+MAASTSETTCPTTGRYTTMRDSTERAALEEFVAFVEARRAAHPGMRIYHYAAYEVTALKR
+LTVRHGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVT
+TAADSVTEYHRYVAAMEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHG
+ATAPRPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGF
+YQREDKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTL
+EPGSSLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKI
+PTQDVEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDI
+LARRPPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKT
+HVGSHAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWA
+TVSDAKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLL
+GDPQQLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSY
+AGELGAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGP
+DDPGRPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAAS
+SPQEVPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>NAFOICDF_00750
+MASFSPVDPASFLLSPSDITAAATCEYGWLRGAVDPKLGRADGAPEDDAFLARVSALGDA
+HEARTLDALVAEHGAGGVVVLERPSPYTPEGIAAAAERTRQALASGAAVVFQAMLHDGSF
+GGLADFLVREPTAEHPEGAYQVVDTKLARHARVTALLQIAAYADLLDGMGVPRTRHGSLW
+LGDGARHTVDLAEVIPVYRHQRARLERVLRTHVTEGTPVAWGDERHAVCGQCRWCEEAIA
+EHRDVLLTAGATRVQRTRLRAAGVRTVEELAASTAPPEGMSRRTWEALRDQAAAQLEPAG
+ADGVPPHRIVDPAPVRALPAPDAGDLFFDFEGDPLWVSPRGDMEGLEYLWGWVEAAPGRT
+TEGTGFDQFRFTGLWADTRAEEKAALEEFVRFVEARRAVHPGMRIYHYAAYEVTALKRLT
+VRHGVGEAELDDWLRAGLFVDLYATVRASLRAGVPSYSIKKLEPLYMGADHRAEDGVTTA
+ADSVTEYHAYAEQAERAGEGDADAAAEAARLRAGIEDYNRYDCVSTARLRDWLLGQVGGA
+STGVAVDAGEPAEAGEDAPAATDEDAALEQALLDLVPADPADGDDETLGLAMLAAGLGFF
+RREAKPMWWAFFDRGISPVDEWQDPRANVVADRVDVAEDWHRPSSRARTRQRVLRVTGRL
+EAGTQLTPGAEAKTVYEDVPAGRVEGLQPNAVRWVGAAAVVEDVEDHPDGTSTLRLREKV
+ALDAEPHPELPMAAFAHTVIPSATLQERIREDGLRARALGALPRPEEGAAPTAAFDILAR
+RVPETAGRPLAQITADARAGRLEGADALVEALVSARGSYVAVQGPPGTGKTHVGSHAVKE
+LASRGWRIGVTGQSHAVVENFLAKLVAVGVPAGHVGKEKPRGGEDRERPWTVLDDRGDAF
+EHLSQPGHVLGGTAWTFAHPKAPDLDLLVIDEAGQFSLAMTLAAAATARTVLLLGDPQQL
+PQVSQGTHPQPIGDAALGWLMEPGEEVLPPERGFFLDTTWRMHSALTAPVSRLSYDGQLR
+SRSEATDARHLEGIVPGLHPVPVEHTGNAVSSTEEARRVVEIIEDLVGRAWTPGSGEEPR
+PLTPEDVIVVAPYNAQVATVRAALDDAGLQGTTVGTVDRFQGREAAVAILTMAASSAQDV
+PRGLDFLLNRNRLNVSLSRGQWAAYLVHSPALADALPTTPADLPLIGAFLRLLQP
+>MHAAABBN_01738
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLTRPERYTPEGVQAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPTRWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAVSVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVTGLPAPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALEQFVAFVEARRATHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVTTAAD
+SVTEYHRYVAAMEAGDTEVAKAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHGATAP
+RPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGFYQRE
+DKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTLEPGS
+SLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKIPTQD
+VEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDILARR
+PPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKTHVGS
+HAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWATVSD
+AKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLLGDPQ
+QLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>LFPAFLNI_01966
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPARWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGIMTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALERFVAFVEARRAAHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGVEHRAEDGVTTAAD
+SVTEYHRYVAALEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLAQVEPEEAAVADRP
+VDDAATGNEPLVEAAPSLQEQDAALAASLQALADVERDEAGGTGAPEAELDGGRRGIALL
+AAGLGYFARENKPLWWAMFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTL
+TVTGRLEPGTEVRPRRNSQERFKLNALYERPPRWAELAPNAVRWQSRSPVDVTEVEEIAP
+GRFRVSLLQRLSTKHEPEPHGEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPDGAV
+FDILARRAPRTTGRTLAAIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVG
+SRAVKELLDRGWTVGVTAQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGPHRWTSLGSS
+EVHAFLAPGRVLGGTAWTFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQ
+QLPQVSRGEHPQPIGDAALTWIAEGAPVLRPDRGFFLDTSWRMHSALCAPVSELSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000112.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00909e2568f3aad70ed79237e243301538f86aab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000112.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00872
+MSALLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLAGL
+MGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVDSF
+EADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDAAQVPVA
+VRQGRVLATSFHPEVTGDHSFHREFLRGL
+>MOLHKGIG_01985
+MSPQKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>NAFOICDF_00808
+MSPQKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>NAFOICDF_00818
+MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA
+RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD
+SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA
+ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL
+>MHAAABBN_01679
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR
+>LFPAFLNI_01911
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000115.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb879176fa21b48bb281ed0ce01e521b16ef58ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000115.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_00920
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+>MOLHKGIG_01939
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>NAFOICDF_00854
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA
+>NAFOICDF_02134
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR
+>MHAAABBN_01635
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>LFPAFLNI_01858
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000116.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dd87aa9d32cfb2f01f380744ce9da7827ae8ae4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000116.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01016
+MTTTLASQTDLDPMRTPAAAAAHRIAPGTAAPDGSGGTPALSVRDLVLEYPDGERGVLRA
+LDEVSLDLHAGTFTALVGPSGSGKSSLLAVAAGLVPPTSGTVTVAGRELTGLSRTERTGL
+RGREIGVIFQQPNLIPSLTAAEQLELSVHLDRDATRTDRKAARDRAMALLERVDLADQAG
+KRPHQLSGGQRQRVNIVRALMASPALLLVDEPTSALDRERSAAVVDLLGALTRDEGTATL
+MVTHDHEFLAATDRTLTMVDGRLTD
+>ACLBLIBL_01058
+MSTTTPVIQLSSVTKTYQRRDLYTDASVTVIPGRAHAIVGPNGSGKSVMMRLMCGFLLPS
+SGSVTIDPRYLDGRRTFPDKFGVVIDKPGMLPHLTGLENLRRLAEIQKKIGDERIREVMQ
+SFGLDPDARQRVHQYSLGMKQKLNLCQAVMEDPEVLVLDEPFNALDADSADALRGRLASF
+VADGGTLVFTSHDSRDVEQLADSVIRLENGRVTQEDASPRT
+>MOLHKGIG_01852
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGVIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARAMELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSVTDRTLTMVDGRLSAE
+>NAFOICDF_00958
+MTISTHTPDLSAYRSPAAARVTAHDAAPAAPDAAPVLSVRDLVLEYPDGEGRTLRALDGV
+SLDLTPGTFTAMIGPSGSGKSSLLAVAAGLIAPTSGSVTVAGTELTGLSRAARTRLRGDR
+IGVVFQQPNLLPSLTAREQLELVVRLDPKSTRADRTAAAARAQELLERVDLGRRADQRPH
+QLSGGQRQRVNIVRALMGTGSGAPALLLVDEPTSALDRERSAAVVELLGELTRQEGVATL
+MVTHDHEFLGATDRVLTMVDGRLAA
+>MHAAABBN_01548
+MTALTAPQADLDALRTPAAAAAHRVAAERPATAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRKAARARALELLERVDLADQARK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLHAE
+>LFPAFLNI_01772
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGCVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARALELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLSAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000117.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3aedddd77ad7e506dc95fcd14cf8325d8388b10d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000117.fa
@@ -0,0 +1,71 @@
+>ACLBLIBL_01024
+MSPRRRTGSTAAPETSTLSVVDPAAARDLRVLGVRAEETLEYTPEERRHVRRRSWALLRQ
+LAGPAKGMLWLTVVLVVVSNAARAAVPLVIAWAIDWGLPQVVEAVRTGADAWGVVVLVGG
+AYALTGVTGGVLLGLYQWLTARASQRMLLALRVRVFRHTQRLSLGFHEKYTSGRVISRQT
+SDLEALRELLDQGVSSLVSGVLFMAFTAVSIVLLDPPSALVLLVAFIPVAVAVRWYQKRS
+EEAYRRSRVSSARAIVHFVETMTGIRAVQAFRRQRANEAKYTRLATDYRDDMVHTLTLFG
+VLQPVLVVTGNLTVAALLVFGGLRVLSGDLEVGVLVALVLAGRRVFQPMEMVAMFYSSFQ
+SAGAALEKVSGLLEEEPAVVEAPEPTPLPGAAAAGEGVASGRIEFRDAVFGYGPEKVVLP
+EFDLTVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKELASADLRRNVV
+MVTQEAFLFSGTVAENIALGRPGASEAEIQAAARAVGAHEFILDLPEGYDTDVSKRGGRL
+SAGQRQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLST
+VEIADRVLVVHDGRVVEDGSPAELVAAGGRFAALHRAWEDSLVPDDA
+>ACLBLIBL_01331
+MPALFVGRRRLLLLGLAGLGLLQAALSVAVAVLTPRLLTAGAGAWGLAAALLVAALLVGG
+ARILERVAAEDLGQDYVRETRRLLVTSALVPEKSLNLGSTIARTTNDLTAVKNWIALGIS
+PIVVGVPLIVGIVIGLFVLLPTLGLVVVVTLGVFFTGLWALSRVFFRRAVAVRRVRGKMA
+GYVADTVTAAGSIRTAGGVQREVGRVDRISGQLQDAAHRRAVVSGTMRGSAASITTVLGV
+LVAITGSAAGSTGAAITTAVFIAGMLGAPVTELGRVGEYRQNYNAACRVLRPIIENARGH
+ARRERRQKRARTRMRHHGNPRGLSRDAVHLADLRDAEGTIPALVAAPGSRVLLTGGSRER
+LERVTREITGDMPASDAWITVAGRHLYAMTAKDRRELIGVAARDVPLQRGTISRIVRYRH
+RGAGETVAQVLDRVGMAERVARLPEGDATRLKRGGEPLSINERALLKIAGAVAGNPPLLV
+LDHVDDQLDARDRPILRRILADYPGCVILRSASPHELLERYEVYNVDELAPTLVVAPSVL
+HSRIQGERPTTYVIGADRDPFGPPVRHSAVELAGTRAASAPRLGESADDLEGVDE
+>MOLHKGIG_01844
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>NAFOICDF_00965
+MSRRADTAPVTSTLTVVDPAEAAGLRVLGVGAEESLDYTPAERRHVRRRSWALLRQLARP
+VRGMLWLTAALVVLSNAARAAMPLVIAWSIDDALPRALEAVRAGTDPTGVVVQTGALYAV
+TGLVGGVLLGLYQWLTAKASQRMLLALRVRVFRHTQRLSLGFHETYTSGRVISRQTSDLE
+ALRELLDQGVSSLVSGVLFTAFTAVSILLLDPPSFLVILVAFVPVAIAVRWYQVRSEEAY
+RRSRVSSARSIVHFVETMTGIRAVQAFRRQRAGERAYARLATDYRDDMMHTLNLFGVLQP
+VLVAVGNLTVAALLLFGGLRVLSGDLAVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATA
+ALEKVSGLLEEEPAVVEPAHPVALPGAERPGEGVASGRIEFRDAVFGYGSDAVVLPGFDL
+TVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKDLAGADLRRNVVMVTQ
+EAFLFSGTVGENIALGRPDASEAEIQAAARAVGAHEFILDLPEGYATDVSKRGGRLSAGQ
+RQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLSTVEIA
+DRVLVVHDGRIVEDGSPTELVAAGGRFAALHRAWEDSLVGEG
+>MHAAABBN_01541
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>LFPAFLNI_01765
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLLTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGLSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIIEDGSPA
+ELVAADGRFAALHRAWEDSLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000120.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80d61251fa6ef1d8599a65a199db3b495580313e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000120.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01086
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>MOLHKGIG_01790
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>MOLHKGIG_02051
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR
+>NAFOICDF_00729
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR
+>MHAAABBN_01757
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR
+>LFPAFLNI_01985
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000121.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdbcb35bf800b6cd7622bc84d9030c2072941701
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000121.fa
@@ -0,0 +1,44 @@
+>ACLBLIBL_01098
+MRVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVRDVVP
+VNATVPAVEAEAVESVLARYGEGITAVKVKVAEHRPGGGLVPGSHSADLARVRRVRELLP
+DAHVRIDANAGWTPAEAIAMLTDLADVGLEYAEQPVPGIKKLARVRRELRARGVSTPIAA
+DEAVRKAEDPLAVAAAGAADLIVVKVQPLGGVRRAAAVVAAAGLPAVVSSALDTSVGIAG
+GAALATHLPALPHACGLGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRAD
+ERTHAWWRDRVAAAHAVLAAGGR
+>MOLHKGIG_01779
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVAVPMRVRFRGTDLRHALLLRGPAGWGEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRETIPVNATVPAVDADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTELA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHAVLAAQG
+>NAFOICDF_01022
+MTVPAAHDDADPRPGSALPPLPGAPGGPALPDVDELLEHAVAVTLPMTVRFRGTTERRAL
+LLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVRSEVPVNATVPAVDAADVE
+SVLARYGDGITAVKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDE
+DRAFAVLGALQDVGLEYAEQPVPGIAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVA
+QAGAADLIVVKVQPLGGVRRAAAIVAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFA
+CGLGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAA
+HAVLAARGR
+>NAFOICDF_01806
+MSPAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSDGTVGQGSAAET
+VAVTGEDAASIETAVDGVFGPALTGATGGLDGLLARLPAPARGATSARSAVDVAVHDAVA
+RAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAGTRILKIKLGRDVA
+EDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISGMEDEGLPVDLVEQPVAAADVAGL
+ARVRAAVTTPIMADEALWSSEDARRLIEAGAADLFNVKLAKTGGLADAVAIADLAAEHGI
+GCMVGSMMEPRISIAAAVQLSLAHPAVTMVDLDAPLWFASDAPAGGYTQEGADLRLLPGE
+GLALERLDPGTDPV
+>MHAAABBN_01486
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHECAAWLAAAIEAGWQGWPGPVRQTVPVNATVPAVAADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTALA
+DVGLEYAEQPVPGITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHAVLAAQG
+>LFPAFLNI_01708
+MSTAPALPPLPGAPGGPALPSIEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRQAVPVNATVPAVDAADVEAVLARYGDGIT
+AVKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTALA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHAVLAAQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000124.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19d9f24bd7feb0c1e816e10e91bdbd9016bd1791
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000124.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_01218
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIGR
+FLRDNITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAHGIDLFEERQSTDYLP
+GRAINLGALDELHSVSRAGAEYLRARHPEFVEKIKVSYLGTEDHGVRPPRSSSQVLRLVS
+CSEVAPVKRLELLVEALREVSDSIQVEWSHYGEGPDMDRVRAMASTLPGHVSATFHGWTR
+NDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSCGLPTIATDVGGTGEIVSDGVNGRLI
+SANPMPREIAAAVEEFARMAPEAFARRSAAARETWSTHFDSDRNYRQFVAKMLS
+>ACLBLIBL_02441
+MTPEAATTTPAPLTLWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAP
+ALVSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPI
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGVGPLEGQLRAQAEALGVADAVDLPGFVEPWGAMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVMRATVEGPGEVRVGDVETMARATA
+EATLEVLGRRAGKTSG
+>MOLHKGIG_00509
+MIPEAARTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGAGPLEGELRAQAEALGVAEAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVVRAAADGPGEVRVGDVETMARATA
+EATLEVLGRRVGKVGTR
+>NAFOICDF_02325
+MIPEAATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRL
+TLAGSGPLEGQLRAQAEDLGVADAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVTRAAAEGPGEVRVDDVEGMAEATA
+RAERDVVETQDARRRKTR
+>MHAAABBN_00229
+MIPEDATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRV
+TLAGSGPLEGQLRAQAEDLGVADAVHLPGFVEPWGTMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPEAIADAVVRAAAEGPGEVRVGDVETMARATA
+EATLEVLGRRVGKGGHR
+>LFPAFLNI_00508
+MIPEAARTALAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGSGPLEGQLRAQAEALGVAEAVDLPGFVEPWETMAEHDVLAQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPAAIADAVVRAAADGPGEVLVGDVETMARATA
+EATLEVLGRRVGKAGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000127.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a5f0cda9da18e53fa15efeb01622e8e45e4abec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000127.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01252
+MIPVLLIEDEERIAAFVTKGMAAEGIAVTTAGTGAEGVGLAMTGAFELVILDLGLPDADG
+FDVLARIRRQDAHLPVIILTARSSAQDTVEGLTSGADDYMPKPFRFAELLARVRLRLRPG
+APAPEPTDTVMRHGDLELDPASHTARVDGRTVALSAREFALAEEFLRSPGQVLSREQLLD
+GAWGEDFESGSNVVDVYVRYLRAKIGAERILTVRGLGYRLAGEDELSG
+>ACLBLIBL_02602
+MQSQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVGDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRAADKR
+>MOLHKGIG_00359
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>NAFOICDF_02461
+MQSQTPEARLLVVDDEPNIRELLSTSLRFAGFEVRAAGNGREALEAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRLFPVVFLTARDGTEDKVTGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTAPLDDDSAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGRDKMIHTKRGVGYMFRTADKR
+>MHAAABBN_00075
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>LFPAFLNI_00366
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLS
+KAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000129.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5b645da99f9a839f5c8e48bea343dbea163fb7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000129.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_01273
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQNESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>MOLHKGIG_01624
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+KAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>NAFOICDF_00781
+MSHAHHHGGGSSAAVLDSSLTRLGLVGSPNSGKSTLFNALTGLRVKTGNYPGVTVSRAEG
+VMVAEDGTRVVLEDLPGTYSLDPISPDEQVVADLLALDPADADHPQALLLVADATTLRRG
+LTMVAHALAVELPATLVLTFGDELALRGGSVDVTRLSRALGIPVLAATAGDARQREAVRA
+HLATDPAGWAVPPVAPPTDPAGIAAWIDSVLEAARYAVPRPDGRTRRIDDVLLHPVWGTL
+VFLVTMFAFFQVIFTVAAPLQALVEELFGWLGERAAALIPIEWLGRFVAEALIGGVGGVV
+VFLPQILLLFLMISLLESTGYMTRAAFLMDRVMSRFGLEGRSFVALLSSLACAVPGIMAT
+RSLPSARDRLATMMAAPSMTCSARLPVYVLLISLLVPSEVRWGPVGLQGLVMFALYLGGA
+TASMLTAAFWSRVVGRRQAAMPFYMEMPPYRLPKARTVVTSMWASAEGFLRKVTSIILVT
+TALLWVLLNVPVRSEEEMAGAGVAMDDPAAVAQYTIDHSAAAAVGKAVEPAFEPLGFDWR
+IDVGVLASLAAREVFVATLGQMAAAEDPEDPGDALASWTVTDDAGVERPLFTPDVVAALL
+VFFMLALQCMSTLAVMRRETGTWRWPLLAFGYYFTLAWLAAFAVRHVVLALT
+>NAFOICDF_01182
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>MHAAABBN_01330
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+QAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>LFPAFLNI_01551
+MGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERL
+PRLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRVFDDGD
+VVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALQAALAVL
+ERGETIFAAKDKDTLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADA
+VFLDAKLESDLVELSEEEAAEMLEMAGQDESGMDQLARVGFSTLGLQTYLTAGPKETRAW
+TIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKD
+GDVVEFRFNV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000130.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6036b1ea473cea53b5c73e2325fbcc3a33c15fd1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000130.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_01275
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN
+>ACLBLIBL_01290
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>MOLHKGIG_01604
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>NAFOICDF_01198
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER
+>MHAAABBN_01316
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>LFPAFLNI_01531
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000134.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11a58392b6a4594d4abfc2c0e2bd14f8f7ec2415
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000134.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_01340
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA
+>MOLHKGIG_01582
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA
+>NAFOICDF_01234
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA
+>MHAAABBN_01292
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW
+>MHAAABBN_01293
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA
+>LFPAFLNI_01509
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000135.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdd959b4e84e1cc2b3b26579cb8e6bee0bcaeaf0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000135.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_01342
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR
+>MOLHKGIG_01581
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR
+>NAFOICDF_01235
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR
+>NAFOICDF_01767
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R
+>MHAAABBN_01291
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
+>LFPAFLNI_01508
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000143.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..860a1f277dddfe46f5bc3e4d0897eacd9498cc40
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000143.fa
@@ -0,0 +1,81 @@
+>ACLBLIBL_01524
+MSSTRRDPLVGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHPHLAEDPVLV
+GRFEQEAKTAARLSHPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTP
+REALRHLRPLVDGLAAAHRAGLVHRDAKPENVLVRTDGRITVADFGLSRAATAHTSAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPV
+PSSLQPGLPEALDDLVLWCTEPDPADRPADAGEVLDRLDAVAAELGPAELDRPPVLVPDA
+VEGRPGPEHDETTTLDALDRLDPKDPLDDADGDETTSLDAGDHHATRVLPSLPADALPTE
+ALAADDVVRRSPARRRRRP
+>MOLHKGIG_01369
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHGAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIEAVAAGLDPDAPDRRPAAQPAE
+GPGADPAPAGPAADGLEDAAPDGNLETRALDAGDHHATRVLPALAESDLDEDMTDVIDTR
+VATHGGDPRPAARPAEPIGPLGLDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAA
+IGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTAR
+HDELRTEGTVVASSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARF
+TVEVAERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAH
+TTLADEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG
+>MOLHKGIG_01953
+MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLA
+RTKFILVELKYYSGVLRGTGLRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGA
+GRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNETASNLPSIEHLVLAPATDRFP
+LIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI
+RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLA
+PLPLWLESRAATLSQQNRLDLLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRIL
+VADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAPTSGALFRAPEDARRVSSLGR
+YKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD
+PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAV
+GLLVDDAQTGSRQVLKVALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPFDVGGRRALL
+LTSAGTRTLSEVLRERQRLSLDHLERFGSELLEAAQALDAAGLRHRDVKPANIGVVRTPK
+HGEHLVLFDFSLARARSTDVRAGTPPYLDPFLEQGGRTGYDSAAELYAVAVVLYEMASGQ
+KPFYGDPEANPAAVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWE
+ALFRNDADPVTAQDAETLAARATLETPLSEAGLSARGLSALEAIKVTAGPGGVAVEPHDV
+RTVRDLVLVDPIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQVPQGTLPTPLD
+AAELLLRHAGAAHAEGVRAQLRLVLGLDGEVPALSTHAVLADARGVTPGLVPQLFGRAQQ
+AWTDVAETRSLLDSLDGALRAAVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIV
+QGLLWLLLDRERAAARGEADVPALVQRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGA
+GDPESALVPADLVQTRVAAVLDAVDGLPEALRSWRRAAALAAHVSATTCLSAAGEWHHRL
+LAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDE
+DLGPQGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVP
+AQRLARLESALVRRFHAEPLDLTDLFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQG
+LNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHLGVLARWADLAEYRARP
+VWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT
+>NAFOICDF_01419
+MSSTRRDPLIGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHPHLAEDPALV
+GRFEREAKTAARISHPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAP
+RRAVALLEPVVEGLAAAHRAGLVHRDVKPENVLVRTDGRITVADFGLSRAATGHTSAGQT
+VFGTPAYLAPELISGTGGDARADVYGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPV
+PSSVRPGLPEALDDIVLWCTEPRPADRPEDAAALLPELRRVAALLPQTAPADEAPAADDA
+PTVALAVSPTVPTVPVPDAADATARLEPRRPDPRRAEPVPTPATATAASPSSDLSSAVPE
+APRPAPVAPRPASARQRRRTARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSG
+GISGPAGVVVPPLWGLEQQEAAARLAEAGLTSAVVSRHDERFSDGVVLDVSPAAGSTVDA
+GGPVRLTVSDGPAPVPAPDLAGLTVTDAHAVAEDGRVGVVVADRVADRAVPAGAVVSQSP
+EAGAEMTPGDEVAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDVRTLPLPGPSGD
+AARVLRQGTPAGTVLPEGASVQLWTL
+>MHAAABBN_01089
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRHPAEGPGA
+EPAVAAPAADGPEDAAPDGNLQTRALDAGDHHATRVLPALAESDLDADMTDVIDTRAATR
+GADRRPAAHPAEPIGPLGLDPAPADRHPGRESPRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHNEL
+RTEGTVVASSPAAGEPAGRGTPVELTVSAGPAPVPVPDLTGVVIRRAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDVTGQDPETARTTLA
+DDGWDARVHRLPLPLAGRGESRVLHQSPAAGTALPEGTAVHVWVG
+>LFPAFLNI_01324
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRRPAEGPGT
+DPAAAAPAADGLEGAAPDGDLPTRALDAGDHHATRVLPALAESALDDDVTDVIDTRAATH
+GGDPRPAARPAEPVGPLAVDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHDEL
+RTEGTVVDSSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAHTTLA
+DEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000144.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faa48e39ba1c89478536f2daf30d530f0917a98b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000144.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_01551
+MTTHTTTAQRSSKHPTTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQPAMAEP
+VAATLAAITAELDARDKAPAPTAPLGVCFPSIVKDGVCLSANNIDPSWIGTDLKAAFEEH
+LRRPVRVVNDADAAGLAEARYGAGRGVSGLVLVITLGTGIGGAMVHDGVLVPNFEVGSLE
+LDGVMAETRASAKAREREDLSWAEYAQRLQRFFSHVEHVFSPDLFIVGGGISKRPDDYLP
+LLSLRTPIVPAQLRNNAGIVGAALAAHDSLADAR
+>MOLHKGIG_01341
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQTAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGTFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGMLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>NAFOICDF_01415
+MHRSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGADPA
+SAVTRAAADALSRAGVRVPDGAGFACAAWLDPATGRARASPHLPSLVGIRPAALLTPVLE
+AAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDLPGAPTLFVALGTGVGGAVIVDGA
+VLPGARGMHGEAGHICVDPDGPACPCGARGCWELYASASALARTLPGRPIADVLEAAVAG
+PGPERDAVLDAGEWLGRGLAPAVCLLDPVRVVVGGGLMAAGELLLPTARAALRRALPTAA
+ADRPPELVAAALGNDAGWIGAALADGARV
+>NAFOICDF_01447
+MSFPNTGVIPRLPPAPSKHPSVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQP
+ASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIVQHGVCRSANNIDPSWIGVSLQD
+TFEEALQRPVTVVNDADAAGLAEARYGAGAGVPGLVMVITLGTGIGGAMINDGVLVPNFE
+VGSLELDGVMAESRASAKAREREGLDWPEYALRLQRFFSHLERIFSPDLFIVGGGISKRP
+HDYLPLLQLETPIVPAMLQNNAGIVGAALAAHADPADGLLR
+>MHAAABBN_01061
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>LFPAFLNI_01296
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000145.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2c5f85708de70b395f2373cbfef7a02bf7dc7a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000145.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_01557
+MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAEHHNMPAIA
+SSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGRTRIPGIEAYPGKGTDVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTREEADR
+EWEAARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTMLECTAVGTGEETATWLRDFA
+AKVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>MOLHKGIG_01334
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>NAFOICDF_00131
+MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGEHHLNPGVLGSNPALT
+LALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDLGLGRAAAPGGPPPGT
+RAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAAPDLSAALGSPLRAAS
+RALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARPAVDVEPWVLGSGPGVSA
+EVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVVSVSAEVLIADTAAEARR
+RASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRLQTRFVGTAEQVAERLDA
+LARLTGADELLISASAHRVEHRVETLTRLAEIWRTA
+>NAFOICDF_01453
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRAPGTDQRTLQALRRSPEAADRFPQDVLELQGYLRGESRMPGIDAYPGRGTDVPLWI
+LGSSAFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHFIAAANVVVA
+DTDEEAQRLWEATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGMLRHTAVGTPDVV
+RAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR
+>MHAAABBN_01055
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFTAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>LFPAFLNI_01290
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000151.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76483ecf03a05ee7f4611b6743a49ce9808cbda3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000151.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_01792
+MSINPAAAAHAADATAAQDALARHGLVLRTLAPLSRGFDGADPARAEHPAHVRHTAAVEK
+GFYEEVPQGAAADQDLGVSADDAKVLRGVYLSADDPARREPVGTFVDWTSRLTTSPGAEL
+PVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASESTIYGRFGFGAASTA
+RTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHDRVRRGTPGSVHRPTG
+HVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGKEPTTVSVEVFLAATD
+AAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRVRTKSVWDDLYLRVLDVPVCL
+GGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADGVGRAERLADDARADLALDVAHLSAV
+WLGGVRAGALVRAGVVDEREPGAAARLDALLAPAAAVHLLTGF
+>ACLBLIBL_01793
+MTPRTDAPDAWLDPAPATAEALAAHGLELLRVPSPWETGDADPDAPFDHARRWADAPAVR
+RHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTLVDFTKD
+LNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATEATLYRR
+FGFGVSTYHRSVWLDVTRGVQLRGRRPDGSFRFVEPTASGALIDGLWRRAFEAQAGSVER
+IRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTAELVADDPVTATV
+VALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRIYTRGVHHHLWHR
+VLDVAACFEARPYLHEGAVTVTVEDDLGYAAGTWEIAAADGVGRVRPAPQDAAELTLDVA
+ELGSVLLGGVKAEMMREAGILLAHRPGAAADLDTLLRQARPPYSLTGF
+>MOLHKGIG_01102
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTSPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVGLDAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>NAFOICDF_01683
+MRPHTDLQPTATPRADAEVLAEQGLALVVAPGRAADPAFERHTTAVERGFYEQVPSGEAM
+AQLLEAGEADGRRMVDVLPLGADPATTRPVATFEDFRSELTVSPGVAVSAWLISGVTVDP
+GFRRRGLLRTMMTRSLADAVAAGVPVAALTASEAAIYGRFGFGAATRWRRARLDTRGDVR
+LRGAPSAGRVTREEPREVGALADELYQHVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGS
+GLYAAVHRDAAGTAQGIALYRPQGWDVEPPTVTMELFLALTPDARRGLLTHLTSLDLIER
+IVWERAPEAGWPEALLEDERRLRTERDGDDLYLRILDVPAALGARADLGDGEVVVDVTDP
+LGHAAGAWRIRARDGVAEVTEAAEGEAELGLDVADLSAVWLGGHGSAGGVAARVATGLVR
+EVVPGAGARLDALLRPSVPVRSLVGF
+>MHAAABBN_00821
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGEDPAARRPAATFEDFVQPLTTWPGRAVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPALTGAPAGGRVTVEEPREMPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>LFPAFLNI_01051
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTWPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000157.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43cc12abd4267bfc043a660287569748aca3db8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000157.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_02080
+MSGAPATGQATTTAAGGSPSSPAPAPPEWDAVLFDLDDTLLDLRAAQHAAFDATVRRQWA
+GAADVDPARMAEATEAFASDAAGHYERYVAGELTFEQQRLARAADALRALGAPEESATPL
+EALWTADYEDVVRGHWALFPATAEVLAQVRSSGRGVGIVTNNVEAYQRAKADALGLEWVD
+VLIGSDTAGAPKPDPAPFLAGCARLGAEPGRTLMVGDSLTHDVAGARAAGLVPVWMSPAA
+PARGAAEDPVWDPERGCWRLRAIGGLRAWLRR
+>MOLHKGIG_00175
+MTPPAALLLDLDGTLLDHGRAARIALGQAMQEAGLTDADHSSALLLWGELERIHFQEYLD
+GQTTFEEQRVRRVRAFLAHYGRTRLDRTSALAWFDTYRTAYERAWS
+>MOLHKGIG_00854
+MSRDASTTPAGGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATDAFASDAGGHYGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLRTWLAA
+>NAFOICDF_01975
+MIRTPGTPSAPVVDGVLFDLDDTLLDLRGAQLPAFAETVRAQWPDAPPAEAGVFVRAADH
+FAADRSGHYQRYIAGELDFAGQRLARARDALAVLGAPGAVAEPDPALWTDEYEVRVRAHW
+ALFDDVVPTLATLRSSGVALGIVTNNVEAYQRAKADALGLEAITVLVGSDSAGAPKPDPA
+PFLEACRRMGTTPGRTACVGDSLSHDVRGARAAGLVPVWLRRGAGAADGGGEGRWDAAEG
+AWTIGGLGALAAWFPGSGADLASGREVL
+>MHAAABBN_00576
+MSRGASTTPADGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLQTWLAA
+>LFPAFLNI_00813
+MSRGASTTPADGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLQTWLAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000159.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0221123252ecda3ed8cf2d84fa82e1c1896da849
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000159.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_02182
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTAGFCLALGTWSTVAGQAADAVLAGRWGAAGRIW
+AAHLGLGLLAAAAGWGLGLGARLLVA
+>MOLHKGIG_00747
+MLSGFCLALGTWSTVAAEAADAALARRWGAAARLWTAHLGLGLVAVVVGWGAGLGLHAVL
+AG
+>MOLHKGIG_00748
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG
+>NAFOICDF_02077
+MSAGTVLLTVLLAGLAAAVGAGLRHLADHRWGGRGVLLANVTASALAGALFAIGFGPGSA
+DPEGPAGAALALGAAGAFVLALGTWSTVAFQAAQEVLAGRTRRAVRVWLVHLASGTAAAV
+VGVLAVGFLVR
+>MHAAABBN_00478
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGLMLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAARL
+WTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>LFPAFLNI_00712
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGLVLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAARL
+WAAHLGLGLVAVVVGWGAGLGLHAVLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000163.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08f4898fdaf9db23571de02ed477ad350bdf1108
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000163.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02319
+MTSVPTVPFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGYRHIDTAAIYGNEEGVGRA
+VAASGVPREELFITTKVWNSAHGYDEALAALEESLGKLGTDYVDLWLIHWAKPTQGRYVD
+TWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVVPVIHQVETHPYWQQRELRELEER
+HGILHESWSPLGQGGELLEDPEITAIAEAHGATPAQVVIAWHLAKGFVVIPKSVTSERIV
+SNLAAADVELTEDEVARIDALDREDGRIGPDPATIEF
+>MOLHKGIG_00644
+MTSVPTVPFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLE
+TWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAHGFVVIPKSVTPERIV
+SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF
+>NAFOICDF_00584
+MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY
+RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV
+LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA
+PVDQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEPVAAAAARTGRTPAQV
+VLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPDEFGH
+>NAFOICDF_02178
+MTTVPQTPFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGYRHIDTAAVYGNEEGVGRA
+VAAAGVPREELFITTKVWNSDQGYDEALAALEASLAKLGTDYVDLWLIHWAKPAQGKYVD
+TWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVVPVIHQVETHPYWQQRELREVESR
+HGIVHESWSPLGQGGELLSDPVITAIAEAHGATPAQVVIAWHLAEGFVVIPKSVTPERIV
+SNLTAAELELTAEEVDQIRGLDRADGRIGPDPASITF
+>MHAAABBN_00381
+MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLD
+TWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEVRGATPAQVVIAWHLAQGFVVIPKSVTPERIV
+SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF
+>LFPAFLNI_00614
+MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDASLDKLGTDYVDLYLIHWAKPAQGKYLD
+TWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVVPAIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAQGFVVIPKSVTPERIV
+SNLEAAGVELTADDVARIDALDREDGRLGPDPAVIDF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000164.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0cee2b2314cea567acb04f7ee422c886674b3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000164.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_02344
+MSTPTRNPTPANSSTSGTTSRKAKTIVWVVLAAVVVAGVIAGVVAVGAARNATPDAAATQ
+AGQSAAQGSGPTTAEEAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGAAYPVVEEL
+RAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDK
+SPVFRGYAEELGLDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLTS
+LEQFRAEVDAAASN
+>MOLHKGIG_00611
+MTSTDPTPAKAASAPNRQRRAKIIVWVVLAALVLAGVVAFFAARAPSTPEAAPAQAGQAA
+SSGTGQTAASEAAPVVRPDSRVLSQAPNEKAVLVEFLDFECEGCKAAHPVVEELRAEYAD
+TVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRG
+YAEDLGLDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLNTLEQFRA
+EVDAAASN
+>NAFOICDF_01190
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWI
+NDGLMMTFFLVVGLEVRQEFAHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEG
+LGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVVDDFLAVSIIGIVYSDEIRLV
+PLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALA
+NAGVDLRGGVLVDSFQSSVTWGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVF
+GGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMVLATALGWLIFRVAAKRWGEE
+TADLPMVLTPPVDPEVDHIRGPEDAQLTLVEYIDFECAYCAHATGSWDDLRSRFGDDLRY
+VVRQLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDALEREDLIRYAEELGLDVAQF
+TADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRT
+QEVRS
+>MHAAABBN_00327
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
+>MHAAABBN_01771
+MTSPDPTASTPSSPTPSRQRRAKIVVWVLLGLVVAAALIGYLVARGTATAQQQDPNQSTA
+QSTGQSTGSAGQLVRENSRVLSQAPNEKAVLVEFLDFECEACAAAYPFVEDLRAEYADTV
+TFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYA
+EELGLDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVNSLEEFTAAV
+EAATQD
+>LFPAFLNI_02008
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000171.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58bc794e8df59934f8967226b923b1e456106978
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000171.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_02569
+MTDEQTTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVE
+NNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPLVVVASQIPLSGLGAR
+RKGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLL
+GEVLVPPVQDALAVPYDHPPRAELVDESVRWLRDAQRVAIVAGGGVRRSGRAAMESLREV
+AELLQAPVVCSPGGNTAFPWQHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYF
+TLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAEDAPVWHGRTP
+AEVVAETMGRVAARLDAQDLGVERRLLADIRAAVPSAMQTYWDMTIAAYWAWNCWDAREG
+EFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSIAELAAARQHD
+AAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGAL
+ERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>MOLHKGIG_00386
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>NAFOICDF_01756
+MSARHDAAVPQEAADMAAAAGGAGGGTARRNGGDLAVETLHALGARTVFGIPGQHALGLF
+DALSRSSLRFVSSRVENNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVP
+MLVIASQIPLSGLGARRKGMLHQLDDQKASAKNVTKAQFTVHHASGIPSAIQDAWAEAVT
+VPQGPVWVEIPQDVLLGEVMVPPVQDALAVPYDHPPRAELVAESVRWLRGAERVAIVAGG
+GVRRSGRAAMASLREVAELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRHVTELLEDAEV
+LLVVGSSLGEVTSNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALAALADALRA
+DETARPAERPWHGRTPADVVAEVNAKVTARLDAQDLGRERRLLADIRAAVPSTMQTFWDM
+TIAAYWGWNCWDAQDGEFHSAQGAGGLGYGFPAAFGASVGLASAGRDARVLAVAGDGSAM
+YSIAELAAARQHDADVTWLIIDDGGYGILREYMEGAFGKATATELARPDFAALATSFGVP
+AETVGVEDVRGALERAFQEDGPNVVVVQTRLAMWAPSHLEAPVPADEAGPGLAETTRPEG
+RAA
+>NAFOICDF_02444
+MRALEDRRPRNSRSETLSGRGVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQ
+DVLLGEVMVPPVQDARAVPYDHPPRAELVAEVVRWLRGAGRVAIVAGGGVRRSGRAAMES
+LREVAELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALQALAAALRESGSVARDAAVWH
+GRTPAEVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWD
+AQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAA
+RQHDVDVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>MHAAABBN_00110
+MSDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHLLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>LFPAFLNI_00392
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTALAGLQEAYATGVPMLVIASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESVRWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIEGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000172.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a01e3d538910fef2d9460764675b9b3d7cbbf6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000172.fa
@@ -0,0 +1,41 @@
+>MOLHKGIG_00614
+MGSHHHAPTGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDAAHMLTDAGGLLMALL
+AATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQRLFAPPEVASGPLLA
+FGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIAATGWTRADA
+VAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQALPHVVSVHDLHASQIA
+TGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHSTFQLEPAAHAHHEHPT
+HH
+>NAFOICDF_00544
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP
+>NAFOICDF_00702
+MGAGHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDTAHAITD
+ASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIRRLFEPP
+EVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVIIAAIVIA
+TTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILELDHVKDV
+HDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHSTFQIETE
+HIAEHEPEISKHD
+>MHAAABBN_00326
+MVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLLIALTATTLALRPATDKRTWG
+YKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVESTAMLWFGVIGLAGNLIGLAIL
+ASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWNRADAVVSLLIAALIVPRALI
+LLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHASRIDSDTPVLSAHVTVHNGC
+LTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHTETLHP
+>MHAAABBN_01774
+MGAHHHASPAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDAAHMLTDAGGLLMALL
+ASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQRLFAPPEVASGPLLL
+FGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIATTGWAQADA
+VAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAVPHVVSVHDLHASQIA
+TGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHSTFQLEPAAHAHHEHPT
+HH
+>LFPAFLNI_02007
+MSGHDHSHALPAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLL
+IALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVEST
+AMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWN
+RADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHA
+SRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHT
+ETLHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000173.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80e54bd4c0d6f1570ab3a164775b9cae4a79bf95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000173.fa
@@ -0,0 +1,36 @@
+>MOLHKGIG_01601
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTRSAPVTVPTTYVWGTRDAALGPRAAELTAGQVAGEY
+RFVKLDADHWLPEREADAVARAILDRVR
+>NAFOICDF_00271
+MLHRREYGDPDGVPVLHFHGTPGSGREAAALDAAARAAGVRLIAPDRPGMGRTPHLPGRR
+LAHWPAEVTRLLDELGIDRAAILAWSGGGPYAVACLARIPERLTAVALLAPAGLLRGIPW
+ANRLFPRLYLPAAGAIARARDWAPAAALGVFRWRRMRSRLADGPPAASPEREPLAPSSAA
+VLAASWREAFRQGHAGPVQDEQVINEDWSPLLTSARRAPVPVRIWHGRRDRVVPHRHSRR
+LAAALGAFLVDAHDGDHPGALLTAGPEALGWLAASAE
+>NAFOICDF_01201
+MTGGDALWGRVDAFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDSTSWRHVEPLLHAAGLR
+TLAPDQRGYSPGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATA
+HPERVASLTVLSTPHPAALARALRGSDQLRRSWYIAAFQAPALPERILSRRLGSLLQRGQ
+VPGAEHYARRFSTPQSLRGPVNWYRANPDLVTTTRSAPVSVPTTYVWGTRDAALGPRAAE
+LTAGQVAGEYRFVALDADHWLPEREADAVARAILDRVR
+>NAFOICDF_01824
+MTIPGFALEHIPLPSGVTLRVATGGEGPAVVLLHGHPRTHATWHRVAPALADAGLRVVCP
+DLRGYGQSSAPEPSDDLHTHSDRTMAGDIALLMTHLGHDHFSVVGHDRGSYVAYRTALDF
+PERVDRMAVLDCVPILEALERADARFAEKWWHWFFFASPHAERVICADPLAWYQPDAQKM
+GQENYQDMVAAISDPQTVRSMIADYRASLHVDRDADARDRARGHQIQCPTLVAWSKHDDM
+EDLYGNPAEVWESWCAHRPESAVIDSGHHMAEDNPEQLTAVLTEFFLPS
+>MHAAABBN_01313
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
+>LFPAFLNI_01528
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000175.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8d2bd33d90a1ead5bda6b6f8ddfc7c904b1dce0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000175.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00005
+MSNSKQAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGH
+DAVRATVRLLDPSGAEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLH
+AATVKLAAGVDVELMLAEGAALFRAAAEDAERSAQDRAAFEETARVLADEGLVPAQRLAG
+AESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEAAGTWSS
+GTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGG
+HDAVHPDLGTIADFEDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAY
+AENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGWVGRGVHIFRVDNPHTKPLWFWEWLIA
+RVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEISHETPAF
+YRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESI
+DNEKYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSK
+TRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNPHHVAEATLDLDLSALRLRPEDLDESG
+SFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG
+>MOLHKGIG_00330
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+AHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVAEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG
+>NAFOICDF_00006
+MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRAN
+VYREGHDAVRATVRLLGPDGAEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDP
+VGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGAADRAVFEEAVRGLEDASLAP
+VQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA
+AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAI
+GGEAGGHDAIHPGLGTFEDFDAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRV
+DGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGWVRRGVHIFRVDNPHTKPLWF
+WEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT
+AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARP
+GAEEYIDNEKYEFRPRDWAGEEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPE
+LLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDPHRVAEATLRLDAEALRVRPE
+DRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG
+>MHAAABBN_00046
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASSES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+GTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG
+>LFPAFLNI_00337
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLFDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGVDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPGGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000177.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dbc1ced9511fd1761d3d7ee216a8de655493a9b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000177.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00011
+MDGADVDGTADAVTEPALLHAEALECGYAGVPVTGRLDLVVRPGERVGVVGANAAGKSTV
+LRTLVGDQEPVAGRVRLEGLPVLPESAAHRRALSVLTDEDAYFPTLTVAEHLTLVALGHG
+VPEPDRVVDRELDFFALREAADAPPSRLSSGQRRRLLLAAALLRPFRLLALDEPEQRLDA
+GMRERLTARLAALEPASALVLVTHDPDVLAGAATRCLIVDGRVREAAVAEGAAWIRERT
+>ACLBLIBL_02586
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEIMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGELTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
+>MOLHKGIG_00377
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
+>NAFOICDF_01180
+MSNAPALATRGLTRRFGPVRAVDGVDLTVPAGEVLALLGPNGAGKTTLLDMALGFSPPSD
+GTVRILGSDPVAAVRQGRVGAVLQTGGLLEDLSVRETVAMVAGCHRRHIGVSAALERAGL
+TGLAGRRVKKCSGGERQRLRFALALLTDPELLILDEPTAGMDVRARHDFWDTMHAEADRG
+RTIVFATHFLPEAEDFADRIVLMREGRIHADGTPAELATGGSVTLTGRWAGGGGDPDAPA
+RLAAALGLPRDAVQLEPQHLSPGRLRVRVPAGGRVTGDDVARHLLNERLVEDLAITHASL
+DDVFLSLTDAGQSAPSEPQESLA
+>LFPAFLNI_00383
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000182.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de9b2a9504e6aa83a259b83bc4a0cbcd733ddf3a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000182.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00016
+MSRILIVEDEESFSDPLSYLLEKEGFEVAVAADGNEALGVFERDGADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EPEELVSATLGAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRHLVTVRGLGYKFEA
+>MOLHKGIG_00321
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
+>NAFOICDF_00012
+MSRILIVEDEESFSDPLSYLLNKEGFEVAVAADGNDALEEFERGGADLILLDLMLPGMSG
+TEVCRQIRQRSHVPIIMLTAKDSEIDKVVGLELGADDYITKPYSSRELVARVRAVLRRGG
+EPEELVTSTVSAGPVRMDVERHVVAVDGEPVNLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRAKIEPDPSSPRHLVTVRGLGYKFES
+>MHAAABBN_00036
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
+>LFPAFLNI_00328
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000188.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8479acd98101799d70a97383a81d5aebc07a15f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000188.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00023
+MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR
+IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE
+DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA
+MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR
+RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR
+IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>MOLHKGIG_00314
+MTASAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQC
+EVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRI
+FLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVEQ
+VAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAM
+ALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRR
+RRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLARI
+DAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>NAFOICDF_00019
+MTGAPDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQCEQP
+DPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWRIFLM
+EDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPEDVAA
+LLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDAMAMA
+ARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRRRTRV
+TRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVARIDAV
+HLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR
+>MHAAABBN_00029
+MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV
+ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL
+MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA
+ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL
+AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR
+AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA
+VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>LFPAFLNI_00321
+MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV
+ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL
+MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA
+ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL
+AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR
+AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA
+VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000190.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..955ad69ac2704d407dda62228873341d68220b6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000190.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00026
+MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH
+AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL
+GQGSSDSVGRHAERTLAHLDRAEELAARL
+>MOLHKGIG_00311
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>NAFOICDF_00022
+MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV
+HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF
+RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL
+>MHAAABBN_00026
+MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGAGL
+>LFPAFLNI_00318
+MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH
+AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL
+GQGSAESVGRHAERTLGHLDRAEELGARL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000199.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..002b4099ec4569be4d1eaa8b013dd18afe106a2c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000199.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00056
+MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR
+LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL
+AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA
+>MOLHKGIG_00298
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR
+LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM
+AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV
+>NAFOICDF_00034
+MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR
+AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF
+AELDRQRVRDLVSLPAEFLGLRRLPGA
+>MHAAABBN_00006
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH
+>LFPAFLNI_00305
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000200.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f927ccdeb3aa1616b8d3712198dc024dfa92a56e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000200.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_00058
+MADNATTSFADRALQDAPTDYAQLREWVAQVAELTQPDAVQWVDGSEEEYARLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPEKMHGILDDV
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVELTDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGQEDVPWPCNSTKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTSPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAIAKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPASETPAAHPNSRFCTPIEQTDMLADEYRDPKGVKLDA
+ILFGGRRKTTVPLVTESFDWEDGILKAATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVEESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGRAD
+AVETPIGHVPSPEALDLTGIDVSAEDLEDALKVDAEEWAKENELIEEWLGRFGESLPAMV
+RERFEAQKERFARA
+>MOLHKGIG_00296
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPEFGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEQWLGRFGESLPAVV
+RERFEAQKARFAQA
+>NAFOICDF_00036
+MADNATTSFTELATKDAPTDYAQLREWVAGIAELTQPDAVHWVDGSQEEYDRLAAELVAA
+GTLTKLNEKKLPNSYAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPKEMHGILDDA
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVKESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAG
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKARFAQA
+>MHAAABBN_00004
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPHSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA
+>LFPAFLNI_00303
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000204.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f7987129cb8b8d32af93e73af17f940d0aaa5b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000204.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00063
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQRG
+>MOLHKGIG_00291
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQRD
+>NAFOICDF_00042
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG
+>MHAAABBN_02314
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQRD
+>LFPAFLNI_00298
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000205.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76cc296b66120b8778e13447db76738712796dfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000205.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00065
+MATSGRRGRLTRRAVLGLGAGALALGGGAAVANLAGVPPAPVGPDVNALFGMRSSTGHRY
+ADLPGRAGRVDVYRPQGPGPFPVVVWNAGSGWRDDRGYHDGQTVARGLVPHGYAVAAFSV
+RSSKQGRFPAQVEDATAAVRWVRAHAVELDLDASRLTVAGTSSGGWNALMAGLTGGRDLD
+RAHVPPPGREVPPGGHAIPEEDRVQAILDFFAPTDFLAMNAQMPPGACADYNRQRRLEHC
+HLDDHSTKSAMLGVPVLASYGLTRLASPIAHVRPDSPPMMIVHGLKDPTVPWRQSLELYE
+AAEAAGVRAAFYSVADAGHDLGMMGGGWGSAEVLRSGVPLSAVHATISWAAVAAFLDTVL
+PG
+>MOLHKGIG_00289
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+ATLPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVQAIVDFFGPTDFLTMNRQMLPGACADYNRANRLKHC
+HLDDRSTKSDMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAETAGLRTAFYSVAEGSHDLGMMTAKTRSAEVLRNGVPASAVHATISWSAVASFLDAVL
+PR
+>NAFOICDF_00044
+MGGDTSTARAPRVRRRTLLGLGLGALAVGGTATALGHGSPVDSPALRQTMGALFGTTVIS
+GIVYADLPGAAGRMDLYLPEGEGPFPVLAWNAGSGWRSDRGFQGGDAVARGLVPAGHAVA
+AFSVRSAREDAFPAQVLDATAAVRHLRENAGELRVDPGRIAVGGNSSGGWNALMAGLTGG
+RDLDRSAVPAPGDEVPEGGHAIPEEDRVQAIVDCFAPVDFLQMNVQMPRGACEEYDRRNH
+TRHCHLDDASTKSRMLGAPVMARPELARLANPAVHVTPAAPPTLIVHGRADREVPYVQSR
+GLYQAYVGAGVPVAMYSVEGAGHDLQMMARRVGRTDVVRSGLPRQAVHGSISWSAVAAFL
+DVAMPRPRR
+>MHAAABBN_02311
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR
+>LFPAFLNI_00295
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000206.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1969fb0f62b0f870793e6984929acaff011c89af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000206.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00066
+MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>MOLHKGIG_00288
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>NAFOICDF_00045
+MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI
+LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV
+WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA
+>MHAAABBN_02310
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>LFPAFLNI_00294
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000208.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6add9237d8deafe7f8c15fbbe21845f06ef6d671
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000208.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00070
+MAVPSPSPARNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFAAGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPHEDPLPVAHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGVDDLVPLHRLDRATAGVVMFSVDPATRGAYHLLFERRAVAKTYEAVSALPP
+DADDDGLVLGRFPLTVRSRIRKDKGVLRSVVEEVPAAASGRRAGAPVRTRRSNAAHAGAN
+AESRVEVLGVGESAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFYPDLLDA
+APDDFSRPLQLLSRSLRFTDPLTGREREFVSPAQLQERPR
+>MOLHKGIG_00283
+MAVPSPLPPRNGVNATRLRLPTSGWPTAQDYVLHRFGHVDPEGIRARFARGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLPD
+APDDGARGPGAPTDPILGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRRS
+NRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDP
+FYPDLLDLAPDDVARPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
+>NAFOICDF_00056
+MAAPSPLPPRNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFARGEVVARDGSP
+LTPTTPLGVHEDLWYYRDVPHEAPLPFQHTLIHRDERLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGIDDLVPLHRLDRATAGVVMFSADPATRGAYHLLFERRAVTKRYEAISALPP
+ARDHADDDAAAWLDRFPLVMRSRIRKDKGVLRSLTEEIPAAASGRAAGARVRTRKSNLSH
+AGANAETRIEVLDVGRSAGTLAGAPVVRFRLSPRTGRTHQLRLHLAALGLGIAFDPFYPD
+LLDAAPDDLARPLQLLSRSIAFTDPVTGEHREFVSPAELQERPA
+>MHAAABBN_02298
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVVLLP
+EAPDDGARGPGAPADPVLGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
+>LFPAFLNI_00282
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLP
+DAPDDGARRPGAPADPVLGRFPLTVRSRIRKDKGILRSVVEEIPPAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000214.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78ac9594ff668e6f7b23ff950cfc0b9466f679b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000214.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00087
+MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF
+IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD
+SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH
+RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR
+AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE
+NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG
+RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV
+DRIRAALQDGTYAELKEETLGRYYAPKG
+>MOLHKGIG_00270
+MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA
+TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>NAFOICDF_00064
+MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ
+TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP
+TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT
+GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL
+TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA
+IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY
+TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT
+VSLVDRIRASIQAGTFAELKAETLGRYYAPKG
+>MHAAABBN_02285
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>LFPAFLNI_00268
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000218.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f24eab487ef843415b3ab9645f221d0dbf8a1108
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000218.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00096
+MARMSTPAEDTLTALIHLLDREGYDAVTADQLAREAGMSRASFFRNLGGKEEVVFADHAT
+LLAHLEELLRGTGLGVREALDEAVLQVFRHHTRDPERAQARARLLRGSQALRTRELLTSH
+RYEELFSAWLADALPDTPARGGVAVGLAAAVVAVHNRALRAWLHSPDDDAEAGLRADLAE
+VVARLTAEPSAAERTLEAVRRLLG
+>MOLHKGIG_00267
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>NAFOICDF_00067
+MNPMTAVPEDTLTALIHLLDRQGYDDVTVDQLAREAGMSRASFFRHVGGKEEVVFADHEQ
+LLPRLEDLLHSTSLPLPTALREAGLQVFRHHVQHPERARARARLLRGSRALRTRELLASH
+RYEQLFSRWLAERLPDTPTRGSVAVGLAAAVVAVHNAALRGWLHAEAPDPTAAEAALGAQ
+LDEVILRLTREPGEAEVRLAAVRALLD
+>MHAAABBN_02280
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>LFPAFLNI_00265
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000221.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10de3ee173b94bb03a5cf0b259547f05cacea0e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000221.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_00099
+MLEFLTGTGLATSAGLNAYIPMLALGLLDRFTGLVDLPAGWTWLSADASLWILGVLLLLE
+VVADKFPGVDAVNDAVQTVVRPAAGGIVFASGVGTETTAVHDPGTLFGGSGWVSVLIGAG
+IALAVHLAKAGTRVGANTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLVVAVVVG
+LWLLARRFRARRTRGRAAAAAGGSEWTA
+>MOLHKGIG_00264
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>NAFOICDF_00070
+MLALGLLDRFTPLVDLPPAWAWLSSDVALWVVGILLVLEVVADKIPAVDAVNDVVQTVVR
+PAAGGITFASGVGAQTVTVQRPDTLLDSQVWVPTLIGAAMALLVHLTKAGTRAAANTVTM
+GTAAPLLSTAEDASAVVLTAAALFLPVLVLVVLLAVLVGLWAVPRRFRAGRRGGRRATMA
+S
+>MHAAABBN_02277
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>LFPAFLNI_00262
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLAADASLWILGVLLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRDRRTRGRAAAVPGGPEWTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000223.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86d37f0f31142cb5486ad4a2e7dd834005754cd3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000223.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00105
+MRQNSPVPGSLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVDPHRMGAA
+ERRGLARTEAAASGAFVAAEAASSLRLAGLPGRVGPAAGGLAAGAATAALALSTVPLNDR
+IDGALVRFLERAGASAPRAVLAGTAALSVLAGNESVRRERRNALEEAAWPAWDDLSEEEQ
+SEPTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVASMAEAIRDEDEVPD
+WTPLVVETDGPVDRAVPHDHVWPVRGRFAVGEDGHEVELRLQVIDGELGALVITLPADED
+ADPDAWDAFQELEAFPGVEDLTFQVDGERRD
+>MOLHKGIG_00262
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG
+GAVAAVALRTAGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>NAFOICDF_00075
+METPRTPETRTDPPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRPPVVR
+TVVTESERIERPVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRVLRERLATPEPTPLER
+LADAGRGAGLPLALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAGEDD
+VDGLPPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVR
+TAASVAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFTTEDGHELELRLQVI
+DGELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP
+>MHAAABBN_02275
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG
+GAVAAVTLRATGLNDRIDGALVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>LFPAFLNI_00260
+MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALRGLGGLAVG
+GAVAAVALRATGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDAVDEVEPEATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVTSVAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000225.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f1cde28769ce81a0db8f1bbfb5f48d83a7ec1ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000225.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00112
+MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG
+GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM
+ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY
+QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA
+YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG
+>MOLHKGIG_00257
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>NAFOICDF_00080
+MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD
+GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE
+QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD
+ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG
+DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG
+>MHAAABBN_02271
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>LFPAFLNI_00256
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000227.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96ebaab49dd8a5bf555e9a165fd43939357621e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000227.fa
@@ -0,0 +1,90 @@
+>ACLBLIBL_00114
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTLTVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGALPASAHEGAVA
+TPAVPEALRRSSAFMTHPVFNTHHSETQMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGGFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATEHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLQEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEDAVADTADED
+>MOLHKGIG_00255
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPESLRRSSAFMMHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEGAVADTADED
+>NAFOICDF_00082
+MTSPLTPTEPRDTASAPFVARHIGPRGEDVRHMLQTLGLGSVDELVDTAVPSVIRQSAPL
+DLPAPLTEAAALEQLREIAGRNVVKTQMIGQGFYDTVTPGVILRKVLENPAWYTAYTPYQ
+PEISQGRLEALLNYQQMVEDLTALPIANASLLDEASAAAEAVLLMHRANRKKADGITLLD
+ADLFPQTLTVAQMRAEAVGLEVRVADLSAGIPEDVRAEVEEKGLCGVVLQQPGDSGRLHD
+HSAVIAQAKEAGALITVAADILSLALITPPGEQGADIAIGSTQRFGVPLFFGGPHAAYLA
+VREGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAITASMY
+AVYHGPAGITAIARHAHAQAHRLAIALAGAGVEVAHAEYFDTLTLNVPGRAEEVVRAAEE
+AGVNLRLVDADIVRVACDETTVDEDLAAVLTAFGADPASLPAAPHEGAVQTPAVPEAQRR
+TSAFMTHPVFNTHRSETQMLRYITRLANRDLALDRTMIPLGSCTMKLNATTEMEAISWPE
+FCAIHPFAPDHQTEGWRFLISDLEERLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLA
+HGDGERDVCLIPASAHGTNAASAVLAGLRVVVVATADDGTIDSADLDAKIAAHEGRVAAI
+MITYPSTHGVFDGDVTEVCDKVHAAGGQVYIDGANLNALVGLARPGAFGGDVSHLNLHKT
+FCIPHGGGGPGVGPVAVGEHLVPFLPSAERLVTAAPHGSAGVLPISWAYIAMMGGEGLKD
+ATEQALLNANYISRRLADHYPTLYTGEGGLVAHECILDLRELTAQTGVTAEDVCKRLIDY
+GFHAPTLAFPVAGTLMVEPTESEDLAELDRFIDAMISIHAEITATTPETVEQSVLRRAPH
+TLGATTGEDWDRPYTRAQALYPLPSLVDDKYLPPVGRIDGAYGDRNLVCSCPPPEAFEEA
+AASPESTEPVSAADTASTSH
+>MHAAABBN_02269
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPESLRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEDAVADTADED
+>LFPAFLNI_00254
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPQDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLKAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPEALRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIEDLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEGAVADTADED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000228.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..460ac5bc7f8f0a7249078d92ac945d61f10acabc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000228.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00119
+MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA
+GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA
+RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR
+DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR
+DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS
+GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV
+EAIYSYEGSYGMNTLIVGRALTGVSAFV
+>MOLHKGIG_00251
+MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>NAFOICDF_00087
+MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE
+ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV
+AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI
+AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS
+KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI
+LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA
+AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL
+TGVSAFV
+>MHAAABBN_02263
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
+>LFPAFLNI_00251
+MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW
+DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI
+AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI
+GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA
+DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ
+AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG
+LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000229.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a767cd6d5963ff8657f81d4d3e98f22ba87fde22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000229.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00121
+MKNAPLPQDPIREAARNWERHGWGDVARPMAAVTSIMRAQQILLGRTQAALKPFGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLESAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNEEVFGRTGFDEADVDALIDVFGRFRAGAGDFEADGADTTTERPS
+A
+>MOLHKGIG_00249
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSRENRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFGPADVDTLIDVLGRFRAEAGDFQVDGPDAGAPATA
+EHTSS
+>NAFOICDF_00089
+MSTRDPLPQDPIREAARNWEHHGWGEVAAPMAAVTAIMRTQAILLARTQAVLKPFGLTFA
+RYELLALLNFSRERRQLMSKAGALLQVHPTSVTNAVDRLEAAGLVERQPHETDRRALLLA
+LTDEGRRVADAATEALNAEVFGATGFTDDDVAALNEILGRFRAGSGDFEA
+>MHAAABBN_02261
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS
+>LFPAFLNI_00249
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000231.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e537c96e41111f39cdc5f1467033330da293eb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000231.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_00123
+MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS
+EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE
+FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG
+RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR
+QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE
+VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL
+AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG
+APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV
+GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL
+EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE
+QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA
+>MOLHKGIG_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>NAFOICDF_00092
+MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD
+DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA
+ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL
+GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV
+PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS
+GIIETVREAGKDTAA
+>MHAAABBN_02258
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>LFPAFLNI_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000238.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b37b6765c281aea2cc970deaf3d9777ac10431d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000238.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00136
+MAIHPVDATLQAAKIDPEERTERLQGVKLDGAGWKYALGRAFKEFGKDGGTDLAAKLTYF
+MVLSLAPSLLAVFSILSLVLASNRGAIDDLMAQMTGLVPGEYQPLVTDLVTTMSESASGG
+GGIVALVVGILTALWSASAYVKAFNRSVNTVYGYEEGRGFVKLTLSNLLTTLIMIVGIVV
+VLISLALNRSLVDGFLAPIAGPLGMTGAVNFLSDTFLPIWAWVKWPVVVVILLLLIATLY
+YTTPNVRKPSFNLFGPGNVFALVGMVLAAVGLSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGVEIDAEVERAKQLVAGLPAEEAVRLPPKDASALEKRVEKQTALQERGYELRA
+THEDR
+>MOLHKGIG_00235
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGELTGLVPSDYQPLVTNLVTTMSDSAGSG
+GGIIALIIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLLSLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWAKWPVVVVILLVLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTVMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA
+VHEGR
+>NAFOICDF_00101
+MAIHPVDATLEAARIDPEERTRRLKGVKLDGAGWKYAFTRALKEFGNDGGTDLAAKLTYF
+MVLSLAPALLAVFSILTLVLSSNRSAVDDVVRQLTELVPADYQGVVGDVVDNLLGQAGGG
+VLALIIGILTALWSASAYVKAFSRASNQVYNYSEGRGFVKLTLTNLVTTVVMLVGIVLVL
+ISLALNRSLVDGFLAPIAGPLGMTDAVNFLSDTFLPIWAWLKWPVVVALLLVLIATLYYF
+APNVKKPSFHMFGPGNIFALVGMALAAVALYFYFTTLAGYSAYGAIGGVMALLFALWIFN
+IVLLLGLEIDTEVERAKQLTAGMPAEDAVKLPPKDVSALEKKVEKQEELEEKGYELRALH
+DDGSDSDSDEGKGVSRAPRHAAGSHGA
+>MHAAABBN_02248
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG
+GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLLLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA
+VHEGR
+>LFPAFLNI_00236
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG
+GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLVLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRVEKQTTLEERGYELRA
+VHEGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000240.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a979e9c82dc7c8dbaac4ea7aa2ab655107e562e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000240.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00138
+MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT
+PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV
+SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL
+GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA
+WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD
+GGDDPVDGRR
+>MOLHKGIG_00233
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>NAFOICDF_00103
+MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT
+SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI
+VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW
+VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG
+LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG
+GDPVDGVR
+>MHAAABBN_02246
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>LFPAFLNI_00234
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000245.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cc4bf63481e1bdbd03a6ca38ce06bc1b0ef9d30
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000245.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00151
+MTFEDLIGTLNDVIWSLPLIYLCLAVGLYFTVRTMFLQFVNIPDMIRQLREGEDSKDGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWAMALLGAATSFIESTLGQIYKER
+DRDTGEYRGGPAYYFTKAYSHKPWGKALVVYGVLFAIVTIFATSYFLPGVQANGVAAAVE
+QAWNVEPWIVAVAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIVLALIILVLNADQIP
+VVFGSIFSSAFGMDAVFGAIVGLAIQWGVRRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYEGESEAGAVIFEGGSLPATASVGPAYVQSG
+FDAMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFITRNFSNPLFRRVALRALQGLI
+LVSVAYGAVATTGAAWGLGDIGVGSMAWLNIIGILLLQGPALKALKDFRAQKRQGLDPQF
+DPRPLGIHNATFWEERADGRITPGVAGTAPTPVVDADGGSPRA
+>MOLHKGIG_00230
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAAG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD
+AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVVLRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
+>NAFOICDF_00108
+MSFADLVTEINDVIWSPALIWLCLIVGLYFTVRTMFLQFVNIPDMVKQLREGEDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYRHTAAGGAFKVYAILFAIVTVFATSYFLPGVQANGVAAAME
+QAWSLPPWVAAVGMVILLAFIVLGGVKRIATFAVYVVPIMAIAYIILALVVLFMNWEQIP
+EVFGTIFSSAFGTHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVFEGESETGRVLFEGGTLPVTASVGPAFVQSG
+FDAVFAGFGPTFVAIALAFFAFTTIVAYYYMAEVNLVYLTRTLRNGTVRRVALRLLQALI
+LVSVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKKQGLDPQF
+DPRPLGIKNADFWEHRADGLITQGVGGLSTDVRADTADGAGSHRA
+>MHAAABBN_02243
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD
+AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFLTRNLRNGMVRRVVLRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
+>LFPAFLNI_00231
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDGSGSGLLFEGIVSPTASEGPAFVQTGFD
+AMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVALRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000252.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7d14f09f0d4a97d36432ce86d6d55858010b0a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000252.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00166
+MDRSNEIPPELQGLDWGEDDAPRRRRPLITLVAWLCIIGLVLGVAAGLFSIL
+>MOLHKGIG_00215
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
+>NAFOICDF_00119
+MADLPPELEFAEFDDDPRPSAPSPWVRVLAVVVLLGLVGSLAAGLFGGI
+>MHAAABBN_02208
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
+>LFPAFLNI_00215
+MDRELRTPPELEGVDWHDGAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000259.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3011c0e2d9f6dea027a229874ed0c976270595f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000259.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00182
+MPRQNPTGRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSVRMVTEL
+RSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRFTVERRG
+ASGEDRPAYVERWTAAPHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDADGIRRSGQD
+AVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGDVEPLQAPP
+SDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG
+>MOLHKGIG_00209
+MRQRQTQTRRTRRGLSLAALGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRFTVERVGA
+SGEDHPAYAERWTATPYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>NAFOICDF_00128
+MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV
+RLTTEARNDSGAAPGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERFT
+LEQPGGVSGEGRPAFAEKWKKAEPLPGDASMRSILDGVLTAVPQAGALQGADVRATDIRR
+QGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNAVEPV
+TAPATEDMAQDTATAK
+>MHAAABBN_02202
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>LFPAFLNI_00209
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGEVDPVQAPPA
+DEVLKQDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000261.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc5292ce48add17b7b51a59a59330def2da2587d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000261.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00188
+MTSYADLAARFADAFDAVGHGERAREAGRHLPFAVQRGLQEAGFGRVSVPEVAGGDGASH
+ETALRLLMDLAARDVNTAHLWRSHLVFVATVLDQVPAAAEPWLERVVAGDWAGSALAERG
+TAAPGRAATMAERDEGGTWVVTGEKYYATGSAFATWTIATVGVDGDGLVSRRNSKRAGGV
+VREPGRAVAVVRVRQPRVRVKDDWDGFGQRLTATGSVVLDGAAAEALLEVPRREGPVPVL
+QEASLLALQVGVGRAALAEGVELLRARRRTFNTGTEALPAQDPQLLEIMGRLAGQLAAAE
+ALVRQVGGLMDEAEERGTAGDDDGAARLMEEAMVAAYRAQAVVPDAVLGVCTGIFDTLGA
+SATSAALQLDRHWRNARTLATHDPAAFKVRMAGDHLVNGTPPTAYTSAGVVDDD
+>MOLHKGIG_00203
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPEDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD
+>NAFOICDF_00143
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRDRWLRHIVAGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRKRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGEDGADGAGLAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGDAQD
+>MHAAABBN_02198
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALAELQAAGFGKVGVPEDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD
+>LFPAFLNI_00205
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGEDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAYKVRMAGDWLVNGTPPTAYTSAGEVPEGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000262.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1853fac150d5e930710feaa146cc062e496acd1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000262.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00190
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR
+>MOLHKGIG_00202
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST
+>NAFOICDF_00144
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR
+>MHAAABBN_02197
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST
+>LFPAFLNI_00204
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000263.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7056a41c4bd268de103e2522fed88a5f73f2924
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000263.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00198
+MTVLDRPGGRTAVGLIVPALLLLLWWALTAAGVFSGVQLPPPAWVAEAAVDLAARGTLWH
+HIAISVQRVLVGFLIGGALGLLVGSVLGLSRWADALLAPTIGALRAVPSLAWVPLLILWM
+QIGEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAYGYHGVRLLGTVQLPAVVPA
+MFSGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKISDW
+LLGFVERWAVRRWA
+>MOLHKGIG_00204
+MSAALTTPAATTGPEARERSGHDDGDTGARRRQRPRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>NAFOICDF_00140
+MSTALTTPAATTGPEARERSGHDDGGTGARRRQRSRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>MHAAABBN_02199
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
+>LFPAFLNI_00206
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000267.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de1be6d170ffb799072d3ad3922a661b41bf0c9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000267.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_00206
+MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI
+GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD
+VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP
+LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE
+PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN
+ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG
+PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS
+VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA
+>MOLHKGIG_00194
+MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>NAFOICDF_00153
+MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRTRDGAVVPAEQEA
+>MHAAABBN_02190
+MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA
+GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ
+ALTEATGRTRDDDGAPAAPKEA
+>LFPAFLNI_00194
+MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA
+GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL
+EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS
+AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP
+IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG
+EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS
+WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL
+QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ
+ALTEATGRARDGAVVPAEQEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000268.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cabec345de0cd8be45eb5b786d8edfff1ce0f06c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000268.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00207
+MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>MOLHKGIG_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>NAFOICDF_00154
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>MHAAABBN_02189
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
+>LFPAFLNI_00193
+MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN
+PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW
+NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000274.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32568d6dd2fdd4475e99270fa79ae212af1ab27a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000274.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00217
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEIAAERGVRVPMEATIRD
+>MOLHKGIG_00184
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
+>NAFOICDF_00162
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRIPMEPTVRD
+>MHAAABBN_02180
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRVPMEATIRD
+>LFPAFLNI_00181
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000275.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77523baddde85d57d1dafebb851e857bf38039ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000275.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00218
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS
+>MOLHKGIG_00183
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS
+>NAFOICDF_00163
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD
+>MHAAABBN_02179
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS
+>LFPAFLNI_00180
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000276.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7364420d81a7aff152e7063af4a104b3df64cd1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000276.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00219
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR
+>MOLHKGIG_00182
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR
+>NAFOICDF_00164
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS
+>MHAAABBN_02178
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
+>LFPAFLNI_00179
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000278.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c163f917ed14cc7aa84f45aef7937bea10cdf80
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000278.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00221
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ
+QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI
+HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA
+AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL
+LPAHRVWERFGTTGRFAD
+>MOLHKGIG_00180
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE
+LLPAHRVWDRFPTTGRLAD
+>NAFOICDF_00166
+MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ
+QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI
+HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA
+DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE
+LMPAHRVWERFPTTGRLAD
+>MHAAABBN_02176
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD
+LLPAHRVWERFPTTGRLAD
+>LFPAFLNI_00177
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ
+LLPAHRVWDRFPTTGRLAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000283.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c14999e75ca6c1b5d3e10472b73edde136d2a451
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000283.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_00233
+MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD
+QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS
+TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL
+VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP
+FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA
+AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG
+>MOLHKGIG_00150
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD
+>NAFOICDF_00172
+MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA
+SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC
+TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY
+QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN
+EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD
+IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV
+GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD
+>MHAAABBN_02164
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD
+>LFPAFLNI_00158
+MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP
+TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS
+VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA
+QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA
+WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD
+FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP
+RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000284.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ded6e56c283b8f671c29228d5cbf892cfa44a84
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000284.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00234
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA
+>MOLHKGIG_00149
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA
+>NAFOICDF_00819
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA
+>MHAAABBN_02163
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
+>LFPAFLNI_00157
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000285.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9efd86ac9d9ce383fd3fb4d3b6393bc162c18f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000285.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00235
+MTTQPHHSTPASAEQLQHDWDHNPRWAGIERTYSPDDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGDFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYHERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>MOLHKGIG_00148
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>NAFOICDF_00820
+MTEQTVQQIAQEIQKDWDTNDRWTHIERTHTAEDVAKLRGRVQEEHTLARRGSEKLWEQL
+TSEHAKGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYPANS
+VPAVVRRINNALLRADQIEWSEGIKTVEDYLVPIVADAEAGFGGPLNAYELMKGMIASGA
+SGVHWEDQLASEKKCGHLGGKVLIPTGQHVRTLNAARLAADVAGVPSVIIARTDAEAATL
+ITSDVDERDAEFITGERTAEGFYKVKNGVEPCIARAKAYAPYSDLIWMETGTPDLELARK
+FAEAVKSEFPDQMLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYTFQFITLAGFHALNH
+SMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAISTAVNPESSTV
+ALKESTEAGQFH
+>MHAAABBN_02162
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>LFPAFLNI_00156
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000287.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cee38f0cf89a899b8aea70091a7299b9a7d6be43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000287.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00238
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>MOLHKGIG_00146
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>NAFOICDF_00173
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>MHAAABBN_02160
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>LFPAFLNI_00154
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000289.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..579faedaa828c795faace9ceffd93f20a0819ff6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000289.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_00241
+MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR
+YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM
+VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL
+SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGGVPTSSS
+>MOLHKGIG_00143
+MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTE
+WAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGS
+TRSINAGVAAGIAMHAWIRQHAAVP
+>NAFOICDF_00175
+MGSGEGVDAREVGREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYRYWTVEAIVADL
+DRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVHHH
+ETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSEEVRAASEAV
+LSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV
+>MHAAABBN_02157
+MLDHYRYWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRW
+NRRGAMVTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFG
+QEGPGLSAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAAVP
+>LFPAFLNI_00151
+MPREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYRYWRLEAIVADLDARRHPFHVAI
+ENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTEWAA
+GEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGSTRS
+INAGVAAGIAMHAWIRQHAAVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000292.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f824ca951c6d587be58c8604a6c381884e327ca8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000292.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00244
+MGGMTDAQTPTVPTPEQDRERLKELIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGVQFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRDVVVLEDTSTTGGSALTAVEGVRRAGGRVQAVAVIVDRATGAAERVAE
+EADVPYLYAFGKDELGLD
+>MOLHKGIG_00140
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>NAFOICDF_00178
+MTAEHTSVAPTPEQDRERLRELIKELAVVHGRVTLSSGAEADYYVDLRRVTLHHEAAPLI
+GRVMLRLLEENGIEFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGMGRQ
+VEGPGVEGRRVVVLEDTSTTGGSALTAVEGVRKAGGDVQAVAVIVDRATGAAERVAEEAG
+VPYLYAFGKDELDLD
+>MHAAABBN_02154
+MGGMTDAQTPTVPTPEQDRERLKQLIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIEFDAVGGLTMGADPVATAMMHQAGTVGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>LFPAFLNI_00148
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000293.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1465e1a9edf21037b1a9a4c984cab0f3afe0af0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000293.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00245
+MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS
+RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>MOLHKGIG_00139
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
+>NAFOICDF_00179
+MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN
+ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA
+VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA
+>MHAAABBN_02153
+MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS
+RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA
+TADVPRDQIDDAVRVLRRIARNLGHPDA
+>LFPAFLNI_00147
+MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR
+AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT
+ADVPRDQIDDAVRVLRRIARNLGHPDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000296.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..837ae56bebec567bde132ba5866df628d7f70e8b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000296.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00248
+MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE
+VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE
+TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDADRAHPDEEDGPGRDEDGPSGR
+HRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRHA
+PDAELIAELTVMVEWLGAFHPDSHVELDYGGLTRHVWPDDSVFDLWTLIDALGEGDEATA
+GVAQGRLNRRWAAVGMLARLT
+>MOLHKGIG_00136
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHSAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAVEDPQDEDGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWVELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWATVGMLARLT
+>NAFOICDF_00182
+MRTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAEVEAEAAERARRRLLRLPADPFPAPG
+EDDLVRVLERGGSAFYCPDELALRMEMAAEMLEASAPEALYAAAVPAAARAMNRGRALVA
+LEDEWGLSPDPDAPAPDDPQDAAHQDQDADAGTHRLQTRTSLWGVPHAWLAAFDPEEPAR
+RLVDGEDVAYRRTPVAEAVERVGHAAAVLAGAAPDAELLGELAVMIPWLQAFHPDAVLEL
+DYGRALTSLVWPDDSVFDLWTLLDALEEGDEVGAGMAQERLNRRWARVGMHAHDG
+>MHAAABBN_02150
+MTHDDGGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHALDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
+>LFPAFLNI_00144
+MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA
+RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA
+ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD
+PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP
+DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000297.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5bb7ce280cb3cf481ea04d7b31d1cca9f5d0cce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000297.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_00250
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>MOLHKGIG_00135
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>NAFOICDF_00185
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG
+VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT
+SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG
+QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS
+PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV
+RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE
+HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR
+VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH
+LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR
+>MHAAABBN_02149
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>LFPAFLNI_00143
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000301.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a341d887f98ad3b4633681238434da9e75301568
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000301.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00259
+MSAQTQPAAPREDAPLGVLVGVDGSEQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWGY
+GADAGGTVLDDSRLREGVQVLLDEVAAKLDADGVRPELRVEVGDAAGVLVDLSKAASLLV
+SGGRGRGGFIGRLLGSVASALPGHAHCPVAIIPAGVEASRAADGAAVVAGVDGSEQGRAA
+ALVAAEEARIRQAPLKLVCALPPVGGNAAWLGVTLDEAAREQELRERLDAGAAWIASEFP
+GLEVVTELVDGTPVDVMREQTATARLTVVGTRGLGGFTGALVGSTSRGVTDHAKGPVMVV
+PFRKDARLGTRTKFGPVADQD
+>MOLHKGIG_00126
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADASGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLEAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQTATARLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLGRRASFGPVQDQSGS
+>NAFOICDF_00193
+MSAETTPSTLPAEAPLGVLVGVDGSDQSISAARWAQREAGLRNLPLTLATAYTVPAFWGY
+AADGAGLLTDDGRLHAGVEALLREVAGKLDPAGVAPELRVEVGDAAGVLIDLSAQAELLV
+SGSRGRGGFIGRLLGSVSSALPGHAHCPVAIIPAGVEASRADSGAPVVVGVDGSEQGRAA
+ALVAAEEAQARKAPLHLISALPPISPNAAWLAVSLDEEAREQELRERLEDGARWLASEFP
+GLEVTSELASGVPVDVMVEQTATARLTVLGTRGLGGFSGALMGSTSAGVANHAKGPVMVV
+PFREDVRLGRRAEFGAVVDQDDPRV
+>MHAAABBN_02140
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLSRRASFGPVQDQPES
+>LFPAFLNI_00134
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLGRRASFGPVQDQPES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000307.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaea668e520a68b138583fdfa349bb2198c432eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000307.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00271
+MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN
+PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA
+QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG
+TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA
+QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA
+>MOLHKGIG_00116
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA
+>NAFOICDF_00203
+MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH
+PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA
+QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN
+GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK
+AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA
+>MHAAABBN_02129
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA
+>LFPAFLNI_00121
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000309.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e364a1676879946e4b80713bcffa677203f848e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000309.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00277
+MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV
+EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD
+>MOLHKGIG_00113
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>NAFOICDF_00218
+MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG
+RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW
+YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA
+EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD
+>MHAAABBN_02126
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
+>LFPAFLNI_00108
+MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG
+RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW
+YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV
+EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000310.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60dd3d2999fea392c607f931edc35ea94a071746
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000310.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00278
+MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA
+SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE
+TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR
+EVAWALQSALEALGRVNTDLGMVLVRES
+>MOLHKGIG_00112
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>NAFOICDF_00219
+MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA
+ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE
+TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR
+EIASALRDAVLALDRVNTDLGVVLVRES
+>MHAAABBN_02125
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
+>LFPAFLNI_00107
+MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA
+TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE
+TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR
+EVAWALHAALEALSRVNMDLGMVLVRES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000311.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad889cd2aa6d03141f092cdc1f477ae9439a62f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000311.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00279
+MTPGLAVVALLLCALAAMMGFRDAPNAVALPVRFRALTPRLALVMTALINAVGALLGIGL
+ITLSVHYFTSPAVRGDVGPLAVGVTAVVAVLWGLLLWWRRLPGSTTHAVLSALAGAHLAV
+QLSLHDDLAGSILESVRVEVVLSLLLSPVIAWGLARLLTGPVVQVATTGTTVNVQRRARI
+ALAVSAGAMAMGHGLQAGQRVGVLWAAVLVGSGAALSPDALTAEFVVGSVLFALAIALGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVVPAGLLFVGSLVLHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVGGWWLLTPVVCAALGLLGTLALLPLA
+>MOLHKGIG_00111
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
+>NAFOICDF_00220
+MTAPLLVPVLVLLLAVGGLMGFRDAPNAVALAVRFRALTPRVALILSALLNAVGVLLGAL
+MLTLGLPLMVAGGTARPEVLALVGVAAAVTLGWGVLAWRFRAPTSTTHALLASLAAAHVA
+SVSALGSGLDPAFENGARWEVAASLLLSPVLAWGLARLTARPVLRLATTGTTVNVQHRAR
+IALAVSTGLIALGHGVQAALRLLPLAVLVATAAVGTGLPPGTELSAAFVAAAAVGIGTLG
+GAWGIAWTLTERLVILDPLRAAVAAVVPAVLLFAGTMLLHLPLSSTHTGVAGIVGAGQTQ
+SYASVRWGAVARVAVWWVATPLVCGSLAFAAGAVLLPLLG
+>MHAAABBN_02124
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLRLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
+>LFPAFLNI_00106
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPATRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000320.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0106379c28a15ac0e58fba47a50590b38de12bc7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000320.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00289
+MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ
+QA
+>MOLHKGIG_00101
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA
+>NAFOICDF_00235
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA
+>MHAAABBN_02114
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA
+>LFPAFLNI_00096
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000325.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2502b46492950bdb9e9aa1926e6ece7a919c90f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000325.fa
@@ -0,0 +1,61 @@
+>ACLBLIBL_00296
+MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL
+LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK
+MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY
+MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV
+SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL
+IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI
+TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM
+QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA
+LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI
+VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT
+AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR
+SGGARPGARAAAAVALLTAIAVLMRQARRG
+>MOLHKGIG_00095
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>NAFOICDF_00241
+MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS
+TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA
+AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG
+PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA
+LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT
+IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW
+KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ
+MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL
+QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE
+RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL
+RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG
+>MHAAABBN_02108
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>LFPAFLNI_00090
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP
+AALAVAGTALLAAVVTALVRARRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000329.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..972eecba2f650d0d02387fbbf43c43c06b35ba95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000329.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00300
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGDAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGLKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR
+DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFNVAGHRSVSAFRRGRNVPD
+>MOLHKGIG_00091
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP
+APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>NAFOICDF_00245
+MTPERLAAAFDGPTPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGLKLLSGPGNLGQGLGITLQMGHVPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR
+DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>MHAAABBN_02104
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPAAPARFLLAPP
+APRDPAAPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>LFPAFLNI_00086
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP
+APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000333.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c434f63eaf0bd1527216195abb35801a6130f32e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000333.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00304
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG
+VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA
+>MOLHKGIG_00087
+MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA
+>NAFOICDF_00249
+MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE
+AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA
+DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA
+SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP
+TIDPLTGEPVAEDPYDQTRDGGRA
+>MHAAABBN_02100
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
+>LFPAFLNI_00082
+MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA
+GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ
+GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA
+AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG
+VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000340.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63def35786a80cd2d925a160ea2bae2688accaea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000340.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00315
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP
+>MOLHKGIG_00078
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT
+>NAFOICDF_00256
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT
+>MHAAABBN_02091
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
+>LFPAFLNI_00072
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000341.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fa4bcd55d8843b6cd9567475775858073de9694
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000341.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00316
+MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR
+TRRDAS
+>MOLHKGIG_00077
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>NAFOICDF_00257
+MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET
+VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR
+GA
+>MHAAABBN_02090
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
+>LFPAFLNI_00071
+MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA
+DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR
+TREDLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000349.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be2a109073bf282308447e7b82b2388ce340f628
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000349.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00329
+MEKKLVCLDVDGTIVDHDGHLHEPVREAVKAVVAAGHHVVIATGRSRGATLPVAQSLGIE
+AGYMVCSNGGVTLRLDPALEDGYEVTDCRTFDPRSVLSQLRSRLPGAKYAVEVPDGSFLS
+TERFQDMSFGVAAEGTTFEELKNTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLHVAPEHTVAVGDGRNDLEMLAWAGRGVAMGQAVREVK
+EAADEVTASVDDHGLADVLWSLVPEADRPEGVRVQEPAAA
+>MOLHKGIG_00066
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
+>NAFOICDF_00268
+MTKKLVCLDVDGTIVDHDGRLHEPVREAVRAVIEAGHHVVIATGRSRGATLPVAESLGID
+SGYVICSNGGATLRLDRALEDGYEVTDLRTFDPQSVLAQLRDRLPSAKYALELPDGSFLS
+TERFQDMSFGVAAEGVGFEELMATTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASALEALRTVLHVDVADTVAVGDGRNDVEMLRWAGRGVAMGQAPDEVK
+EAADEVTGGVDEHGLATVLRTLL
+>MHAAABBN_02079
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGID
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGLGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPTAA
+>LFPAFLNI_00060
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRAATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEITDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKMAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000353.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37fa27dd027041e0c9ccf505ca2d2162afc860c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000353.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_00335
+MQLRDALAAGELSAREVTQAALDAAERHAGLGAFTLLDPEGALARADELDDDGARASLHG
+LPLAYKDLTDVRGLPTRHGSALLAGAPAAEEDAPLVRRLVGAGTVTLGKTTVPEFGLDSY
+SENLVSAPARNPLDPARTPGGSSGGSAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGFK
+PGRGELPVDEPADTVRNLTVSGPLAHTVEDAALLYDELLTPEGLPGRVLADLRRTVETAR
+AGGAVEGRRIGVTTASPFAPDVPITLARPAVTALTKAAAALSAGGHAVQDLHPAYGEEYH
+RDFRTVWTSGLLRAPLPEDAEERVGAIAAHFLRTARSAGRQEIDDAVRRLEAWARGVRGQ
+FAAVDVVMTPVLAAAPPPVGHFLAMEPEDNYAAQCAFTPYTSMVNVLGLPAASVPVLRDE
+RGLSWSVQLIGRPGTSGALLALAAHLELLLAG
+>MOLHKGIG_00060
+MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA
+ALAAAQTHADLGAFALLDAEGARARAAELDAAHPRVAPRAVPGPRTSPAPDDDGAPASLH
+GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS
+YSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL
+KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA
+RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY
+HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA
+QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD
+ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
+>NAFOICDF_00276
+MAVSEPLSPSDQPTSPTPAPDAPARLLGRTALALRDALAAGELSAAEVTEASLAAAHAHA
+GLGAFVLLDEDGARVRAAALDARPDDAAGASLRGLPLAFKDLTDVAGLPTRMGSAVLAQA
+PAAAEDDPLTTRLRAAGTVLLGKTTVPEFGLDAYSENPVDPPARNPLDPSRTPGGSSGGS
+AAAVAAGILPFAPGSDGGGSVRIPAAACGLVGLKPGRGTVPTDPGEDAVTNLTVSGPLAH
+TVEDAALLFDVMTSPEGLEGRTGPDLRRFLDARAAGEPVAPVRIGVSTASPFSPDLEITL
+ARPALSALARSGAALAAGGHAVDEFVPHYGERYHRDFRTAWTSGLLKAPLPDGAEALVGP
+VAASFLASARAAGPEQIATAIGRLEAWAADVRGQFAAVDVVMTPVLAFAPPAIGHFLALD
+PEENYAEQCRFTPYTSMVNVLGLPAVAVPVLRDEAGLSWSVQLVGRPGAEGRLLELAGHL
+RLLLAG
+>MHAAABBN_02073
+MTRATPVRLGRMQTSDAAPAADDDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTE
+AALAAAQAHADLGAFALLDAEGARTRAAELDAAHPRVAPRAVPGPHTSPAPDDDGAPASL
+HGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRGAGTVTLGKTTVPEFGLD
+SYSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVG
+LKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVMLTPEGLPGRVLSDLRRTVET
+ARAGDAVDVRRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGED
+YHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWAHGVR
+AQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLR
+DERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
+>LFPAFLNI_00055
+MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA
+ALAAAQTHADLGAFALLDAEGARTRAAELDAAHPRVAPRAAPGPHTSPAPDDDGAPASLH
+GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS
+YSENLVTAPARNPLDPARTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL
+KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA
+RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY
+HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA
+QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD
+ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000354.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98267b04bf499342da88823eee002355f5ae1b15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000354.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00337
+MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL
+RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT
+WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE
+RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE
+AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL
+TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR
+RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG
+WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL
+AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG
+VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV
+REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE
+ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP
+>MOLHKGIG_00058
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT
+VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>NAFOICDF_00277
+MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL
+RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL
+ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA
+ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG
+DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR
+ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE
+VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL
+LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM
+DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE
+LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD
+GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH
+EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG
+>MHAAABBN_02071
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>LFPAFLNI_00053
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000356.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03e5b6bd45fb515c2baf39be04dfeee7ecb7b244
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000356.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00339
+MVSTDMDTTTQTPDERTLLRAAGLRVTRPRVAVLTALGECPHADAATVLAAVRRELPAVS
+HQAVYDSLHTLTDVGLVRSIQPAGSTARYEIRRNDNHHHLVCRDCGTVVDVPCHTGQAPC
+LEARTDHGFLIDEAEVYYWGLCPSCRADPGAAAS
+>MOLHKGIG_00056
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>NAFOICDF_00279
+MSTVTVEQPEESALLRSVGLRVTRPRVAVLQGLRRHPHADAGSLLSAVREDLPQVSHQAV
+YDCLHVLTDAGLVRSLQPAGSPARYELAAHDNHHHLVCRGCGDLVDVPCQTGVAPCLHAP
+EDHGFLIEEAEVYYWGLCPDCRSGGYTTTSDGTPAPAPPAP
+>MHAAABBN_02069
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLTAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>LFPAFLNI_00051
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000357.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0caec7a6d5555d04ca3e42c881fa792a8a35ba1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000357.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00342
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK
+TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD
+CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG
+>MOLHKGIG_00055
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG
+>NAFOICDF_00281
+MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND
+DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT
+PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA
+DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR
+EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN
+AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS
+QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF
+VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK
+AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI
+YAESFLGEEHLKQVQQEAQAIVDAVIS
+>MHAAABBN_02068
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG
+>LFPAFLNI_00050
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000359.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eeb72ec05d7c691c091f898485b0640e0040ea14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000359.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00348
+MPRVSSRPHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFAALVG
+VSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMALLAAL
+PLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAVAGFLTAGPYRL
+TAFLGWALLGAVLVRTVHGTTTALPRSGRLVGLGWGVGGVVLAGLVILLSRVQTGAAPVP
+YTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPGSMTLSVYVAHQAYLGWVLT
+AGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRPFRAGPLEGVVRLVTDPIGR
+RSRGEH
+>MOLHKGIG_00047
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYVSAFLTDG
+PYRLPLFLTWALLGAVLVRTVHGTTTAAPARSARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
+>NAFOICDF_00295
+MTLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFAALVGVSAHLE
+QRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSVLALLPGLVQL
+LLVPAAAWAGVRVGALTADDVAARLEPARALVPAQVRPGPAVVAEQAAAFFTVGPYFLLF
+FTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLLVGGAGVALARQ
+RTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPGSMTLSVYVAHQ
+AYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEPWRRGPLEGPVA
+LVTHGLARR
+>MHAAABBN_02060
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGPFRAGPLEGVVRLLTAPFD
+RAR
+>LFPAFLNI_00042
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000361.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa6dcfde2bf0225cce1df57cd4a4b4350ee2f0ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000361.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00353
+MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD
+EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD
+DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG
+AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA
+>MOLHKGIG_00050
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT
+>NAFOICDF_01218
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE
+ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP
+HDRAVTVAARLLPRTVLRGMGAMHRRGAARR
+>MHAAABBN_02063
+MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD
+EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
+>LFPAFLNI_00045
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000362.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2e748ab4febbd2d102c6ac7c327b69ab11d158c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000362.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00355
+MPALPLPPRRPRLIATDLDGTIIGYRHTRSGYLSPRTVAALQEAHETGVEVVFVTGRPLR
+WLGALSEQLGQVGPVICSNGAVVVDTATDEVLLHHSMDRDAVWDAVGRLRALDRSATFGA
+ETLDGFFWESAFSEWGELEEGFRTAQRLEGVLPAHVDVVKLMARSSTMDPDVFLAAAREE
+LGALLNATHSAPGVSLVEMAAPGVHKAATLAEFAARRGVDARDVVAFGDMPNDTEMLAWA
+GLGLAVASGHESLLAVADAVVGECDDDGVAQAIELLLELPAE
+>MOLHKGIG_00045
+MPALSLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIVALRDARDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVVVDTATDDVLIAHPMRVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLMARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPADVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>NAFOICDF_00297
+MSALPASARRPRLIATDLDGTVIGYAHTRTGRISPRTVAALRRAHAEGIVVVFVTGRPLR
+WLGPLRAQLGEVGPVICSNGAVVADTATDEVLLHHALDRAAIDHVVRRIRALDPAATFGA
+EALEGFFWEDAFASDELGQTRAASLEAALPGDATVVKLMAKSGGIEPDVFLAAVRELGDG
+LVTATHSAPGMSLVEMSAPGVHKAATLAAFARGTGVEAADVVAFGDMPNDAEMLAWAGLG
+LAVASAHASLRAVADGVVGACDDDGVAAAIEALLALPEA
+>MHAAABBN_02058
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>LFPAFLNI_00040
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000365.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92a1ff0e88b12353877e6fd393c5d23727d06897
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000365.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00358
+MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV
+TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL
+AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG
+VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI
+ARVRGTEPVSEDDEAYEASEAGRLG
+>MOLHKGIG_00042
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV
+TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>NAFOICDF_00300
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG
+>MHAAABBN_02055
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>LFPAFLNI_00037
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEEFEASEAGRLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000367.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df496b61c3c13716c4a237c873dfa75e58955b99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000367.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00361
+MMASKTPHQNTTFDLPSKDASHDGDQVGHGYLALPESGSGPAVIVIQEWWGLVDHIKDVC
+DRLAAEGFVALAPDLYGGWIAHDGDEAGEMMQKLPAEEGARQLAGAVDWLLAREEVTSTT
+VGAIGFCMGGGFVLALAAQQGEKVSAAVPFYGVGQGVPGDFAGVKAAIQGHYGEQDSMFS
+VEDAKKQEQQIRDESGAEVEYFYYDAPHAFHNDDDPQGNYRPEAAALAWGRAVAFLKEKV
+R
+>MOLHKGIG_00039
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP
+VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
+>NAFOICDF_00302
+MMASKTPHQNVSFPLPTKDAAHGDQTGHGYLALPAAGKGPAVIVIQEWWGLVDHIKDVCD
+RLAEEGFVALAPDLFGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSSRV
+EAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGSFEGVTAAIQGHYAEQDDFFPV
+EDAKKQERQIREESGAEVEYFYYDAPHAFHNDENPQGNYRPEAAQLAWDRAVSFLKEKVR
+>MHAAABBN_02052
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVTGDFSGVTAAVQGHYAEQDDSFP
+VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
+>LFPAFLNI_00034
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP
+VEDAREQAQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000368.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec9cc23a9f697c0cbb2f7d43f846974d24615dac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000368.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00362
+MAQVTTGTWNLDPAHSDVDFVVRHAGISKVRGTFAAVEGVLVVAEDFNASSVEVTVDVAS
+INTKNEGRDQHLRSGDFFDVEQFPTMTFRSTEVRGAAEEFTLVGELTLHGVTRTVELEAE
+LGGQDVDPFGTTRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLPEAD
+AQA
+>MOLHKGIG_00034
+MHAITPGTWNLDPAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>NAFOICDF_00303
+MAQITPGTWNLDAAHSDVDFVIRHAGISKVRGTFHTVDGQLVVAEDFNQSSVQVTVDMAS
+INTKNEGRDQHLRSADFFDVEQFPQMTFRSTEVRGEAEDFTVVGELTIHGVTKTVELEAE
+FGGQDKDAFGATRVGFEAKGEISRKDFGLTWNAATEAGGVMVSDKVKIEIGAAFVLPEA
+>MHAAABBN_02051
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>LFPAFLNI_00033
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGLLVSDKVKLEIGAAFVLPEAD
+AQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000371.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae7399b1777e416110a2b1f4f34fe0e6895e1a15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000371.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00372
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>MOLHKGIG_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA
+>NAFOICDF_00354
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED
+>MHAAABBN_02042
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>LFPAFLNI_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000374.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30025f5737c3be647d1caf0f12cb5d89fcbc1740
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000374.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00375
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E
+>MOLHKGIG_00021
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E
+>NAFOICDF_00357
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E
+>MHAAABBN_02039
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+>LFPAFLNI_00021
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000375.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2afd8f29ba75b780bb0163a0aae2da7b9bc9988e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000375.fa
@@ -0,0 +1,64 @@
+>ACLBLIBL_00376
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV
+RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE
+TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA
+GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF
+ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE
+DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV
+DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE
+PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA
+GGSASPTAEESPTA
+>MOLHKGIG_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG
+ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA
+QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD
+DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP
+SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT
+TDPSADARGAEASSADATPSA
+>NAFOICDF_00358
+MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV
+RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG
+DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP
+AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA
+QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA
+VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD
+TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST
+EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG
+>MHAAABBN_02038
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF
+ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE
+DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV
+DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA
+SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT
+GESTTDPSADARGAEASSADATPSA
+>LFPAFLNI_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA
+GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL
+GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD
+AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV
+DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE
+PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP
+TTDPSADARGAGASSADATPSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000377.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..beee3c9b7ff3d3da5ed47d13bce26a5ecea960b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000377.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00379
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD
+>MOLHKGIG_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>NAFOICDF_00360
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD
+>MHAAABBN_02036
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>LFPAFLNI_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000384.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df5fb90dc5132db2ceac0ad060bb05cd10580388
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000384.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_00388
+MARCTVERLMRAAGLRGISRAKGPRTTVPGRGPDERQDLVQRDFTAAAPNQLWVADITYC
+RTFSGWVYAAFIIDVFSRRVLGWQLSKSLRTDLALDTLEMAFWTRQRAGQDVAGLRHHSD
+KGVQYVAVRYTQRLAQAGAVASVGSTGDSYDNALAEAFNSLFKAELIRNKGPFKSIEDLE
+IAVAEYIDWFNHRRVHGEIRLVPPVEFEDVYHHENPVPAPAGTALTSL
+>NAFOICDF_00330
+MHTCCRLLGVSRQGYYRYQKRPTSATELRRRWLTGLIREIHIASRGTYGYRRIHAELTMG
+MNIPCSSRLVWVLMTRAGIGGLPGPARIKRLKGVATADDLVNRKFHRLELNELWVTDITE
+HPTREGKVYCAAVLDACSRKIIGWAIDSKQDSTLVVNALDMAIRARQPDPGGIVHADHGV
+QFTSWVFTQKIRSAGLLPSFGTVGDGLDNAMMESFWSSMQIELLNRKKWKTRIELANAIF
+EYIEVFYNRHRRHSSLEYATPNDYDLARTPQALATTGS
+>NAFOICDF_00656
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGVYGARKVHAQLRREGLQVARCTVERLMRAAGLRGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGLQYVAVRYTQRLAQAGAVASVGSTGDSYD
+NALAEAFNSLFKAELIRNKGPFKSIEDLEIAVAEYIDWFNHRRVHGEIRLVPPVEFEDV
+>NAFOICDF_01209
+MQIGAWAQGGEIELANAIFEYLEVLYNRRRRHSCLECATPYDYDPAGTPRALTTTGS
+>NAFOICDF_01831
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGLYGARKVHAQLRREGLQVARCTVERLMRAAGLGGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGVQYVAVRTPSGWPRPAQSPRSARRGILTI
+SVLAEAFNSLFKAELIRNKGPFTSIEDLAIAVAEYVDWFNHRRVHGEIRLVPPVEFEDVY
+HHENPAPAPAGTALTSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000385.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..911d4435e906f4602d83c146245c3068faca49be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000385.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00406
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>ACLBLIBL_00753
+MSTETSAAGRAGHSVRLVVLATVIVLILGAAGWALGRLTAPVTSFPSAASPEAGFARDMQ
+VHHLQAVEMSFLVRDRTEDPEIRQLAYDIARTQQHQAGQMYGWLSIWGLPQASPEPAMAW
+MDEDAGHSSPHDTGQQSTAMPGMATAAQLEALTDAEGSEAEQLYLELMISHHQAGTTMAQ
+AVLDRTDNEAVRALAQSIATSQQTEIRYLEQLLRTR
+>MOLHKGIG_00634
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATAASSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>NAFOICDF_02195
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>LFPAFLNI_00597
+MKRTMTLTALTLASALTLTACGTGAQDENAGAEASATATGSAPAATPAATDTATPSATES
+ATSSATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVID
+AQGPEIERMNAMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARL
+YLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000387.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5142615e36a91c3a83c4e6d8cd4e68629bd8b18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000387.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00415
+MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED
+>MOLHKGIG_00009
+MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED
+>NAFOICDF_00367
+MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG
+>MHAAABBN_02014
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
+>LFPAFLNI_00009
+MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000389.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3bdc97b9599013a272b3d7841faa694e8c23264
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000389.fa
@@ -0,0 +1,82 @@
+>ACLBLIBL_00418
+MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA
+DIDPTDPAAAPEGLFEEDADGEGADGGEQ
+>MOLHKGIG_00006
+MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY
+AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA
+IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD
+MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT
+REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT
+ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY
+KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR
+GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ
+DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI
+PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT
+NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL
+VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR
+PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK
+VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR
+IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>NAFOICDF_00370
+MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD
+YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT
+AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV
+DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA
+TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV
+TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL
+YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL
+QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI
+QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL
+IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF
+TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN
+GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA
+LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG
+GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP
+DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA
+EAAGEDADGGEQ
+>MHAAABBN_02011
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>LFPAFLNI_00006
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000397.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34ca321905715918d7931bafc8afd1c562574c4c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000397.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00426
+MAVTPSPFTVLEPSREWGPVRALPSALLAGLLTVYRAVVSPLYGQVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>MOLHKGIG_02310
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>NAFOICDF_00379
+MPASSPYTVLEPSHEWGPLRALPSTLLAWLLTAYRAVVSPLYGPVCRFFPSCSAYGLEAV
+HVHGAVRGSWLTARRLLRCHPWNDGGVDPVPPGRRRWPPGREPRIFALNHPPIPPDPSQE
+D
+>MHAAABBN_02003
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ
+ED
+>LFPAFLNI_02251
+MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA
+VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILALNHPPIPPDLPQ
+ED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000402.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce43fa434de43045e224ed02ca0bcf6de7661230
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000402.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00433
+MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD
+ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG
+>MOLHKGIG_02304
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>NAFOICDF_00385
+MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD
+ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG
+>MHAAABBN_01997
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>LFPAFLNI_02245
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000404.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7fbcf489b8f5540f6c5889ca5a29bdf5d3a2c6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000404.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_00436
+MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVR
+EHDGGLEVAIIARYNRGGRLEWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAI
+DYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERRI
+VDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE
+EPTTADPAPATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVA
+IGLSTDMADIFEIANSLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGT
+LVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNAN
+GRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLGVILQA
+VILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEAR
+DRGELRIPGTEAWSTEMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTR
+QDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPLGRVFGSTAETSMVAGIAVGAVLLAL
+ALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMALWVAIA
+SSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGF
+AWETIVTALITCAVAAAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG
+>MOLHKGIG_02301
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>NAFOICDF_00388
+MSSRTAPRRALPADDAPRPKEVEDVVLPASDPEAPAQAQEEVPEGERRAGRSTAIMAAGT
+MISRVLGFVRAALLTIAIGTTVGTVADIFEVANSLPNVIYLLLVGGVFNVVLVPQLIKHA
+KDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTVFALWCLP
+QMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTP
+EQTLVLAGGHTLGVILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAAS
+NIVLLLSHRYINGASAAREDPSVRVPGTEGWDPAMADALIPGLTAYNQAMLISVLPHSVF
+VLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPLGRLFGST
+AESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTA
+AGAYLLPLWAITYWAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVA
+GAAGAVVAWLLGAYSGGWAWGSILSALVTCAVVGLVMAPVYVVALRVLRFPELASAAAPL
+ARRVPALGRLLGAR
+>MHAAABBN_01994
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>LFPAFLNI_02242
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAFASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAAAVA
+MGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000407.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a16490edff9e766ae3db47787663b5d8fb29948
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000407.fa
@@ -0,0 +1,51 @@
+>ACLBLIBL_00441
+MRPAPAHAATPSEPPTHAVDGPSWAGPDGRAEAGGSAVSAPPSRGPAAVPAPVPAPGDRG
+GRFQLPGGLAANRFTLGGRGGTGSWASPAALAGVLVALAAVVTVLQKAPCLLHGWGAPNV
+YYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVGSVGAQLTQWLPFGAEHGT
+LVFWLVNLLFVVGLWAAVAVLTVRMAGRRWSDGLMVAVAPGVILAGTINWDLWAVALLAL
+GMYAWARERPLAAGVLIGLGAAMKIYPLLILGPLLILAVRSRRWRPFLLAAGGAVAAWAA
+VNVPLMVANFEAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGAFA
+VCCLGIFVLGVRVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVIWLIPLVALALPRWRDFW
+AWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHP
+EDDLVRRDHTDLPGGDPLAGAYRSAQA
+>MOLHKGIG_02295
+MRPAPAHAATPSEPPTHAADGAPSDAVTAPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHILAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA
+>NAFOICDF_00394
+MSSSPAPGAAPDDPPAPAPQARPDVPVGAHRAPRHALTTPPPGSAEGAPSAGSGAVESDE
+ATPEGEVDPRVVPAPGDRGGRFAIPGGLAANGRGRGTGAWAGPVALTALLVALGAIATVL
+QKSPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVASVG
+AQLTQWLPFPASVGTVVFWCVNLLFVVGLWAATAVLTVRTAGRRWTDGLMVAVAPGIILA
+GTVNWDLWAVALMAWGMWVWLRGRPGWAGVLFGLGAATKLYPLLILGPLLILAVRSRRFG
+PFLKATGGAVAAWLAVNLPLMLTHFESWKVFFTFSAERGPGLSSVWHAWDVVAAQAGWAA
+VPDERLGMYAYGAFAVCCLGIFVLGVVAKRPPRLAQLTFLVVAAFVLTNKVYSPQFVIWL
+IPLMALALPRWKDFWVWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLA
+VLWLCARVVLEILDPDDDLVRGPGGDPARDPEDPSAGPADPGMTGVRPVREAVAAGVGAA
+SAQA
+>MHAAABBN_01988
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGALPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA
+>LFPAFLNI_02236
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPAALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGMLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDTDPLAGAYAGPARGRSGRPAAVQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000413.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..838a6ce39b39956217d65737518dea2094dfe6c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000413.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00447
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA
+QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD
+PWSGGGGGGGWDTPSSNEPPF
+>MOLHKGIG_02291
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>NAFOICDF_00399
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW
+REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS
+QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG
+GGWDTPSNGEPPF
+>MHAAABBN_01983
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>LFPAFLNI_02231
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000419.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..938418f14102bc29c7870f85a822a5e201cc9fdc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000419.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00454
+MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF
+>MOLHKGIG_02282
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF
+>NAFOICDF_00406
+MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>MHAAABBN_01973
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>LFPAFLNI_02221
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000421.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..682ce2c402021c18d62474e9438a5e2fb3d4f866
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000421.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00462
+MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEAL
+RERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLS
+RRSMAATFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGD
+DGRVQGVRVREETSGEEFDVHARAVILAGGVWTQEQQELAEADGGLEVLASKGAHITVPR
+DRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPAATADDIDYILEHAN
+AVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTY
+RAMAEDVVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLF
+RYGTVLRHVLDLIDADPSLSVPLAEAPRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEV
+RDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETAHDDVTAAAALAAAD
+AASTH
+>MOLHKGIG_02268
+MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTERI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADADAAPTP
+>NAFOICDF_00493
+MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDA
+GDWAGGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH
+ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAETFPGLDPEAAVGAVEYADAQF
+DDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVIL
+AGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDE
+HWIIGTTDTPWRQDVDHPAATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAA
+GADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAEDTVDFAVRDLFPTRPSLTAHTP
+VLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGGE
+AYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRD
+AEVAAYRALVAARRRAEGLDDDAAAAAELAAAGERAGVVPVTSRETVTPEEKGGAR
+>MHAAABBN_01961
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPVHGKEPVHGHDLPA
+>LFPAFLNI_02200
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+ADEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000422.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be0db256ec1eb973a0bbe1de3158c338f98afb89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000422.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00470
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVRAGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQGYA
+TELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWVDG
+VTYAMLASEFLARV
+>MOLHKGIG_00154
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>NAFOICDF_00420
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDVVGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRGY
+ATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWID
+GVTFALLASEYEGGAAASRA
+>MHAAABBN_02168
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>LFPAFLNI_00167
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVRVGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000423.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..890c4632a5cfe7512dc14f210c9c0321b2d347e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000423.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00474
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT
+PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA
+GEPR
+>MOLHKGIG_02257
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>NAFOICDF_00429
+MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH
+AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA
+GEPR
+>MHAAABBN_01957
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
+>LFPAFLNI_02188
+MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT
+PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP
+LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH
+AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG
+EPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000424.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7df75ae28aa9ae35999e3a2c1157d78a09b90758
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000424.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00475
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q
+>MOLHKGIG_02256
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>NAFOICDF_00430
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q
+>MHAAABBN_01956
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>LFPAFLNI_02187
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000430.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb72cbb56bd4073f51bd267221443fbb00c3b43b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000430.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00502
+MSRGGCLSGGLQSKCGEFRLQFPDRHSPRTACRPHRASAPHLRTAPHVRTFLATLDPDDA
+EPFLEMSPRLVPETWERFRDHALPGIRAVDEDAVERPSARYVLDPVPEEAGPRVEAPALI
+LTGRSWGSGPPRRRGRRGTEAPVREARSAHPLATRPAGFPSATCRGALAPWPT
+>MOLHKGIG_02244
+MTEHTSEHTPENPHVVRRGSGVPLIEVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>NAFOICDF_02088
+MSQPAPHLVRRGSGAPLVLVHGMGVDHRLLLPLDAALEAAGGWERVYVDLPGFGGTPALP
+APGGLPELADWLDGVVGEIAGEDRFALLGNSLGGLLVREVLARRPGQVAGLAMIAPVVDP
+DPERRDVPERVVLEQDEALLAELDGDDAAPFVEMAVIQTRPVWEGFREHVLPGVLAVDED
+AVDRLEDRYALDGPLPEERFGEFDRPTLIVTGRQDDKVGWRDQLALAEHFPRLTLAMLDR
+TGHNAHLDQEAAVGAMVRNWAEDAAREL
+>MHAAABBN_01946
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAESGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>LFPAFLNI_02176
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000434.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9fba43c0dea39f22f236a038edbf01408d15d1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000434.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00515
+MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG
+LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG
+VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG
+LETRLGA
+>MOLHKGIG_02220
+MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG
+LEARLAA
+>NAFOICDF_00462
+MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL
+MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA
+FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP
+AVRAGLEARLAGSAPAD
+>MHAAABBN_01933
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG
+AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLTA
+>LFPAFLNI_02159
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000435.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f457834af5391d5423c306e0be4b68ffb56e800
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000435.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00518
+MKAWQFSGTGKPLELNEVPEPTPGPGEVVVDVKAAGICHSDVSAIDDAGWMPLFPELPHT
+MGHENAGVISAVGEGMDHWKVGDRVGLAPMNSKGEAIGYHTWEGGFGPKLRATDDNLVKL
+PDEVPFDLGAMATDAGLTAYHAVVAKGGVKKGMKVGIIGLGGLGYIGAKVAALMGAEVYG
+AEVNPKTRELKDEIGLTAVAESILEFKDVGLELVVDYAGFGTTTAEGITALKKDGVFVQV
+GMGKLEAPLNTYELITKTISVLGSNSGTKEDLAGIYELMQRGELNPPINRITQADIPDAI
+ETLRAGGVIGRYIAMYDDAK
+>ACLBLIBL_00811
+MHQAYAVYEGDTAIHEIEVETPEATGRSVLLKVLRSGVCHTDTHLREGGYDLGSRGTMSL
+TDRGVPYPLVMGHEVVGEVTAVGDEVQDVRVGQRMLVYPWIGCGECRMCREGRDNACAAG
+KNLGVARHGGYAETLWVPDAKYLVDIGDLDPSWTATLACSGITAYSAVDQVLPLDEEESV
+VVIGAGGLGLTAIALLSARGHRTVVAVDRSEKNLELARQMGASATVVSDDDVAAALKEAL
+GGGAAAVIDFVNNGATATLGFDSLAKAGQMVQVGLFGGEVTLPNALLSLKMIRISGSFVG
+TLQQMKDLVQIARTTDLPKIPIIERQLSAEQVAASLDDLTAGTVSGRVVLTA
+>ACLBLIBL_00946
+MTTMKAVRFTAYKTFPELKEIERPTPGPGEVLLKVAGAGACHSDVAVYDEFEAGMNPLVD
+PEYTLGHETSGWVEELGEGVTGFEVGSAQLVYGPVGCGHCPACSRGQDTYCQNVAEMDYA
+GIGLGRDGGMAEYVTVPARNLVPLGDADPVPASALADAGLTPYHAIKLALPRLNRAGTYA
+LVVGLGGLGLMAVQILKDLTGATVIATDMKPEAMAEAEKYGAVTVPSGEDQVARIREITG
+GRGVDAAFDFVGIAATARAALDSAAVQSRVTIVGIGNGSTIDWSFLSTPYEAELVTTYWG
+TVEELHELAGLYRDGKVEPLYTTYAMDGALQAYRDLQDGKISGRAVVVPHGQA
+>ACLBLIBL_02387
+MKALYESGPHAGFEFTERPEPECGAHDVKIRVFTTGICGTDLHIEAYDAAAQAMIQAPMI
+PGHEFYGEVVEVGDLVEHVEVGHRVSGEGHVVCGMCRNCRAGRRQMCINTVSVGVQRDGA
+FAEYVVIPEANVWVHKGEHVTPELGAIFDPLGNAVHTALSFPLVGEDVLITGAGPIGLMA
+IPIARHAGARYIAITDVSAERLELARSMGADAAIDVSATRIREAQRELGLAEGFDVGLEM
+SGRASALQEMVANMNHGGKIALLGLPAEEIAIDWQTVVTHMLTIKGIYGREMFETWYAMA
+AMLQTNATLRERVESVVTDVIAAADWKRGFDAARAGATGKIVLDWRNL
+>NAFOICDF_00886
+MVTMRAVRFEAYQQFPALKDVEKPVPGPGEALLKVAGAGACHSDVAVYSEFQPGMNPLID
+PEYTLGHETSGWVEELGDGVVGLEKGEAMLVYGPTGCGRCRACSRGQDTYCENVAAMAAA
+AVGLGRDGGMAEYVSVPARNLVPLGDADPIPASALADAGLTPYHAVKLALPTLGRPGACA
+LVVGLGGLGLMAVQIIKALTGATVIATDMKEDAMAQAEAYGAVTVPGGEGQVERIRELTG
+GRGVDAAFDFVGVAATARLALDCAAVQSRVTIVGLGNGSTIDWSFLSTPYEAELVSTYWG
+TLEELHEVARLYRDGRIEPLHTTYSLDDALQAYRDLQDGKVAGRAVVVPHGGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000438.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2808721f74dd94340f01baae207a097effa31059
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000438.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00537
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP
+>MOLHKGIG_02208
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP
+GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL
+ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD
+FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF
+EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA
+LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL
+MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF
+RLALP
+>NAFOICDF_00468
+MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW
+TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK
+PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP
+>MHAAABBN_01921
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
+>LFPAFLNI_02152
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000444.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..447ff741c1214144dd459e61c87a01231067ecfc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000444.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00546
+MIQAHIDEHLNERVVAAWIADPARIVLVGGTAPDEVLGYAMLETAATPEAPVVEHLGETP
+AGHLSKVYVLAESRGTGLAETLVRDGVARLEALGFRHVWLGTNAQNARANAFYERLGFEK
+IGARTFVVGGTRVEDDWVRLLSLG
+>MOLHKGIG_02194
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPSSLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAATPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNTRANRFYERLGFATIGARQFVVGGERVEDDWV
+RLLTVE
+>NAFOICDF_00482
+MPTSPTPRPVPAVIRPATPADVPALVRVAAETFPDACPPTTSQEAKDEHIASSLNAEVIG
+GWVAGPGHAVHLAEAPAGRDDAGRLLGYVMAELAPEEEPAVTAVLGEGAAVGCLSKLYVV
+REARGTGAAAALMAAGLDALRVRGLTHAWLGTSEENHRANAFYERVGFRTVGSRTFLVGG
+RPERDNVRLITP
+>MHAAABBN_01907
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVA
+>LFPAFLNI_02138
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000448.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f2b934bfbc4a0a0e63af3570c7c5a05e11cd00c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000448.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00554
+MAPSRRQILLTGSALLGSGLLAACSSEGGSAPASSSPAGTPAPAPSSSSAAPAGPGPAGE
+PVAWPNTALVPHLFFHSLVVDPKRAFDGDHKEAGYLDFMVTMDEFAAILPQLYAKGYVLV
+SPHELYEVGEDDVVRPKTLMVPENRTPLVFSLDDCSYYLYMEGDGFADRLIVDEDGRVRN
+EYTDADGTTHVGSYDMVPMLDDFLEEHPDFSLNGARGVLAMTGYEGVFGYRTSAREFGDS
+PTFDADVAAATEVADAMKATGWEFASHTWGHRTVPKLELDELQRDLELWHGEVEPILGPT
+DMMIYPFGADVARTGKYEADNERYQYMRSLGYRSFFLVDGTAKAWGQLEPGYYRGSRINV
+DGISLEAAISGKRPVLDEFFDSRSVLDPARPASIRGTQQSPAAPPGGQSGSASPSATG
+>MOLHKGIG_02190
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKARGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAQGTTHVGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYLRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>NAFOICDF_00483
+MEYSRRHVIFGGSALLGAGLLAACAPAQDGAAPSAGGGSSSEAASSSAAPSPSSTRPVIP
+SAPEPAGKPVAWKDVAKVPHLFFHSLVVDPEKAFHVHGESDGYLNYMVTQAEFERILPQL
+WALGYVLVSPHELYEVGRDDVVRARTLMVPENRTPLIISLDDCSYYEYMEGDGFATRLLV
+DDSGRVRTEYTDQEGKTTIGANDLVPILDDFVRDHPDFTLNGAKGVLALTGYNGVLGYRS
+SPTMYPEGPELDEAVATAKEVVAAMKETGWEFASHSWSHRSMAQMSLADLKEDCERWIED
+VQPIVGPTDMLIYPFGADIAGIEKYSGPEYEHLRSLGFRSFFLVDGSSKAWGQLEPGYYR
+GSRINVDGISLAGAKDGSRPVLDEFMDVDSVLDPARPESIHAPSYVPPEERAAASSGAPS
+ASPSS
+>MHAAABBN_01904
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMRHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>LFPAFLNI_02135
+MPPPVPQPTRRQLLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWSDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGTYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRSPRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000454.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db31c39659f8496480684b001543a4396e835c7c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000454.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00568
+MRHPFVDYLEGLLGSLEHVTEGDVARYIPILAEADPSLSAVAVATTSGRVHTAGDADAEF
+SIQSVSKPFTYAGALEDRGVELVDEYVALNPSGEAFNELSLEADSHRPDNAMINAGAIAV
+HQLLVGPGATPAERTERAVSLMSTLAGRRLRVDERTFESEMATADRNLALGHMLRSHGIL
+QDRAEDVVAGYIAQCSVMVTVRDLAVMGATLASGGLHPLTGERVLSSLVCRQVLSVMSSS
+GMYDAAGQWMAHVGIPAKSGVSGAVLGALPGQVGIGTYSPRLDPFGNSVRGVEMCRIMSE
+DLDLHIMEADVIGSTVVRSVRREGDTVHLHLQGVIRFGGGESVLAAMTELGTGADPDPVE
+WAHCFYPFSEEPDTAAGRAAAQDEGRTAAEALEQEAPVRAVVVHLERVDRVAPVGRRLIE
+DGLKRLRADGVQVRVEDPDGVLTGG
+>MOLHKGIG_02182
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASREERLDRAVEIMSLLAGRRLSVDRETYESEMAVSDRNLALAHMLRSYGVL
+QDSAEEIVAGYVAQCAVRVTVKDLAVMGACLATGGIHPMTGERVLPSIVVRRVVSVMTSS
+GMYNAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADRAALSAATGGGAVHEAAAVAARDENDGPIRTVVLNLTRVDWIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>NAFOICDF_00495
+MKHPVPDYLQHLVDSLREDRRGALADYIPVLAQADPERLGIALATVTGRLHSAGDDETEF
+TIQSVSKPFAYAAALQDRGLDAVDARVGLNPSGEAFNELSLEAESKRPDNAMINAGALAV
+HQLLVGPYAGRQERLDRLVGFMSTLAGRRLEIDRETFESEMATSDRNLSLAHMLRSHGII
+QDRAEDVVAGYIAQCSVRVTVRDLALMGACLASGGVHPLTGERVLPSLVCRQVLSVMSSS
+GMYDAAGQWLVNVGIPAKSGVSGAVLGALPGQVGLAVFSPRLDEVGNSVRGVEACRRMSE
+DMDLHLMEGDSLGGTVVRFARREGDTVLLHLQGVIRFGGGEAVVTAMTDLGTGAAGGGRA
+AWSEHDYPEWEDAPHGDVAAEAGDRRPVDAADPEAARAAATGDGSVHEAAACAVAEDGLP
+IRTVVLNLERVDRVTAVGRRLIDEGVDRLRADGVAVEVVDPDGLLG
+>MHAAABBN_01896
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRLGIALATPTGRLHSAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLAVDRETYESEMAVSDRNLSLGHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERVLPSIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALAAATGGGAVYEAAAVAAQDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>LFPAFLNI_02127
+MRHPIPDYLASLITDLGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLSVDWETYESEMAVSDRNLSLAHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERMLPYIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALSAATSGGAVHEAAAVAARDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000458.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..068a5af8595e5dade4ce7a9c36d473b7126d65a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000458.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00574
+MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA
+LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT
+VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV
+LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR
+LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP
+TTQETR
+>MOLHKGIG_02178
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>NAFOICDF_00501
+MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK
+STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR
+HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL
+LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV
+LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP
+RGRGDRA
+>MHAAABBN_01892
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
+>LFPAFLNI_02123
+MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA
+NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL
+VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ
+TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA
+AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000459.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41acc37e07e759de2b99155b29a2a3f5b44a2b06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000459.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00575
+MSGRGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAYMVAVPDLVR
+ILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPDVLGVTSGAA
+AGAVLWQAAATGTGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVVAGIAVAAGAQ
+AVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAWLHGRLEPADT
+GEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARGLAGGRPSLAA
+AALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRAGRRGERTA
+>MOLHKGIG_02177
+MSLQCTAPDDVVARLRRADRRRLGGACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGVLHARLAPADVGPD
+LAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLCQGRTPGGVRSA
+>NAFOICDF_00502
+MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY
+QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD
+VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV
+AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW
+LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG
+LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA
+GRSSEGTR
+>MHAAABBN_01891
+MNLQHTAPDDVVARLRRSDRRRLGRACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
+>LFPAFLNI_02122
+MSVQRTASDDVVARLRRSDRRRLGGACTGLAVAVLVLALLRVVWGTYQVTVPDLVRILAG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAATVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000460.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d495c70975543baa3fac4703c404d4e03e7a6503
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000460.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00576
+MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR
+VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV
+MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP
+AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP
+ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL
+VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA
+>MOLHKGIG_02176
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>NAFOICDF_00503
+MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA
+AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG
+STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL
+LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG
+LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG
+AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS
+>MHAAABBN_01890
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA
+TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL
+GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM
+AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>LFPAFLNI_02121
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000477.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..383d6bd1ae2ddf48fb55888e4e8f708a97380e83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000477.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_00613
+MSPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHNPG
+VFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRAAA
+RGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMVVD
+DEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPESW
+DPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGVDV
+QVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANIDR
+LSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPLRP
+LL
+>MOLHKGIG_02149
+MRRPSLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPG
+VFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL
+>NAFOICDF_00537
+MGYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAERPGTFQAQVGPDALTI
+YTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRAAARGVQVWASYDGFG
+NLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILTVDGRVGFVGGYNVGD
+LYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPEEWEERTVVAANLPTQ
+LVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGVDVQVLVPKDSNHVVA
+DWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANIDRLSLSFNYETNVSV
+VDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPLRPLM
+>MHAAABBN_01862
+MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPGVFDAHVEGSELRIFTSGEDLYK
+EMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAARGVEVYVSYDGFGNLVVPPRFY
+RQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVDDEVGFAGGFNIGDDYARLWRDT
+HVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTWDPRVTVAANQPPLLVYPIRLSY
+LDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDVQVMVPEDSNHIVADWASRGFFG
+KMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDRLSLGFNYESNVVVVDRDFAARM
+EEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRPLL
+>LFPAFLNI_02092
+MHRPPLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPNPG
+VFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000479.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7daae92012915261e19fa29db76de84750c0842f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000479.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00616
+MAWLAVVLAVAVGLLLGLMGGGGSILMVPLLTYVAGLDPKEAIAGSLFVVGVTSLVSVGL
+HARAGNVRWRTGLVFGLAGMVGAALGGVVGGFLPGTVLLIAFAVMMLVTAWAMIRPKRPT
+AAPAEGGHAPGRALGRIVLDGVVVGFVTGIVGAGGGFLVVPALVLLAGLPMSAAVGTSLL
+VIALKSFAGLGGYLTSVTLDWPFLLAVTGVAVLGALIGAALVNRVPDKALEKGFGWFVLA
+MGVVMLVTELVGLLA
+>ACLBLIBL_02658
+MSGTLILTLVLAVGVGLALGTLGGGGSILTVPLLTYIAGMPPKEAIAASLLIVGVTSLSS
+LVVHARHRRVRWRTGLIFGAAGMVGAFAGGLIGGQLPGAVLMVAFAIMMIATAIAMVTRK
+PRRDTDQPTADAGTERAHSLPMLRTMLEGIVVGLITGIVGAGGGFLVVPALVLLGGLSMP
+VAVGTSLLVIAMKSFAGLAGYLTTVTLDWPLVAAVTAMAVLGALLGARLSGRIPADALQK
+VFGVFVLLTGTLVLVIELPPAWAIAAGGLGLITVVLVLVCRLTALNCPFGLARPTPG
+>NAFOICDF_00540
+MVPLALLVVLAAVVGLLLGLMGGGGSILTVPLLTLTAGMDPQEAIAGSLVMVGASSLVAA
+LVHATRGAVAWRTGLTFGAASMVGALAGGFVGRDLPGPVLMVGFAVIMLISAVKMIRPRR
+KGAGHDDAAPVPLGRVLLQGVGVGLITGVVGAGGGFLIVPALVLLARLPMPVAVGTSLLV
+IAMNSAMGLVSQLGATALDWAVLGPMAAAAAAAGVVGVVLAHRVPAAALKRGFGWFVLAM
+GVLILAQQALELLP
+>MHAAABBN_01858
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIIGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGGLIGVPLVKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV
+>LFPAFLNI_02088
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIVGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGALIGVPLMKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000482.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9d3aa32abb83003b0deb871e7dcf6e5e3fd2330
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000482.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00626
+MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA
+DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV
+GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG
+ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY
+SE
+>MOLHKGIG_02146
+MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY
+REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP
+AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR
+PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG
+>NAFOICDF_00550
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP
+CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP
+DVFWGTAP
+>MHAAABBN_01853
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
+>LFPAFLNI_02083
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000485.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea1af9edaa92d9070ff4f8b48f70cecffbd252a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000485.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00629
+MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG
+YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV
+MRTA
+>MOLHKGIG_02143
+MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV
+LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD
+RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD
+YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI
+TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA
+APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV
+MRTA
+>NAFOICDF_00553
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD
+RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>MHAAABBN_01850
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
+>LFPAFLNI_02080
+MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV
+LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD
+RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG
+YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI
+TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA
+VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV
+MRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000492.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b04b608683a63924c21aca10cab9064bf41c8952
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000492.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00647
+MSQTTEAGGRLSAGHVIVKTLESHGVRRIYSVPGESYLDVLDGLHDSQIENVVCRHEGGA
+TYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHREKEAFQ
+EFDPHAWFGTGAKRVMVLDHADRASEIVAEAMFAATSGRPGPVVVGLPEDVIREQIDATL
+HPVIPVATGGMTVEDWKSLHSALKESKKPLFITGGNDWTDEGAQQLTQWLEGHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDLLEETDLIVFIGTVPGDVVTNGFKIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLDVKPEWEEWTSRMRGEQETFAAL
+PPAEPSEGQAKMATLMANLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAGMAEAFGGLGIRVEKDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>MOLHKGIG_02133
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVASGGMTVGDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>NAFOICDF_00563
+MSQNSEAPGRLSAGHLIVKTLESHGVRRVYSVPGESYLDVLDGLHDSAQIENVVCRHEGG
+ATYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTAMVLFVGLIPFEHRDREAF
+QEFDPHAWFDSGAKRVMVLDHPERASEIVAEAMFAAASGRPGPVVVGLPEDIIRVEVDAH
+LHPQIPVAPGGMTVEDWKSLHAALKESQKPLFITGGNDWTDAGAEALTSWLEDHKIPAAA
+EWRCEGTVPFSSPSYVGPIGYGRPDFTQHLLEETDLIVFVGTVPGDVVTDGFTIRQNWDK
+KNFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLAVKPEWEAWTSRLRGQQEEFAA
+LPAAEPGDGQAKMATLMATLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGS
+MGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR
+THQEREYPERVSGTQLKNPDFAAMAEAFGGFGVRVEQDADVPAAVDAALKAVQEEGRFAL
+IHLIVEQRVKAY
+>MHAAABBN_01841
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLYDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIRQEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGAKPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>LFPAFLNI_02071
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDAVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000495.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0827ea720ad39f3085ad2b4313688d5ae62c164b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000495.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_00650
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR
+SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL
+RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT
+LERIERDLA
+>MOLHKGIG_02130
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR
+SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT
+LERIERDLA
+>NAFOICDF_00566
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR
+SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH
+AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT
+LERIERDLT
+>MHAAABBN_01838
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGVASIRAELGEALREA
+VAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVATLERIERDLA
+>LFPAFLNI_02068
+MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGVASIRAELGEALREA
+VAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVATLERIERDLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000499.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..231ae330e631b5eef27cdce19b964c783ef5bb8c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000499.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00654
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>MOLHKGIG_02126
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLAAWFTGHSTSPRVHA
+>NAFOICDF_00570
+MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>MHAAABBN_01834
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>LFPAFLNI_02064
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000501.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d8e487589cffa60f02c49bceb57dfedf64767ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000501.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00656
+MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR
+IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE
+ESGELEQWLEYSRQCLP
+>MOLHKGIG_02123
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>NAFOICDF_00574
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>MHAAABBN_01831
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>LFPAFLNI_02061
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000504.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9eb13a3918b48ad24ebb0b3152e0e0f39ca1395
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000504.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00661
+MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV
+GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC
+HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE
+DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL
+GEEGSDAPPPGEGAPVA
+>MOLHKGIG_02119
+MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDLYPPGV
+>NAFOICDF_00578
+MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA
+RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR
+SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA
+QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE
+GEEQGGAADPAA
+>MHAAABBN_01827
+MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDPYPPGV
+>LFPAFLNI_02057
+MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG
+EAAADAPLPDADTRAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000505.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89dc32a22e04fe2ace87de1c54547ab1aef9ee1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000505.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00662
+MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA
+AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV
+AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP
+ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA
+EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG
+RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI
+ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD
+>MOLHKGIG_02118
+MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL
+WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA
+AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM
+TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA
+DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS
+VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD
+GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>NAFOICDF_00579
+MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR
+RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP
+REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV
+VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS
+LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH
+HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL
+DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA
+>MHAAABBN_01826
+MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL
+SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD
+ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS
+RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
+>LFPAFLNI_02056
+MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL
+SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD
+ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS
+RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP
+RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL
+ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ
+DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000509.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e6fd7b3c14ee018097e2cce71d7a998d136d81e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000509.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00667
+MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT
+LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD
+ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR
+>MOLHKGIG_02113
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH
+VSAVADVVIAGAGVQGYTLAVDWLAAAVRR
+>NAFOICDF_00583
+MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR
+QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE
+FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR
+>MHAAABBN_01820
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLAAAVRR
+>LFPAFLNI_02051
+MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLATTVRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000516.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..449ba28b5c3336fc1a16ad29ce3e36b13225b8bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000516.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00676
+MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD
+SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR
+>MOLHKGIG_02103
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>NAFOICDF_00591
+MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA
+DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS
+>MHAAABBN_01810
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>LFPAFLNI_02043
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000517.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..236c55d76feb92da123e0c1173efa6655e3f282d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000517.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00677
+MTFLDLILVFVGLAAAVLAAVALTGRVRARHAAAIAVAIAALAVLTAVFDNVMIAAGLFD
+YGHDLLSGIYVGLAPIEDFAYPVGSALLLPAVWLLMTGRRRRGGERSPDGGAEPTGDGSS
+TADAGR
+>MOLHKGIG_02102
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
+>NAFOICDF_00592
+MTYLTISLPFLAVAAAVLLASALTGRLDRRRRLGLVLAVALLVVLTAVFDSVIIGLGIVD
+YTQANINGARIGLAPVEDFLYPLAGVALLGGLWTLVRGGTR
+>MHAAABBN_01809
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
+>LFPAFLNI_02042
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVTATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000519.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e8689eda992ddf725893c690eacbdba379f9a24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000519.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_00683
+MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG
+LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE
+SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE
+DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG
+DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP
+TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV
+IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV
+TGQPESVKPEEAADAESGHDEHTDHDH
+>MOLHKGIG_02095
+MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA
+SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA
+DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ
+VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH
+>NAFOICDF_00598
+MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ
+AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP
+DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS
+HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK
+VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID
+EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK
+DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH
+>MHAAABBN_01803
+MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA
+SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG
+DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ
+VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH
+ESDEHTDHDH
+>LFPAFLNI_02034
+MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH
+GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV
+MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA
+LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW
+KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP
+ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000521.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..193ff1a028ac4cdd52430e333442203141bdf8bd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000521.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00696
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR
+>MOLHKGIG_02087
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>NAFOICDF_00606
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR
+>MHAAABBN_01792
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>LFPAFLNI_02026
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000526.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5fc9f7b51197b4768379dc06e1532e2443bf6051
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000526.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00701
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG
+>MOLHKGIG_02082
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>NAFOICDF_00611
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG
+>MHAAABBN_01787
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>LFPAFLNI_02021
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000531.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0b2845854f0185bf66ed6f75f45a59d5a65db6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000531.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00716
+MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA
+LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL
+AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA
+IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET
+LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA
+MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW
+HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT
+LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV
+EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH
+>MOLHKGIG_02141
+MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD
+PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI
+LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP
+RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP
+FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM
+MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA
+TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD
+AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG
+IHAEVTGLNEASAAMHARLTGRLGA
+>NAFOICDF_00554
+MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL
+GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL
+TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS
+VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL
+RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT
+AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI
+AAEVTGLNEASAAMHARLTGRTGA
+>MHAAABBN_01849
+MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL
+GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL
+TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS
+VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL
+RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV
+TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH
+AEVTGLNEASAAMHARLTGRLGA
+>LFPAFLNI_02079
+MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG
+VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI
+QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL
+LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI
+LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ
+TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR
+PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD
+GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR
+HGIHAEVTGLNEASAAMHARLTGRLGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000534.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31d57c22fcf9a6d00e220bb126aa5f7ec986663c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000534.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00763
+MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD
+VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS
+KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG
+RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD
+EAVAAESAEAAAGDPAAVNPAGASAEARP
+>MOLHKGIG_02057
+MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY
+ERFLDHAVAAELR
+>NAFOICDF_00727
+MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA
+RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT
+DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD
+EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA
+ETVAAYEAFLDDAVARELA
+>MHAAABBN_01763
+MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY
+EHFLDHAVAAELR
+>LFPAFLNI_01991
+MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT
+VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR
+ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL
+LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000537.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c94bbc1bfdc181df3670f9c3ebb862b5833a9440
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000537.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00770
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>MOLHKGIG_02052
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
+>NAFOICDF_00740
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>MHAAABBN_01758
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE
+>LFPAFLNI_01986
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000538.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74e6e53129319fa87961e0c91fae0fd28089c295
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000538.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00778
+MTGTHETALPASTTDGRAASAPLRRIGFDRAKYIDLQSQHIQERRREIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLERIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHATARIVSEE
+GFGRNEWSQTTRDLVVVTAPGPGSGKLATCLSQVYHDHQRDIPSSYAKFETFPIWDLPLE
+HPVNVAYEAATADLDDINLIDPFHLAAHGEQVTSYNRDVEVFPLLAALLEKLTGTSPYRS
+PTEMGVNMAGAAIVDDEACREAARQEIIRRWYKAAVEEAANGESDEVSERIALIMSRLGL
+TSEDRPVVGASLLVAERTGEPGAAVQLADGTLVTGKTSALLGCSAAMLLNALKVLAGLSD
+EVHLLTPESIEPIQTLKTVHLGSTNPRLHTDEVLIALSVSAATDPNAKAAVEQLASLAGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>MOLHKGIG_02040
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDANARAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>NAFOICDF_00746
+MTGTADMAPQKISRPLGFDREQYIALQSQHIQERRRQLGGKLYLEMGGKLFDDLHASRVL
+PGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEEDVLRLVDVFRERGFL
+VEHVVVTQLEDSNHLALAFIEKLGRLGLKVARHRVIPGYPHAMATIVSEQGFGANEWSET
+TRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLEHPVNAAYEAA
+TVDLDDINLIDPFHLAEYGEKVTSYNRDVEVFPLLSALLEKVTGTTPYKSPTDMGVNMAG
+AAIVDDAVCRAAAEQEIIRRYYKAQVNEALEGADDTESERAALVMSKLGLSSEDRPVVGA
+AQLVAERTGEPGAALELADGTIVTGKTSELLGCSAAMVLNALKVLAGIDDDAHLLSPASI
+EPIQTLKTQHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGCDVHTTTILGS
+VDEGIFRSLGMLVTSEPVFQKKGLYRKR
+>MHAAABBN_01744
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>LFPAFLNI_01972
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000542.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..332af3914b356926583159c3e0f54d5e6336a68f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000542.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_00783
+MTTQPAGPSPASTDHRRSLADSGAALGPLDGRYRAAVAPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHAVLPGLTPLTDEQKAGLRAIVTDFDADSVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAAQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+TQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAIQTVMRAEAIAGVPGM
+DNPYERLKELTRGHRVDGERMREFVRGLGLSDGAQARLLELTPAGYTGVAADLAREFGPA
+QG
+>MOLHKGIG_02034
+MGAMTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+QD
+>NAFOICDF_00749
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVSELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+SAQG
+>MHAAABBN_01741
+MTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEWFIH
+LAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADRLEG
+LGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAETPML
+SRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDADWP
+ALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYFAQI
+PVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQRNIG
+VALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGMDNP
+YERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPAQD
+>LFPAFLNI_01969
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAAPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEAAQARLLELTPAGYTGVAAELAKEFGPA
+QG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000546.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aca8f88063236b7a12567f7995954a2a432b391a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000546.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00793
+MPHSSTAPRRGRPGYDRQTLLTVCVDVFNRHGYEATSMGMLAQHLGISKSAIYHHVESKE
+AILEQALDDALDALEASLDGVMADFAGPGEQVEAAVRGTLRVLVEKMPEVTLLLRLRGNS
+AVELAAMERRRAITRRLGEMIAAAQEAGAVRGDITPRNLARLALGMINSIVDWYRPESDS
+PGHKSVTEMVDAVTRVVLGGLRG
+>MOLHKGIG_02026
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGVDAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQEGPGQMIDAVTGVVLGGLRG
+>NAFOICDF_00754
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRLGDLLESAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDGAD
+PGHKSVEEMVAAVTGVVMGGLRG
+>MHAAABBN_01735
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG
+>LFPAFLNI_01963
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000550.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7db7e3ff53623d959eda835c466ea36234449a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000550.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00797
+MRCGLDETEREPTVFSTNAAQEAGVPPGRLRRSDLEPWGRGLWRVRDAVPDVMDHLRALQ
+DLHPEGVFTHVTAARVLGLWLTGPLARDPAIHLGAPRHHGTGSRREGVRSHRLYGDVPVR
+IVDGVRVTATGWTFVDLAAAAATVETLVALGDSAVRSAPTERRRRDLPPGVTSLEELRGA
+VAERPRVKGIRLARDAVDLVRPGADSPQESRLRVGLVLDGVPEPQVNPRIVLSTGQWLRV
+DLAWPAARLVVEYDGDQHRTEQRQWREDRSRDAGLRADGWEVLRVTADVFRPAEWELFVR
+RVRARLGRDAAGRAAAG
+>MOLHKGIG_02022
+MRCGLDGLLRDPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGIEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
+>NAFOICDF_00758
+MPRSPAPLPPMRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP
+DPLDHVRALQDLHPEGVFNHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS
+HRLRADAPVRIVDGVRVTAPGWTFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG
+VTDVAELRAAVEERGRVRGIRAAREALELVRPGVDSPPESRLRVRLVLDGVPEPAVNPCI
+RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF
+RPGHWELFVRQLRGLVAARTKPGRVPPSWI
+>MHAAABBN_01731
+MRCGLDGLLRAPTVFSTPAARETGVSAARLRRGDVVSLGWGLWGLRGVEPDPMDHLRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLDHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRARLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
+>LFPAFLNI_01959
+MRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRSHRLRADAPVR
+IVDGVRVTAPGWTFVDLAAHAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDMAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000555.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd7ae034bbb240d6ef57a137066db9bc289be632
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000555.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00829
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG
+>MOLHKGIG_02013
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>NAFOICDF_00766
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP
+>MHAAABBN_01723
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>LFPAFLNI_01951
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000563.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cce4a1fb9cf3c3197ed4fb42dba5bf95d53c97a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000563.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00838
+MAEDDGGPAPAREGAPSQTLSRALALLEAVVEAAEPPTIAELADGLGVHRSVAYRVLRTF
+EAHGLLRRDPLGRVHSAPGLAVLARRVEQDLRTAAMPHLSAVSADLGMTAFLVVGDGSTC
+LTLATVEPPRGNLVTQRPGTRHPLGIGAPGMAVALALPEQEWEQRRGDAAPERPELGEAR
+ERGWAVSRDEVITGVSSVAVPLSVPGQLPAALAVVYATRPEDPERLGGRLKEAAQAVAAS
+LGAA
+>MOLHKGIG_02004
+MAEHDGGPVREGAPSQTLSRALTLLEAVVEAPEPPTIADLADGLGVHRSVAYRMLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAAPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
+>NAFOICDF_00775
+MDPHDDSVPAVSAPPPSAPGVRPGAPSQTLSRALTMLELVADRPTPPSIAELADDLGVHR
+SVAYRMLRTFEVHGLLRRDAAGLVHGAPGLVTLAGGVEQDLRAAAVTELSRVSDALAMTA
+FLVVWDGRDCLTLATVEPPRGNLVTQRPGTRHPLGVGAPGIAIASVLPAEGQDRPAVREA
+RARGWAASRDEVITGVGSVAAPVPAAAGMPAALAVVFTSPAVDEEAVGAELAAAARRLGA
+VLGEG
+>MHAAABBN_01714
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRMLRTFEA
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
+>LFPAFLNI_01942
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRVLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGIGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000569.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4f6353667f51ace03bc40d84c5ffb1cea1a5236
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000569.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00863
+MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD
+VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF
+ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD
+GFSYTRAEEGEDSMPEYKKGEYKLGNQL
+>MOLHKGIG_01994
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESLPEWKQGEYKLGNQL
+>NAFOICDF_00801
+MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD
+GFSYTREDEGEESMPEYKQGEYKLGNQL
+>MHAAABBN_01688
+MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
+>LFPAFLNI_01920
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000570.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de715bff50efd0c166d2e510f2e8b8dadfa69c87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000570.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00864
+MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA
+AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA
+ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG
+NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT
+GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG
+SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH
+LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK
+YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF
+YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>MOLHKGIG_01993
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>NAFOICDF_00802
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA
+>MHAAABBN_01687
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>LFPAFLNI_01919
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000571.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..597ba7544f8defd8fea1ab1bf502d39992c94d7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000571.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00865
+MSRTDIGTVGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLSAARE
+VNATMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWTRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLAHQGELS
+>MOLHKGIG_01992
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTGEDLAAARE
+VNATMRAMTESETAWDPMAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA
+>NAFOICDF_00803
+MRRTDIGTLGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARD
+VNAAMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA
+>MHAAABBN_01686
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESETAWDPVTFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLRAYLEHSAEPSA
+>LFPAFLNI_01918
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESERAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHGAEPSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000572.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b2f8c10b1c938bc1bf98607ab16e7cffd14c071
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000572.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_00866
+MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQLQKRGIQNATIDGPRPIHQGRR
+VLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLAL
+RAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQ
+PGDVIVGDDDGVVVIPPSLLQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAT
+FDEYRKTLPDAPAPEGDA
+>MOLHKGIG_01991
+MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLAR
+SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGRLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAEAASSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>NAFOICDF_00804
+MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIAR
+SGDAVERPAGTELLAYEGEIALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY
+GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLL
+TPELRAKIDAIAVATLTAQLQKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFK
+EFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDS
+AAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA
+>MHAAABBN_01685
+MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAG
+SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>LFPAFLNI_01917
+MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAR
+TGDTIERPAGTELLAYEGEIALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLREVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000575.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4956f41f5c7aa923f0034d0624107cfaca5b6362
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000575.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00869
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>MOLHKGIG_01988
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>NAFOICDF_00806
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA
+>MHAAABBN_01682
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>LFPAFLNI_01914
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000577.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..797a6df66d06971a75df7fe200e5ffc4b23c844e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000577.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00873
+MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD
+PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI
+PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG
+PLGLDPRKDARTTADVLASA
+>MOLHKGIG_01984
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
+>NAFOICDF_00809
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>MHAAABBN_01678
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>LFPAFLNI_01910
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000578.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c116fdafeeca5c86b7b300840157b737334b261d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000578.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00876
+MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS
+VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL
+LETEAALEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNVV
+LETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREHI
+HWFSRFTTAGPDAAGG
+>MOLHKGIG_01982
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
+>NAFOICDF_00811
+MTAAPAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQTGRVPA
+AG
+>MHAAABBN_01676
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
+>LFPAFLNI_01908
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000590.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bf58f3f635eea2e52a39bc704f86436b391c760
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000590.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00894
+MPLRASSVPRGIDMQLYRRIHWGDLATFHLLGTRQYRSDQANLDLVKVVDADARDPRRTI
+TGAAQEAWLREGFETSVARWDLITQQVPFVQYDRISGPLLWGDMDSWDGYVASRDRVVSA
+WTAAGVRNPVVLTGDIHEAFASDIKRDFNDLSSESVGVELITTSITSGGDGSDAAAEALA
+WNPHIKFNNDLRGYLRVDLSAHMLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>MOLHKGIG_01963
+MTSHTDPSHPAAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRAQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSRLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHELENNWADETPEIWDPSFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGDLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRTSGPLLWGDMDTWDGYVASRDRVVSAWTAAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
+>NAFOICDF_00439
+MSSPSPTLSRRRLLGLSGASAAVLALGVNAPDAAHAEPLPQRDGLFGLGVASGYPRPDGA
+VLWTRLAPEPLAENGHGGMPLRSVPVKWEVARTADFRRIVARGTALAQPELAHSVHPRVE
+GLAPGTEHFYRFVVGPQTSPVGRFVTLPAAGAATDDYTVGLISCQAWYHGHFAAHRHLAQ
+EEDLDLTVFLGDYIYEYGITAANLWRQGAEVTPAHAVEIETLEQYRLRYALTKSDPHLQA
+LHARAAAVAIWDDHEVQNNYVGAASSTGIPEELFAHRIAVAYRAFYENLPVDIDALPEGP
+ESDIVAGLDVGALARISLLDTRQFRDAPPADAADRERENRTMLGAAQERWVTERLRTSQS
+QWNVLAGGVVLAPISDDRTDQWDGYPAARRRLLTEMKRAGNAVMLTGDIHKHVAAELRGE
+SAGLPAGPAGVELVTTSAASDGDGAKTDKYTPDWVRHDYVRHYDGRRGYLHLRFTPAQLT
+SSFWVVPWVESDDTAPKELSARFTTPAGSSRLIEA
+>NAFOICDF_00834
+MAAAALISTPAGTAHAAAGPNPFTLGVASGDPWPDGFVIWTRLATMPLNRDGFGGMPDAS
+FTVEWQVSRHADFRSTVRTGTTTTSRAQGYAVHVTLTGLRAGTEFFYRFRCNGHLSRTGG
+AVTAPALGSMPGHLTATEAERLIRAAGFAPVRLGGIDESIRMEVTGELHPFGGLDGTLPT
+TANVEQLRG
+>LFPAFLNI_01889
+MSSHTDPAHPTAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAATGPTPFTLGVASGDPW
+PDGVVLWTRLAVDPLALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRTQGYAVH
+VTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPARGSNPSSLTMTVASCANWEHGYFTAYG
+HMAAERPDLMVHLGDYYYEIMPYGYPVSSGVPRAHRNGESRTLAQYRARMAQYKTDPHLQ
+DAHAAAPWLVIFDDHEVENNWADETPEIWDPNFLARRAAAFQAYYENMPLRASSVPRGID
+MQLYRRIHWGNLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGF
+ETSVARWDLITQQVPFVQYDRSSGPVLWGDMDSWDGYVASRDRVVSAWTTAGVRNPVVLT
+GDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEALAWNPHIKFNNDLRG
+YLRVDLSAQLLEARFRVVDYVSELGSSVRTRAVFGVGDGEHRLHRIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000598.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43fab542dac68017a3f155c5ce0a50aa89872663
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000598.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00918
+MAAPHTRRPHDSDPHDARRAADEHSGHTDRGGTPPAEGSGVGPTNPQMDVEQPGERSTGR
+IVLFAIIALLVIGILLFVLGRVFDLFG
+>MOLHKGIG_01941
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
+>NAFOICDF_00853
+MATPHHPDQPADAHRSDHLARATDENSGHAVAGDTPPAEGLGVGPTNPGMEADKSGEGGM
+GRILLGLLIALVVIGVLLFVIGRISSIG
+>MHAAABBN_01637
+MATPHTPDPQDARRAREATDETSGVAFDGDTPPAEGAGVGPHNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLVFILGRVAGLG
+>LFPAFLNI_01860
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000601.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..761a21c33f9978fe40b8dc7ea170044b3487b018
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000601.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_00923
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR
+>MOLHKGIG_01936
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
+>NAFOICDF_00857
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG
+>MHAAABBN_01632
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA
+>LFPAFLNI_01855
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000604.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e81bdff87aedbc0bdec72ace692d4db01a12b9f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000604.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00926
+MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK
+YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL
+VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD
+VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+SRWVNSLIASDLKGMERRQHSLLERLRVGRRGEGRAGKADAEAVAGADVAAAGVEAALDV
+DDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAAPAPGR
+>MOLHKGIG_01933
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGKDEDRAPTDGGDDDGPATDEVTG
+GAGAAPGR
+>NAFOICDF_00860
+MSASAPPAVTGTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAPVFL
+GLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPKYAG
+QFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLLITV
+IMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLDMVA
+LVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVLNFV
+LQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPNSRW
+VNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQGDDDVAPERTAEDA
+APAQDRRRVRAAAQEARLEGPPPSTLRAPRVDLPGEPEPATADGSAPPEAGAAPGR
+>MHAAABBN_01629
+MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDDGPATDEVTG
+EAGAAPGR
+>LFPAFLNI_01852
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDEGPAADEVTG
+EAGAAPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000610.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..793308522e97fa6e8673fabc9b2746784a988e0d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000610.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00935
+MTLTLDDRTRVWDTDLSHHNLRSGLSAFPTGVVAVAGLAEDRREVMVSSSFGVGISWEPA
+LVAFSAQNTSRTWPRLRQAASLGISLLAADQTHLCRQLASREGDRFAGLDVHVSPNEALL
+IEGAALWLETRLHAEVPAGDHTVVMLEVTGFADHTDEVAPAALHRNLFHGLRAL
+>MOLHKGIG_01926
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL
+>NAFOICDF_00866
+MTLIHAPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLAAREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDDAPPAALHRNLFHGLRAL
+>MHAAABBN_01622
+MTLTHEPHTATWDTDLSLGNLRSGLSAFPTGVVALAGLADGVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL
+>LFPAFLNI_01845
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTALADHTDAAPPAALHRNLFHGLRAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000622.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92c94b84d6f253c6a8e3161271d522bf9782ce35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000622.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00952
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA
+>MOLHKGIG_01906
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
+>NAFOICDF_00892
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA
+>MHAAABBN_01602
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA
+>LFPAFLNI_01826
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000623.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9d64cb3cabfef46c8eab8699e0e58778db8773f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000623.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_00953
+MAAAPAASDASTPASAGSGAGTGEASEAPAEQGSAEAGESAEAGALPAWVWAVGVAGLLV
+LVVALILMGRRARALGHLDDGR
+>MOLHKGIG_01905
+MHHQTTPVRRAARAATGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGSTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEAAAGQGDAASAEATAQADAS
+DAAQPADTDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>NAFOICDF_00893
+MNPTPMHPSTPRRAARAAAALTLLPGLAVAAAAPALAHDELLKAVPADGAALAEAPDAVS
+LTFSGDLISGQGIQSIVRVTDAAGNQWQKGDVQVSGPTLTAPLCPDLAQGEYTAAYRVVY
+SDGHSEEQSLDFSVTDPSAPAAGTAPSGCGVAAAGTASSTAAPASSAEQTGAEQSGAAST
+PAAASSTPAESGASAGVPATVWMLGAAGVAVIAVGLAVMGRKARALGRD
+>MHAAABBN_01601
+MHHQTTPVRRAARAAAGLALLPALVVAGAAPAAAHDELIRTAPAVDETVTTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGSAVAGASIAASPEATASQGDAASAAATAQADAS
+HAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>LFPAFLNI_01825
+MHHQTTPVRRAARAAAGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEATAGQGDAASAEATAQADAS
+DAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000624.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ec2f0805b4db8eeb72e91e76dec830f590e9bec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000624.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00954
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH
+>MOLHKGIG_01904
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH
+>NAFOICDF_00894
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH
+>MHAAABBN_01600
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH
+>LFPAFLNI_01824
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000628.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34590c301a3898aa7404c7a1927c395cf958b42a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000628.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00958
+MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRG
+KVVILDFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYT
+IEHPVLDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEA
+KGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTGHHRLLEVAEDLTTV
+LRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDV
+VVADTVNHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAEDVAVDLSDLPGEPT
+AISLSSPWDVAWDPAAGRVVIAMAGTHQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWF
+AQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGLFDFGFVDGEAAQARL
+QHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEH
+DADGAPAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPS
+GQKLDDRWGDPTQLKVSSSPEELLLEGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDG
+EKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRGIH
+>MOLHKGIG_01900
+MMVGMTAPQTPNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPS
+GLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHPL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>NAFOICDF_00898
+MRRPLPADARRAWAMMEGMTEQQTSAPSVPRSGSRVRASSLVGRRWLNTGGTEVSLEDLR
+GKVVILDFWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERY
+DIAHPVLDDPTLVTWQAYSARAWPTLVVVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHE
+AKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTGHHRIVELAADLTT
+VLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVD
+VVVADTVNHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDESAAADLSDLPGDPT
+GISLSSPWDVAWDAAAGRVIVAMAGTHQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWF
+AQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGLFDFGYVDGAPEQARL
+QHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEP
+GEDGAPAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPA
+GQKLDDRWGDPTQLKVSSSPEELLLDGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDG
+EKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRGIH
+>MHAAABBN_01596
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKVSSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
+>LFPAFLNI_01820
+MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL
+DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV
+LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH
+RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG
+GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS
+VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL
+SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPS
+GLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGLFDFGHVDGEADRARLQHAL
+GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG
+NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL
+DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ
+PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000631.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61f1e5f86c55ca18dec8932baa2b0190392577a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000631.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00967
+MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGPTAS
+RAHLDFHLTRIDR
+>MOLHKGIG_01891
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
+>NAFOICDF_00905
+MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ
+EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF
+VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP
+TASRSHQDFHLTRIPR
+>MHAAABBN_01587
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIE
+>LFPAFLNI_01811
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000632.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3774b584c0adf64f4c83b14103c876efef395e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000632.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00968
+MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG
+PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP
+QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI
+VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR
+ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV
+ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA
+LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV
+IPVIVLVLIVGGVLFARVTDPVTRSAEPAP
+>MOLHKGIG_01890
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>NAFOICDF_00906
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR
+>MHAAABBN_01586
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL
+GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>LFPAFLNI_01810
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000639.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2081bfa6a7c09adfcde78ce1cc6c9586e42ca630
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000639.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00975
+MNTLAQKALSTGITLVGGIIGSRVVAGGWKLVTGHDAPDDAADETLPIVEALSFAFISAG
+VAAILKVAGQRGAGAALRKVTESTAHRVDNEV
+>MOLHKGIG_01883
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>NAFOICDF_00913
+MDKVIQKVLATGITVVGGIVASRLVAGGWKLVTGHDAPSDATDETVPLVEALAFTFASAG
+IASVLKVAGQRAAAEGVRKVAQKTSSDVDNEV
+>MHAAABBN_01579
+MNTLVQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPDDAADETLPLVEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>LFPAFLNI_01803
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000641.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49ee83ce4be0cffb40e0a7d2088a8bf7d0380dbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000641.fa
@@ -0,0 +1,99 @@
+>ACLBLIBL_00977
+MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ
+DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA
+RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL
+DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA
+NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ
+VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ
+LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA
+GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV
+SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP
+AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>MOLHKGIG_01881
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
+>NAFOICDF_00915
+MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK
+EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA
+RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL
+DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK
+QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA
+RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE
+QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED
+GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG
+LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV
+GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG
+LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA
+AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG
+SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA
+GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS
+AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN
+VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT
+AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK
+WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA
+>MHAAABBN_01577
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>LFPAFLNI_01801
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDA
+RTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEADAGEQRLAEAAAQLDEGQAAL
+DAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA
+QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VAAQFADQEAQLAAGEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000647.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbb46c9f8fb432354048e5f5332eb2940e0548f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000647.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00988
+MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT
+HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP
+GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV
+AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF
+AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR
+TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA
+>MOLHKGIG_01872
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY
+RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA
+>NAFOICDF_00925
+MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL
+DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV
+VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA
+THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR
+TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA
+RVTAGLPVAGGGPRSGQRRA
+>MHAAABBN_01568
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY
+RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV
+>LFPAFLNI_01792
+MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG
+PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG
+YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA
+HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR
+SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG
+DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000649.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2dd2542caea3d7c7dcc2c665c16789dc9a89bee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000649.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00990
+MSTPASPSARRARAALGLAAVALVALSACARTEPAPEPAPSTASATALPPMDMAPFTVDV
+PSLDLDRVPGASIAVLEGTDPDHRGAWLQVPEAPAWTEAMAGSVRGQIDAYRRDTDRGAD
+PRLEVQPRLAVVGEDIAAARLLSTETRGTDSVSSSHVVWYSAREDRVLETRDLFTDEGWD
+AFRTEVRQRMKNDPDVVRERLASAVDSPELVENRRIWDAVVLLPDGSVMLEADQASMAPA
+AAGVLTVRIPRDTAAPWLSDLGDAATDAARTPADLRLPDRSTPSPSTSAPEPAESSWTPE
+ATGAPVPPRVPVPDPTTTAPSVDPGGDRDPSTSSAPPSSRPGTTAPSPVAGPQHPGPHHP
+GPHHLRADRPGARPLDDDGAPAPGADQPDAHADADPVDSHADADAHDAHPDPDRDGDHGP
+ADRPGAGARAGADDAAAERHERLRPRDPGRAGLSRPTPGCPGRPRTGACPARRRPAPPPH
+GLT
+>MOLHKGIG_01870
+MHPVLPSPRRGRAALGLAAVALVALSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVSGAPAWTDAMAGAVRDQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>NAFOICDF_00928
+MHRLSPASTVRLRAGAGLLALGMLGLTACGSGDDAASSSPAPSSAAATQELPSMDMAPFT
+LDVPSLDLDKVPGASLAVIQGQDPEYHAAWLQVPGAPAWTQAMDESVRGLVAQYQRDTDR
+TASPVLDVQPRLAVAGRDVAAARLLSTERRGDRSVSAVHVVWYAAREDRVLSTEDLFTAD
+GWAAFRREVGARMAGDPAVVQDRLRSAVDAPAQVENVRVWDALTFLPDGSALLEVDQAAM
+SPADAGVLTARIPADTVRPWLSALGVSAQDAARSPEALVLPERPSAAPASEGGDAAVPAP
+GQPSSDGATTSAPGQGSVPPAPGLPGAPAPGTPGTASQGGGSPGTAPQDTGSQHTGSQGT
+GSQGTGASAPGASPSATRGDAGPAPTSSSAAPAPTGTGAPAPAPLPMPAPTTSSATPSGP
+APAPTGGTPAPSPTTVAPTEPSPSADPTTSEPAPSSDPAPAPTDTASPAPTASSPSTPAD
+VTGTATASGPLPATGGSTDPVTPTPAA
+>MHAAABBN_01566
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS
+SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS
+SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT
+ESAPEPTATTASASASPTSGDRSSSTP
+>LFPAFLNI_01790
+MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP
+SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP
+RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA
+FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA
+AGVLTVRIPRDTAAPWLSDLGHVAADAASAPADLRLPDRSTPTLEEQQPEPETSSRTQEA
+TDAPVPPPSAPADTAAPTPSATTPVPSSTVPSSTAPSSSVPTSTGSATPSSPTSPASSSS
+PSGTGSGSPTPSTPDPSPTSATPTPTSPSPSGPSTSAPATAPAPDPTESAPEPTATTASA
+PAPPTSGDRSSGTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000653.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2bde4f56b054bdacf0b5e2d4968d9eebacf3158
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000653.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00994
+MFVLAIVVLALLIDWGTIGENVLNFPAVAPLFPNIILVGLGNTLFYTATSFVVGLLGGIA
+LALMRMSAFAPYRWLATAYVEFFRGVPALLVFLAFGYGVPFAFGVSWPIPVVVMTALGMV
+AAAYIAETLRAGLQAFPPGQMEAARSLGMPAWQAMITIVIPQAFRIVLPPLTNEVILLTK
+DSSLVYVLGLAAHEYELTKFGRDGISALDAGMTPILVAGLFYLVITVPLSLLARRFEARS
+TKKGH
+>MOLHKGIG_01866
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH
+>NAFOICDF_00932
+MSTQASPAPRTAAAPSRAGRRRTLSVAVQAAVFVLAIVVVALLADWQAIAENVLNFSAAG
+PMFPNVILVGLGNTIFYTVTAFVVGLLGGMLLALMRMSSFAPYRWLATAYVEFFRGIPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMIALGMVSAAYIAETLRAGLQAVPKGQMEAARSLGM
+PHWRAMLTIVIPQAFRVVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGIAALD
+AGMTPILVAGLCYLVITIPLSLLARRFEARSSRKAH
+>MHAAABBN_01562
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH
+>LFPAFLNI_01786
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGTLTENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000669.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59993f7bbb477beb46235f0708938772d21182b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000669.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01017
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAALDRLEEQGVQRLVF
+GGAAGQEATASFTQSKFTAEQRDAWAATDGVASVEPLGVSQGRAVGLAHGVETDEAGRAD
+VADVPTTGVASTAFLGLVPGGADAPAALAPGEVVLSSDVADSLGAQAGDAVAVSGFVFTV
+AEVVPNEFYSHSPVTWLALEDWRAISHTADDAVLGTAGLVRFAAGADPDAVAAAGDAAAG
+TVSETVRGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GTDGWVLKDALTQAAFVLLGGVLVGTALAAGIGVLAARGVPFELSWATTLVPAAGILVLG
+MLAAVAAVFRVTRIDPLVALGGN
+>MOLHKGIG_01851
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+GGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD
+VSGEPTTGVATTAFIGLTPGGSDAPAGVELGQIVLSQDVADSLHAQAGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVIGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVIAVYRVTRIDPLVALGGN
+>NAFOICDF_00959
+MFLALRDLRFATGRFSLMGAVVALITVLLVMLSGLTAGLGHQNTAALDDLGARGTDRIVF
+GGTAGQDPTASFTSSEVTAAQLDSWCAADGVARVEPVGVAQGRLTGVAGHVDTDAAGRPA
+ETPEVAGVGSASFVGLDPAAPQAPAGLEDGELVLSQALAEALEVEEGGQVESSGRVYTVA
+SVAADSWYSHTPVAWTTLTDWRALSHTEDADVAGTAGLVTLVDGADADAVASAADDAAHT
+VATDVKGAYAALPAYSSEHGSLTMMQGFLYGISALVVVAFLSIWTIQRTREIAVLKALGA
+STGWVLRDSLLQGGIVLAVGVGLGTALAAGAGWFAAQAVPFVLSPATTVLPALGVLALGL
+AGSALAVARVTRIDPLIALGGN
+>MHAAABBN_01547
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+DGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPPGRAD
+VSGEPTTGVATTAFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDADTDVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAAIGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVVAVFRVTRIDPLVALGGN
+>LFPAFLNI_01771
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+GGAAGQEPTASFTQSEFSVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD
+VSGEPTTGVATTTFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVVGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVVAVYRVTRIDPLVALGGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000672.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e13cc5a7a3ea86bca9efb7ea8eca1886c9c4d8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000672.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01020
+MGPRMNSAWLFVGVMFTCALIGFWTLRGLGFARGDLSLPAALGVLAVAAVAAAVITRFVR
+RR
+>MOLHKGIG_01848
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
+>NAFOICDF_00962
+MTLPPLHHGRDDDADRPAASGPGGRGLGGPAGPGAGLRRTYTFVGVLFACALIGFLSLRL
+LGVERGSMTLPAALGVLAVAAVAAAVITRVVGRR
+>MHAAABBN_01544
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRPR
+>LFPAFLNI_01768
+MPPLHHGQPGDDGDPRDPRHRPGAGLGPGLRSVWMFVGVMFTCALIVFWTLRGFGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000673.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ded297a355adaa96922c0c489a7661ff300c06c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000673.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01021
+MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE
+LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS
+RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED
+FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG
+LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA
+GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+AVPAAVGQAGQAGEDAR
+>MOLHKGIG_01847
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>NAFOICDF_00963
+MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD
+LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA
+RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED
+FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM
+ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ
+LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA
+GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE
+ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV
+LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG
+YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV
+GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF
+WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER
+LTGRRFEA
+>MHAAABBN_01543
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
+>LFPAFLNI_01767
+MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE
+LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS
+RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED
+FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM
+DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG
+LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA
+GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI
+TVPGTGGAK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000674.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ccf1ae76d970354716053cd2bc9b93c3ef5f3e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000674.fa
@@ -0,0 +1,61 @@
+>ACLBLIBL_01025
+MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE
+AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ
+RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL
+LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG
+FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA
+TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS
+AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS
+GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG
+APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA
+RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ
+DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA
+ARPPAGRTAGREETR
+>MOLHKGIG_01843
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>NAFOICDF_00966
+MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF
+AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR
+RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP
+LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA
+LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA
+YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV
+GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL
+VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR
+ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR
+QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD
+RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR
+>MHAAABBN_01540
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>LFPAFLNI_01764
+MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000676.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2650b46fe6d52ded7bdbacedf777c7195ae8d467
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000676.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_01027
+MASRTSRRLPEPSSALGRLLAFLGLSALAGLLVAALLLPLAGLTGVAAASGREMLDELPD
+ELPAEPVSVPSRMISEDGEEIAVFYEEDRIPVPLDQISEHMRNAIVAVEDERFYEHDGVD
+ARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGTKNVSDKVKEIK
+LAVAVEEQMTKDEILEGYLNIVLFSGRAYGVEAASRYVFGKSAAELESWEAATLAGMVQS
+PTRFNPARNPEEATERRNLVLGAMKKNGYLTEEEHAEAVAQPMEVVMESRPSGCLYSKFG
+SYFCDYVERQILADPAFGPDPQSRQALLDRGGLTIRTTIDSELQKAAEENLRKSVPNNES
+LGAGHALTSVQAGTGNIVTMAQNTEYAIQDELGHTSLNFNVDREWGGGQGFQAGSTLKPF
+VALTWLRNGNRMVDSVDASRNVYPTGTRFEASCRPGGYTTIGGTWQFKNVIPGMLRQVRV
+DEGLFWSVNTPTVATAYQMDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSIAPLS
+LAGAYAAIAADGLYCEPRAILEVTDTVGNQYDVAGPQCDQVVDPKHIAELMPVLRHIGAF
+NIAEEGAGYEFGGKTGTNDNVSSTWFTGFTTELATAVWTGRYNNMKSMTGETVNGEVRNP
+FYSTSINGPSWLEYNQLAKEKYPPGELPDWDGPQSEDPGAEGEHPDGTAFRIDDLDRGGP
+QPQAVPGN
+>MOLHKGIG_01841
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSELATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF
+>NAFOICDF_00968
+MASRSSRLPARSSALGRLLSFLGLSALAGLLVAGLMMPAAGATGIVFASGRDMLDELPDQ
+LPAEPVSMPSKIYSADGELIATFFQENRQPVPLDQISPYMRNAIVAIEDERFYQHDGVDA
+KGLVRAMVNNVSSSSTQGASTLTQQFVNNMLINSQQVRGDSRLTLSGTKQASDKVKEIKL
+AVAVEKQMSKDQILEGYLNLVLFQGRAYGIEAASQYVFGKPAKDLELWEAATLAGMVQSP
+TRFNPARNPEGTTARRNTVLKAMLKNGYISQEEHDHAVAQPLTYTMKGQSTGCLSAAFGA
+YFCDYVERQILADPTFGPDTASRQALLDRGGLTIRTTIDSNLQKKAEELTRRVIPNNESL
+GAGHSLISLRPGSGDIVTMAQNTEYSIQDELGKTTLNLNVDAKWGGGTGFAAGSTFKPFI
+GLTWLRNGGKLIDSVDGSKDRYPPDARFQASCLPGGYTTAGGGTQGWQLNNVIDGMKKRD
+RIDEGIFWSVNTPTVALAYQMDLCDIVNTLTQVGIVTARDGAPLSPAEPSFVLGKDDVSP
+MTMAGAYATLAANGKYCKPRAITEVTDTTGNQYTVPAPECRQVLDPAQVAEVTPLLRHIA
+AHNIAPDGTGYEFAGKTGTNNNMSSTWFIGYTTELATAVWAGRYTSQKTMRGETINGVVQ
+KEFYGATVNGGTWLEWNDMAKRTFVPGELPEFDGPQSEDPALEGDHPDGRFYRPEDIDRN
+GGTPTSSLGPAAGETAFSSAENAAKFESGVLTR
+>MHAAABBN_01538
+MASRTTRFPAPSSAPGRLLAFVGLSALAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPAEPVSVPSRILSEDGEEIAVFYEENRTPVPLDKISKHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF
+>LFPAFLNI_01762
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRAAVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEEQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGA
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPNMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTAGNQYDVADPQCDQVIDPDHVRELMPVLRHIGGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFTIDDLDRGGPQ
+PQAVPGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000678.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53cae68c84228709f4d2c0e3530a3e4b6677d948
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000678.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01029
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR
+>MOLHKGIG_01839
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR
+>NAFOICDF_00970
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR
+>MHAAABBN_01536
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
+>LFPAFLNI_01760
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000682.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d01b2d0a12de616f82232a95c60b6c3cd4c5bc47
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000682.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01034
+MSTAAIVMMSLAILLVWGGLALSAVHLLRHPDDSSGDLALGDRLAPAAWEREDELGREDV
+RLGARRG
+>MOLHKGIG_01834
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDDLAPAVWEREDGLLDAQH
+R
+>NAFOICDF_00975
+MHTPALIMMVIAMLTVWGGLVLSAVHLLKHPDETSGTLADAVDVDHTL
+>MHAAABBN_01531
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVWEREDGRLDAQH
+R
+>LFPAFLNI_01755
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVREREDGRLDARH
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000683.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b646a459b2414d9e88b16185a53a8f05d7c50223
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000683.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01035
+MTATPSGAAPSPASAEGGAARVVSASLPVVAVDAALSAPPYRQITDAVLAGVASGCLARG
+DRLPPVRALASELGVAPGTVARAYKELEARGTILTRGRAGTFVAASADARADAAHQAVRR
+CLDTLLDRLGYTADEAVELVRRDAAARA
+>MOLHKGIG_01833
+MAFSTRSTGETMRATGPSAAAPSAAPVAGGAAGVVSTSLPVVAVDGSLPTPPYRQIVDAV
+LAGVTSGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD
+ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
+>NAFOICDF_01055
+MNGVEPTLELDLRSPVPPFEQIRAGISAFVDAGVLAPGDRLPSVRALAADLGVAPNTVVR
+AYRELESAGVVRTARGKGTVVADRPRGALTADDDGTARTLEAAVHSALAAGWDRERVQRV
+VEAALVSPPAPVDRKDTP
+>MHAAABBN_01530
+MAVSTRSTGETMRAPGPSAAAPSAAPVAGGAAGVVSASLPVVAVDGSLSAPPYRQIVDAV
+LAGVASGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD
+ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
+>LFPAFLNI_01754
+MAVSTRGTGESMRLPGPFAAAPVADGAAGVVSASLPVVAVDASLPAPPYRQIVDAVLAGV
+ASGSLARGDRLPPVRVLAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASADARAD
+AAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000691.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3432aa90c231bccc813801204d1d388e3bba0810
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000691.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01045
+MTGRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAAL
+AASDARRGLSAGEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPPALAAAVA
+GPPRLQAPQAVPEDPLPDASSPSTPTPSSVPPSVSPDPSATTGTR
+>MOLHKGIG_01824
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEDPPEAPPPEPSVEASAGTR
+>NAFOICDF_00984
+MSGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAALAASDARRGLGAVPDAGV
+LEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPASTAVAVAGPPVGPRGPVA
+GPGRDDAPEDAPDTPGAPPEAATP
+>MHAAABBN_01521
+MTRGRAPVRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAGSADPPEAPPPEPSVEASAGTR
+>LFPAFLNI_01745
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEAPPEPSLEASAGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000692.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63b3217497aee61fd7e79bc47b5de0c6ab7346d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000692.fa
@@ -0,0 +1,79 @@
+>ACLBLIBL_01046
+MSTPPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHPWDEPAP
+LADAVADVVAGLSVSRPGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWP
+SEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHTVVATGTASGKSLAYQLAAGIRLSG
+DPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHANVLMT
+NPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDR
+PEPVFIGASATSADPAGHFSRLIGAPATAVAEDASPHGAVTVAFWEPELTDRRGENGAPV
+RRSAMAASADLLTDLALQQVRTLAFIRSRRGAEAIASAARRQLEELEAGLGSRIAAYRSG
+YLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGR
+GGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTP
+EAFERFGDPERVRALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAE
+SGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVEELDEDAHAVIVTRAWPDFTTQARDVTE
+IEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPARDLFTSA
+VWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSP
+AVFVYDGRPGGAGFAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDK
+AGALTVLRFLLGQADHLVPVVAEGSGETDGGTDDGVGVDGEDASGSGSSGTA
+>MOLHKGIG_01823
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHASVLMTNPDMLHVGILPHHERW
+ATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPAAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSSGGATDAAPGA
+>NAFOICDF_00985
+MTGGPVPWPDDDPWAARGPAEDRSARDVPTPAPGGPGWEPPQELATGDPEARAAFAAALG
+RRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRH
+TVLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLR
+AAPYDGDTAPQDRIWAREHANVLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYR
+GVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPAEHLATLIGAAPGEVEAVTE
+DASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGA
+ETIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGID
+VAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGV
+EDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVRELLDVLVEQGLLRRRPAGW
+FWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLV
+EDLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVIS
+FQRKALLSGEVLGEEPLDLPARDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMI
+GMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAGFAERGFAQARRWVEATAGA
+IAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDVTA
+>MHAAABBN_01520
+MTGHLPEHDPWADPAGGWGPPGTADSAPPVDDAAPDFSGPEPQPVGAVLADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHATVLMTNPDMLHVGILPHHERW
+AAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSADPAPGA
+>LFPAFLNI_01744
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHASVLMTNPDMLHVGILPHHERW
+AAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASSDGSGGASGGATDAAPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000694.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32418e0dbd8981d64af3b077038fce6344696bab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000694.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01048
+MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER
+LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD
+HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD
+RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER
+SAA
+>MOLHKGIG_01821
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
+>NAFOICDF_00987
+MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI
+NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR
+VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR
+DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD
+AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA
+HPDHVCPRCLERTPA
+>MHAAABBN_01518
+MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER
+LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR
+PHPAERTEA
+>LFPAFLNI_01742
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000695.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..868eed747b55df2b3865b2a1e72342e80e2bdaeb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000695.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01049
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA
+RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA
+ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP
+LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE
+FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP
+VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA
+DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL
+EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA
+AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT
+AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED
+>MOLHKGIG_01820
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>NAFOICDF_00988
+MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA
+PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER
+ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA
+LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA
+GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE
+GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP
+AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT
+VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV
+TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL
+DDAGRAGLLAAVRELHEDGFLLEA
+>MHAAABBN_01517
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR
+LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>LFPAFLNI_01741
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA
+EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000697.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01eef765ed8a93b4fa3ad600e452ef2648431b37
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000697.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01052
+MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI
+REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK
+KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR
+>MOLHKGIG_01818
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK
+KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR
+>NAFOICDF_00990
+MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI
+GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV
+RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK
+KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI
+LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR
+>MHAAABBN_01515
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
+>LFPAFLNI_01739
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000698.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca747f3d4fce0a306b614c19137c9c09de7373c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000698.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01053
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA
+>MOLHKGIG_01817
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
+>NAFOICDF_00991
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES
+>MHAAABBN_01514
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP
+>LFPAFLNI_01738
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000702.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab085e14b939fa013a844611b7cee62dbac98ea2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000702.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01061
+MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP
+PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA
+AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH
+HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF
+LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD
+GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS
+LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD
+>MOLHKGIG_01813
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>NAFOICDF_00996
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD
+>MHAAABBN_01510
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>LFPAFLNI_01734
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS
+VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000707.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab2ca7b66c4e041eae8910508acb1bd1b5e18585
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000707.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01069
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>MOLHKGIG_01804
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
+>NAFOICDF_01005
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA
+>MHAAABBN_01501
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>LFPAFLNI_01725
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000712.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..182a2ef73fc1f946b43d8d778c7cf5e44d7ed3e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000712.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01074
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF
+>MOLHKGIG_01799
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>NAFOICDF_01010
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF
+>MHAAABBN_01496
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>LFPAFLNI_01720
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000719.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61002e2089dacc350e2af41d167bef40f0e815cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000719.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01097
+MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD
+TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP
+RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT
+EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV
+LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA
+>MOLHKGIG_01781
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>NAFOICDF_01020
+MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL
+LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL
+AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV
+VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE
+RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR
+AEQH
+>MHAAABBN_01488
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>LFPAFLNI_01710
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000721.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0d6fe65d58c132cb62d4de1c689b14c7173682a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000721.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01101
+MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC
+GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT
+RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE
+APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW
+LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI
+SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA
+VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL
+LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR
+>MOLHKGIG_01776
+MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>NAFOICDF_01025
+MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT
+PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD
+LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL
+ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP
+DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET
+RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH
+AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV
+ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR
+>MHAAABBN_01483
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>LFPAFLNI_01705
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000724.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f3a3402da92dd0a0fce1ebf86890e05326e5d3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000724.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01104
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER
+>MOLHKGIG_01773
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR
+>NAFOICDF_01029
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR
+>MHAAABBN_01480
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR
+>LFPAFLNI_01702
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000728.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c2af277626250b00820d3c0eaaee02316a8dcb6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000728.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01109
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR
+>MOLHKGIG_01768
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>NAFOICDF_01035
+MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK
+AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK
+SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR
+>MHAAABBN_01475
+MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>LFPAFLNI_01697
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000732.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7704c8d6f7387bfef5dd4aabbda4a72f76dab806
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000732.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01115
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG
+>MOLHKGIG_01762
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>NAFOICDF_01040
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG
+>MHAAABBN_01469
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>LFPAFLNI_01691
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000733.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1dd6755842c9813e85272f627eca5fd5d7f7524
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000733.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01116
+MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA
+HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF
+GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL
+WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED
+>MOLHKGIG_01761
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>NAFOICDF_01041
+MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG
+NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA
+FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF
+GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL
+WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED
+>MHAAABBN_01468
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>LFPAFLNI_01690
+MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000737.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c23e991b287fe8fcd507e5e2444f6bad7720158
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000737.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01122
+MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA
+VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM
+VTTVTEIADADGAPVSTVTSTLLVRGEES
+>MOLHKGIG_01755
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>NAFOICDF_01047
+MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA
+VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM
+VTTVTEIVDAAGAPVSDVASTLLVRGEES
+>MHAAABBN_01462
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>LFPAFLNI_01684
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAPVSTVTSTLLVRGEES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000739.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..976b6ba0f9fcc9a52bc3b118624d124c97dbf1e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000739.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01124
+MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH
+GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR
+DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA
+VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT
+ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR
+GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL
+>MOLHKGIG_01753
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>NAFOICDF_01049
+MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE
+GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS
+AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP
+SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG
+MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA
+GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA
+VRDGVKARFGVDLHHEPMIIGTRL
+>MHAAABBN_01460
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP
+GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
+>LFPAFLNI_01682
+MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP
+GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA
+HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY
+RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL
+AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG
+TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN
+RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000747.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f68fa60134c56a6f905bc77b5702081bad2c3fd6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000747.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01132
+MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVILVIAWGWPRQMGAPARLSLSVTLA
+AVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAISVAAFSLIGLIPGVQGRPGVLALV
+VVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATLVSLTAATAPSARPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
+>MOLHKGIG_01745
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>NAFOICDF_01061
+MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVIAVIAFGWPRQMGAPARLSLTLTML
+VAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAFGTMASFIVQLVRGTGRPLRLESTV
+TTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAATLIVTSLIGLTPFMQGRPRVLALV
+MVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGLVSLTAAAAPSSRPLPEDRVVGTTL
+SPRRAGYALAMAPVGAAGVVGHVMLGFLA
+>MHAAABBN_01452
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>LFPAFLNI_01674
+MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVILVIAWGWPRQMGAPARLSLSVTLA
+VAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAVTVAAVSLVGLTPWMQGRPGVLALV
+VIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVLVSLTAATAPSSRPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000748.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1085cfacff793511feebbe8c284ed65b2575b5e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000748.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01133
+MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR
+>MOLHKGIG_01744
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>NAFOICDF_01062
+MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR
+>MHAAABBN_01451
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>LFPAFLNI_01673
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000749.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02c84d35dddd7b1f2d2bb2c758fc1d49f7835a57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000749.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01134
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG
+ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS
+SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP
+>MOLHKGIG_01743
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>NAFOICDF_01063
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR
+ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS
+SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA
+>MHAAABBN_01450
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>LFPAFLNI_01672
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000750.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9af572d0bd96204628fb3e4432a21bafd249a757
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000750.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01135
+MTGAEPAQRSPLLDLASAEPHGPAGGAVEGVGPDAGVAAHYGRPLPEQRALARGRALVDL
+SHRAVLSVSGPDRLTWLHTLGTQHVADLPAGTSTEILFLDAQGRIEHAAHLLEDGTAAWL
+VTDREDGPGLAAWLASMRFSHQVTLRDHTGAVAVVGSTAPVPGWEDRTVWVDPWPHVGVG
+GWAYTADPRPESHPGADWSWREHLVTRADLEATVRTLGTGPLEGWSLAGTTAAEALRIEA
+GRPRMATDVDERALPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLMLDGSV
+HALPPHGAPVILRPAEDTPQARAAARPVGAVTSSAQHHEAGAVALALLKRSVPVDAELLV
+CEDLPGDAEAGDAADAAETGWIAAAQEPLVSPAAGQVVGRPRGVGRLR
+>MOLHKGIG_01742
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
+>NAFOICDF_01064
+MTEPRPEPAPAVRAARRSPLLAPPPAAPGGPAEGAVEGVGQDAGVAAHYGRPLVEQRALA
+RGRALVDLSQKTVVSVSGPDRLSWLHTLSTQHLKDRPAGTSTEALFLDANGRIEIAVHLL
+EDGAAAWLIADPAHADVLVTWLRSMVFSHRVTLRDHTGVVAVVGAMAPVPGWEDRTVWLD
+PWPRVDVGGWPYSPDPDPAAHPGAGWSWREYLVTRGDLVATVDRLGTGELEGWSLAGALA
+AEALRIEAGRPRPAVDADARAIPHELDILRTAVHLEKGCYRGQETVARVYNLGRPPRRLT
+QLLLDGSSHALPAAGAAVILRPEPDTADARAAARPVGTVTSAVQHHEAGAVALAVLKRAV
+PVAAELLVREEAAGGGEPEWIAASQQALVSPDAGQVVGRPAGLSRRA
+>MHAAABBN_01449
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
+>LFPAFLNI_01671
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLITRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSVHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGAAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000755.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93668a42e99becfa10b0cb991c475d953bba9a6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000755.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01141
+MSVPAPRTAVIVDDHAIFRSGLRADLDPARLAIVGEAGDVDEAVRAVLELAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVVD
+AAVRVAGGDAVFSPRLAGFVLDAFRGAAAPAAAPASPAVPDEDVDRLSAREREVMRLIAR
+GYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>MOLHKGIG_01737
+MTDPAPRTAVNVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRAVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>NAFOICDF_01070
+MTVHADPVVPTAVVVDDHAIFRSGLRADLDASRLRIVGEAGDVDEAVRVVLQLAPDVVLL
+DVHLPGGAGGGGAEVASRVLAERPGQRLLALSVSDAAEDVVAVIRAGARGYITKSAAGAE
+VVEAALRVAGGDAVFSPRLAGFVLDAFRGLPTESAPAGPAPSEGDLDRLSAREREVMRLI
+ARGYTYREAGAELFISDRTVESHVSSVLRKLQLSNRHELTRWAARHGWA
+>MHAAABBN_01444
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLVPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGVEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
+>LFPAFLNI_01666
+MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLAPDVVLLDVH
+LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD
+AAVRVADGDAVFSPRLAGFVLDAFRGTAPAPPLVPAAAASGAAAPDEDLDRLSAREREVM
+RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000758.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a1478a9ec9729085f441c98d702f2f89d068979
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000758.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01145
+MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ
+EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME
+DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND
+AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT
+VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI
+>MOLHKGIG_01733
+MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD
+LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR
+ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV
+TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF
+EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>NAFOICDF_01074
+MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE
+ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS
+IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH
+HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD
+DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI
+>MHAAABBN_01440
+MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ
+ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP
+MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL
+DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL
+PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>LFPAFLNI_01662
+MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD
+EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE
+VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV
+YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT
+ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000763.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ee2399e52a825fc17a4e331d1d0f858cfba5027
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000763.fa
@@ -0,0 +1,105 @@
+>ACLBLIBL_01150
+MVASSTSNETATVSPRSGASAGRISFAKISEPLDVPDLLALQTESFDRLIGNERWVARVE
+EAQAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFSEPEFADAKMTEEECKDRDATYA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQMLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTVKGVRDGEAVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAYQIAQANA
+PVAEDGTFEEELVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATAAGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVLVSEGDRVEPLSVIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSD
+PVNVATPVFDGAEAYEITGLLGHVNATRDGDRLMGENGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>MOLHKGIG_01728
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>NAFOICDF_01079
+MVASSTSNETAAVSPRSAASAGRISFAKIHEPLDVPDLLALQTESFDRLIGNERWAARVD
+AAVAADDHSVSVTSGLTDIFEEISPIEDFQGTMSLSFSDPEFADAKMTEEECKDRDATFA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSARIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKALGWTESRILE
+EFGQYDSIRATLEKDGTADQNEALLDIYRKLRPGEPAAVDAAQNLLNNLYFTAKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTIKGARDGEPVEVRVE
+VDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLNALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINPFGFIETPYRRVVDGRVTDQLDYLTADDELAFQIAQANA
+PVDEDGRFVEELVLCRQRGGGGEPVLSTVDDIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLQSEAPYVGTGMEKYVAVDAGDSVTAAQPGVVTEVAADLVTVMNDD
+GSTTHYPIMKFSRSNQGNAYNQRVRVSEGDRVERLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDVVLNPLGVPGRMNLGQVMEIHLGWAASRGWDIEGEPEWIKDLPDFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNKTRDGDRLMGTTGKAQLFDGRSGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDETYRAAEELGIDLSHAEPSSVEEV
+>MHAAABBN_01435
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>LFPAFLNI_01657
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000766.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..086dc154a490be2e294ffed84c2b0872bd61a0da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000766.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01153
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>MOLHKGIG_01725
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>NAFOICDF_01083
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGVRAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>MHAAABBN_01432
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>LFPAFLNI_01654
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000772.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea460f462d2459e153838e431b7ab6200fa3cc91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000772.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01159
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>MOLHKGIG_01719
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>NAFOICDF_01089
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>MHAAABBN_01426
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>LFPAFLNI_01648
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000773.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ee7d6948f4b41a306cb606b7f82b316d3556a3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000773.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01160
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>MOLHKGIG_01718
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>NAFOICDF_01090
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ
+>MHAAABBN_01425
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>LFPAFLNI_01647
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000774.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59e4f71dfd9762c35cd9f8bebbd182c7eb11814b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000774.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01161
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>MOLHKGIG_01717
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>NAFOICDF_01091
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN
+TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS
+>MHAAABBN_01424
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>LFPAFLNI_01646
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000776.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1273398c627a29afa1e24d829966be86112c5b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000776.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01163
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>MOLHKGIG_01715
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>NAFOICDF_01093
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR
+>MHAAABBN_01422
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>LFPAFLNI_01644
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000778.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..243bcca80f7c3a4b087a8f8792018e0ffa0f54bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000778.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01165
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE
+RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>MOLHKGIG_01713
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>NAFOICDF_01095
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE
+RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA
+>MHAAABBN_01420
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>LFPAFLNI_01642
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000780.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89c3a81cdf90fef0f914aa2ac32835c0d0660158
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000780.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01167
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNSSRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQADNNEEAAK
+>MOLHKGIG_01711
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
+>NAFOICDF_01097
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLEDSSRLKAVKRDIARI
+YTILRERELGIRGDVETAGAEKNEEAAK
+>MHAAABBN_01418
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
+>LFPAFLNI_01640
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000783.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b747a8b0ea5a6bf6f075d6e1b30a2bf36411f70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000783.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01170
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL
+>MOLHKGIG_01708
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>NAFOICDF_01100
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL
+>MHAAABBN_01415
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>LFPAFLNI_01637
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000787.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12fd4b06f48247b8e549b5f0fe4e8340a07252a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000787.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01174
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL
+>MOLHKGIG_01704
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>NAFOICDF_01104
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>MHAAABBN_01411
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>LFPAFLNI_01633
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000790.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77661dce2fd995011eb0a45f9c1f44a2f30fc4c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000790.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01177
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKVDAFSASAVEKIQAAGGSTETL
+>MOLHKGIG_01701
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
+>NAFOICDF_01107
+MAENDAIKVHDLRPAPGAKTAKTRVGRGEGSKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSEMFPEGGEVTVETLVSKGLVRKNQPVKVLGTGE
+ITSAVQMKADAFSASAIEKIKAAGGSAETV
+>MHAAABBN_01408
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
+>LFPAFLNI_01630
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000795.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b14ba1e0cc0ed0fe4602fba311dd09f828af9349
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000795.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01182
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>MOLHKGIG_01696
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>NAFOICDF_01112
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG
+>MHAAABBN_01403
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>LFPAFLNI_01625
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000802.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..688675d8da169223fc578a9bc41dbfad200034f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000802.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01189
+MSINEHDDVELTSYTSESTSAGTEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQW
+TINGRTLENYFPNKLHQQEVNDPFTLLELAGAYDVIARIHGGGPSGQAGALRLGISRALN
+EIDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>MOLHKGIG_01689
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>NAFOICDF_01119
+MSINQNDDVELTSYTSESTAASETAAVSERPALTVPGSAVGRRKEAVARVRLVPGSGQWS
+VNGRTLENYFPNKLHQQEVNDPFTLLELNGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>MHAAABBN_01396
+MSINENDDVELTSYTSESTAAAEAPVASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>LFPAFLNI_01618
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000803.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fb89db04a39f5c5e96ea4b73c97275ad4958473
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000803.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01190
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR
+>MOLHKGIG_01688
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR
+>NAFOICDF_01120
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR
+>MHAAABBN_01392
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR
+>LFPAFLNI_01617
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000812.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..627bb957b75b8d3b2dfc0dd07a3bacfb42e68473
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000812.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01203
+MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAV
+PAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD
+AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSA
+EGPAPDRADAWVAGPGLDTQDDARRRWEGVLSALAERPEAALVADASALELVTAAQLRAL
+REGGTPVVLTPHAGEWARLRERLPADGADAADPLAALRSWSAAHGATVLLKGPRTLTVQP
+DGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRARRAEQAPGPVPTAALAAAA
+AWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG
+>MOLHKGIG_01675
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRAAA
+TVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALLADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTAEHGATVLLKGPRTLVVAP
+DGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR
+>NAFOICDF_01131
+MRAHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGN
+NGGDALWALAFLRRRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVV
+VDAMLGTGARGGFTLPEPARHLPSGAAVVACDLPSGVDADTGAVPGEALAADLTVTFGAS
+KTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARDAHKYTRG
+VVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPER
+ADAWVLGPGLGDGDGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALA
+AVDARTVITPHAGEWARLRDRLPVPAADAVDVDEDGAGELARLRAWTAARGVTVLLKGPA
+SLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHGAARGGRP
+SPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGRRP
+>MHAAABBN_01380
+MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRGRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADT
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTSEHGATVLFKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR
+>LFPAFLNI_01605
+MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA
+ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAV
+PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADA
+TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE
+AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSA
+EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL
+RAAGTPVVLTPHAGEWSRLRERVPADGADATDPLAALRAWTAAHGATVLLKGPRTLVVAP
+DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA
+AWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000817.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8eca28f2dccae46c758a082d791cd68cd369bb19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000817.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01208
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>MOLHKGIG_01670
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>NAFOICDF_01136
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA
+>MHAAABBN_01375
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV
+>LFPAFLNI_01600
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000819.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d20df9b0e5f8daa5a256b51e710982d748940fd8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000819.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01226
+MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA
+MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV
+ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA
+DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG
+RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQSGEE
+>MOLHKGIG_01668
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>NAFOICDF_01137
+MSEKRTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQAMRAAWIEDLL
+SLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVGDSLLGLLTA
+EHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVLYADADMNKA
+DWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLADRRATTIDGA
+RPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVGRCADLRERIE
+ELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE
+>MHAAABBN_01373
+MTRQDTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>LFPAFLNI_01598
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVGR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000836.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a0274207b81dd34189a712d030b53bf87c3e9fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000836.fa
@@ -0,0 +1,110 @@
+>ACLBLIBL_01245
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR
+>MOLHKGIG_01648
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR
+>NAFOICDF_01156
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES
+>MHAAABBN_01353
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR
+>LFPAFLNI_01578
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD
+EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000838.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18ae09eac4e32f10eb0730a46837b1efdaa49b4b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000838.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01247
+MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA
+GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD
+>MOLHKGIG_01646
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD
+>NAFOICDF_01158
+MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG
+APSSTPAAPSSGAASSTGTSSGSSD
+>MHAAABBN_01351
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD
+>LFPAFLNI_01576
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGSAGGSTSDSAAGSSTSSTSSSSSAAAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000840.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..846822b76ae9fad0812afb0a0648659d72efd381
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000840.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01249
+MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ
+MVRWHGRQGREGSSFTWGVALDDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGDW
+RDHRTFAITAEEVPEGLLARWLASRPRA
+>MOLHKGIG_01644
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMALDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLAGWLATRPRP
+>NAFOICDF_01160
+MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ
+MVRWQHRQARAGTSYTWGMALDDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQAG
+RGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGAW
+RDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR
+>MHAAABBN_01349
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLASRPRA
+>LFPAFLNI_01574
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLARWLATRPRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000845.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6dbeb7a1152d8821996ab77fccb547c39db29c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000845.fa
@@ -0,0 +1,38 @@
+>ACLBLIBL_01256
+MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV
+LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD
+RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA
+VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE
+GWFMPRDSWF
+>MOLHKGIG_01639
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP
+SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA
+GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD
+PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED
+DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY
+WLVDHGLEDAPEDWFVPRGSWF
+>NAFOICDF_01165
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV
+AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA
+ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS
+RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD
+GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY
+RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR
+LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF
+>MHAAABBN_01344
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP
+TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT
+PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA
+TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD
+QGLEDAPEDWFVPRGSWF
+>LFPAFLNI_01568
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP
+SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ
+AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA
+TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD
+HGLEDAPEDWFVPRGSWF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000847.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cd8da8388042a43f4188e31797e6102efa1c2d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000847.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01258
+MAENGTAETVRPDDAEGAETGVFSAPARELFAARRGDAVADPADVDASATPGYTGGKAQG
+KQDLADRADVLADLQELLFAQSTREAPSGEVPSLLLVIQGMDTAGKGGIMRHVIGAMDPQ
+GVHLHAFKAPTAEERAHDFLWRIRPHLPRPGRVSVFDRSHYEDVLVHRVRELSPLAEVEE
+RYGAIREFESRVRAAGTRIVKVMLRISAEEQAERLLARLDDPTKHWKFNEGDLDDRAYWD
+DYMDAYRIAIERTDTEDAPWFVVPADRKWFARLAVQQLLIETLQGLDLDWPEADFDVEAA
+RRRLLAG
+>MOLHKGIG_01637
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIMRHVIGAMDPLGV
+HVHAFKAPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>NAFOICDF_01167
+MADTPENRFTEPVRTLLRARRADGAPVGPADVDPHGKPGFDGGKSEGRAVLAARSERLGQ
+LQELLYAQSTREADGGLPAPSVLLVVQGMDTAGKGGIMRHVVGQMDPQGVDVHAFKRPTP
+EEARHDFLWRVRPHLPMPGTLSVFDRSHYEDVLIQRVRSLAPAEEIERRYTAIREFEAEA
+VAAGIRVVKVMLHISPEEQKARLSERLERADKHWKFNPGDLDERELWDEYQEAYRVALHR
+TDATDAPWFIVPADRKWYARVAVQELMIETLEAMGLTWPEADFDVAAARRRLLAG
+>MHAAABBN_01342
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIIRHVIGAMDPLGV
+HVHAFKAPTAEERAHDFLWRIRPHLPRPGLVSAFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>LFPAFLNI_01566
+MADTPATAAGRPARATDAHGVFDAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGK
+KDLAARGRELADLQELLFAQSVRDAPVGEVPSLLVILQGMDTAGKGGIMRHVIGAMDPQG
+VHLHAFKVPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEER
+YGAIREFEAAVRAAGTRIVKVMLRISPEEQAERLLARLDDPTKHWKFSEGDLDDRAYWDQ
+YTDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPEADFDVAAAR
+RRLLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000848.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b35de4de5f1133c9b5efcb892d64a0e1483d98
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000848.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01260
+MSEQQQEQTGAPVEGFTSADTSDVAGMSYEQARAELVETVTRLEAGGGRLEESLALWERG
+EALAARCQAWLDGARARLDEVRGAADSPTA
+>MOLHKGIG_01635
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD
+>NAFOICDF_01169
+MSEQEQQGTAVGGFTSADTSDVARMSYEQARAELVEVVGQLEAGGAGLEESLALWERGEA
+LADRCQAWLDGARARLDQVRGEAAPDAD
+>MHAAABBN_01340
+MSEQGMEQTQDPGRPSGVEGFTSADVSDVARMSYEQARAELMETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDVD
+>LFPAFLNI_01564
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000859.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16f7fe4354624de765323198c14ca55467f32087
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000859.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01291
+MRLVGTVTLARDSVVYDHKSSVPTNERAPDMSRILMILTSHDQLGDTGRKTGFWLEEFAS
+PYYVFTDAGHEVTLASPRGGQPPIDPTSSKPEMQTEATRRFDQDDEAKAALAHTTPLAQV
+DVDGFDAVFYPGGHGPLWDLVSDADSTRIILDSDAAGRPLGLVCHAPGILHPITAADGTP
+FVRGRQVAGFTNGEEDAAQLTDVVPFLVEDSLIAAGADYRKGPDGESFVVTDGTLVTGQN
+PASSADAARRLLDLLAR
+>MOLHKGIG_01603
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>NAFOICDF_01199
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+SEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITTADGTPFVRGRQVAGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDQESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>MHAAABBN_01315
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+ALIAAGADYRKGPDGESFVVTDGTLVTGQNPASSGDAARRLLDLLAR
+>LFPAFLNI_01530
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000860.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..118f3d7c9d30752414382cedef7a6e748437b680
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000860.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01292
+MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV
+LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG
+QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG
+GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV
+RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL
+>MOLHKGIG_01602
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>NAFOICDF_01200
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL
+>MHAAABBN_01314
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>LFPAFLNI_01529
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000864.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6a20cf7cee6df1ea04da9196f5f1e58969d9efc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000864.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01298
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
+>MOLHKGIG_01597
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>NAFOICDF_01207
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG
+>MHAAABBN_01309
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>LFPAFLNI_01524
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000865.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07e5d15d0aa9385f59caf0d78b18846683402cae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000865.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01300
+MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES
+QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR
+GSRRRRLEAKRQRSETKQLRRRPGV
+>MOLHKGIG_01591
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>NAFOICDF_01219
+MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA
+QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR
+GSQRRRLQAKARRSEVKQSRRRPRMD
+>MHAAABBN_01303
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>LFPAFLNI_01518
+MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA
+TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000867.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe8be2407e7865ecfd6be820da373f00750688a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000867.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01327
+MPSRLHRSREIALILGRNGLQATALAAGLGRWLPAADARTARDAVLRPDMLVDVFEQLGT
+TFVKLGQLISARPDMFPESICTAFARLTDDTTPVPFEAMAATVLEDFGASVDELYAWFDP
+VPLATASIGQAHRARLHDGRDVVVKIRKPGVVEQVRTDLEILRTVASRLSRASRALQDMD
+VVSLVDEFDRALRAELDYLVEARACEQIAENLRDVPGVRVPWVDWATTSSRVLTMEEITG
+FRVDDLASLDAAGIDRADLAYRAAEVLMGMVFEDGLFHADPHPGNVFIEADGGIGFIDFG
+SVGRISSGMRRRFARMAMALVRQDPDGLVRALVAIAPPRGDLDRRALRLEVSRITGRLEG
+RDLADIRVDQLVGQIFGIVRRHRLALPPELVQLFRMLIIVDGLGKRLHPGFDYTRVLNPF
+AVRVAGEELDPRRVAGRIGQAGLAAAELGLDLPEYARKVIDHLEDGGLDVTLRTGELEPL
+VARMERTGDRVVAALVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWT
+GRPRRMRRRPRG
+>MOLHKGIG_01594
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
+>NAFOICDF_01215
+MALHLQRYREIAHVMARNGLDATARLAGLGRWLAPQDPTARRPLDAEARPELLVRTFEEL
+GTTFVKLGQLISTRPDLFPESYCTAFARLTDRATPVPYAAIARTVEEDFGAPVDELFAEF
+DRTPLATASVGQVHGAVLHDGRDVVVKVRKPGVVEAVTADLEILRTLTGRLVRASRTLAD
+MDVAGMVDQFDRSLRAELDFVVEARACEEIAAGFTGTPGVRFPWIAWELTSARVLTMERM
+AGMRVDDLPALEAAGIDREELAYRAADVLMRMVFQHGVFHADPHAGNVFIEPDGTIGFID
+FGSVGRIGPGVRERISGLAMALARQDVDGLVRALLEIAPPRGPVDRRRLRSEVGRIVARV
+DGRDLQDIKVPQLVSEVFAIVRRHRLSLPPELVQVFRMVLIVDGLGRRLDPGFDYTRVLD
+PFVRRMVMDQLDPRRLARRLRRATITTADIGLELPQYLRTLMERIEDGGIDVNVRTSELE
+PLVARVERTGDRVVAALVVAAMITGGTNVLVAYKDRLGPFAGPLVAAGGAALTSGSAYLA
+WISRPRRAPRR
+>MHAAABBN_01306
+MALHLQRYREIAHVMARNGLRATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDLFPEAYCAAFARLTDSTTAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQAQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLVSEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
+>LFPAFLNI_01521
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000869.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5a6712d16ebd544b4f0ba9ef28f37313891f52d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000869.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_01335
+MSHASSGAAAPSDRAPQGAVSESCRRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATF
+NGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFGALLVCLLV
+FPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLRRGALHEG
+FDQLRSIIERVVMGLIVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLG
+VTMVAAPGVPGGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMI
+VDKIAGDRLIEDSEDEGLERLDDEEAATGADAG
+>MOLHKGIG_01587
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>NAFOICDF_01233
+MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW
+LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL
+SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI
+PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF
+ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ
+PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP
+GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA
+ADPGVAEESPAA
+>MHAAABBN_01298
+MSRSHSDALDASGPDSGGAVAVPRRRVGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>LFPAFLNI_01514
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000876.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcf7300c3395c1305628c350a067731f9f8d87c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000876.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_01350
+MPRLSAVSEPLTIAPRSDDAPSVPSSSSDAPRGPGGRRALVRRRVFRSPLQRRIVYAVVF
+ELLAILFTTGILAAFGNSGGSSLAVAVVSSTVALLWNIAFNSMFEAVERRAGITGRPWWL
+RALHAVAFEGGLILFLVPAVALILGVGLWQAFLIEAGLLVFFLVYAAVYAYAFDSVFGLP
+DSAAGATR
+>MOLHKGIG_01574
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>NAFOICDF_01243
+MTPPHDDAPRGPGGRRALVGRRVFRSPLRRRIVFAVVFELLAILFTTLILRAVGNEGAAS
+FAVAVVSSTVALIWNVVYNSLFERLERALGVHGRPWWARVGHTVGFEGGLVLFLVPAVAL
+LLGVTLWEAFLIELGLIVFFLVYNAVYTYLFDAVFGLPDSAGVTAPGTP
+>MHAAABBN_01284
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGIGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>LFPAFLNI_01501
+MSETRRARPGVDPASTPPFDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000879.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..424bd2e40aefdd5b079e16ab13c24a7a03f8885d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000879.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01353
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMVDVVGAPDPVVSARESA
+PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMGTGTG
+MVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTDLPVA
+SVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLIQTDA
+DVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEETDTV
+SIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASRMSRL
+VNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN
+>MOLHKGIG_01571
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+>NAFOICDF_01246
+MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSGPQVTTRSLDALAASLDH
+AHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQGTGTGMVLTSDGLALTNY
+HVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSGLTTTSVSRDPVRPGEAV
+AAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLIQTDADVVPGYSGGPLVD
+GEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEETDSVSIGADGSLGISVA
+GSRDGVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATAMSRLVNDHEVGDRLSVQW
+RTADGEARQGEAVLQKARHN
+>MHAAABBN_01281
+MTPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFRMSRLV
+NDHNVGDRITVQWRTASGEVREAEAVLQPALVN
+>LFPAFLNI_01498
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000884.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6321e2c8a4c170ac4efe8c529f63bbd5a15b109
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000884.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01361
+MTAHGNDKEGRPMSGKKNQHDAAGTEATAVGTGAGEHGSHSADLDARGAAVPGSSGTGGP
+TPGPATSSMGVVARHDDLDGKPVLAFRDVDVKFGTEFGEVHAVKGVTFDVKPGEVVALVG
+ESGSGKSVTSATAMGLLPSNADITGSVQLAGREVLDMTPGQLRGIRGDEVAMVFQEPMTA
+LNPVLTVGDQLTEALELHGIAYGTEADKRAVELLTMVGIPDAAERLKQYPHQFSGGQRQR
+IVIAMAISCSPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMA
+DRVCVMLHGELVEQGTVHQVLQHAQHPYTQKLLSSVPRLGATYEVAEPEPVTATQTTAKY
+AIEAEDLHLEYDYRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEG
+SLRIQGHDLAAMPKSEQRKLRKNIGVVFQDPAASLDPRFPIGDVITEPMVVHKVGDRRSR
+LARAEELLDAVRLPRSVVNRYPHELSGGQRQRVSIARALTLDPQVLIADEPTSALDVSVQ
+AAVLDMFAELQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTKEVLHNPREEY
+TRRLLAAAPVPDPDQQAERRQERRDFLASLGEGVY
+>MOLHKGIG_01565
+MSANDKKGRSMFGKKKENDVTDGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVKLAGREVLTMTPGQLRGIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>NAFOICDF_01252
+MSSKAFDPKDSGTTETSAEDLRARAETLPGSSGEAPQGVVTTATGSLKVPGPATTTMGVV
+EHHDDLGGEPVLAFQDVAVRFATEFGSVHAVKGVTFDVKPGEVVALVGESGSGKSVTSST
+AMGLLPPSADITGSVKLGGREVLTMTDSQLRSIRGQDVAMVFQEPMTALNPVLTVGDQLT
+EALQLHGLAFGTEATKRAVELLTMVGIPDAADRLKQYPHQFSGGQRQRIVIAMAISCSPR
+VIIADEPTTALDVTVQAEILELLRSLKDKMNTGILLITHNMGVVADMADRVCVMLHGELV
+ESGTVQQVLQRPQHPYTQRLLAAVPRLGEALETAEPEPVTSTQTAVKYAIEAEDLCIEYD
+HRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKAVLGLLPVASGALRLQGEDLATM
+KAAEQRALRRKIGVVFQDPAASLDPRFPIGDVITEPMVIHGVGDRRSRLARAEELLDAVR
+LPRDVVNRYPHELSGGQRQRVSIARALTLDPEVLIADEPTSALDVSVQAAVLEMFAELQT
+RYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTGRVLHHPQAEYTQRLLAAAPVPD
+PDQQAERRRERRRLLASFGESAY
+>MHAAABBN_01275
+MSANDKKGRSMFGKKNQNDVTAGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADITGSVQLAGREVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>LFPAFLNI_01492
+MSANDKKGRSMFGKKNENDVTADGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVQLAGRDVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000886.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ebb4318010704cd098360263647f021cfc9fd74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000886.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01364
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA
+>MOLHKGIG_01562
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>NAFOICDF_01255
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA
+>MHAAABBN_01272
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>LFPAFLNI_01489
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000887.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fd6d60b6d4d5fa43e454a1a5062eaf98da27552
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000887.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01365
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG
+TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT
+YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL
+GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG
+HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA
+ITASDEAVEQAARRLAARGPLRR
+>MOLHKGIG_01561
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>NAFOICDF_01256
+MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG
+TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT
+YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL
+GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG
+GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG
+YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA
+ITASDEAVAAGAARLTARGPLPR
+>MHAAABBN_01271
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>LFPAFLNI_01488
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT
+ATDEAVARAAARLTARGPRTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000891.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..191c40525843f6cb29ca2c64f4ea3be65b006b8b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000891.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01369
+MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN
+AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI
+MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA
+>MOLHKGIG_01556
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
+>NAFOICDF_01260
+MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN
+AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV
+MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA
+AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGRTKPHAGSTAVTIGKD
+>MHAAABBN_01266
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
+>LFPAFLNI_01483
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000892.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13db20c959c07001e44d4a653332ce017b1b3729
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000892.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01370
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN
+VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR
+>MOLHKGIG_01555
+MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>NAFOICDF_01261
+MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH
+IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG
+LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR
+>MHAAABBN_01265
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>LFPAFLNI_01482
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000893.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fcd9bdd388083337850e0686cab1a53fb4622a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000893.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01371
+MFRKKLLTLSAVTAAAALSLTACSPSAQQGGGEGSGSASAGGSQSAGSGEGLRIGIKFDQ
+PGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFATY
+SITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQFA
+SGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYGV
+GIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS
+>MOLHKGIG_01554
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>NAFOICDF_01262
+MARSRILSVAAVAAAAALSLSACSPSSSGGSGSASSASGSTAAQSGSSDTLRIGIKYDQP
+GLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFATYS
+ITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNYAS
+GVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYGVG
+LQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA
+>MHAAABBN_01264
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>LFPAFLNI_01481
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000894.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..602c03f22f91d1d9eb481d6e0b10b16a3fdbc127
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000894.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01372
+MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA
+IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPESFFTAPQHERARDFLGKILAH
+>MOLHKGIG_01553
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>NAFOICDF_01263
+MSEITSGTVHGSTAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVAIVLG
+PSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNLFAHK
+SILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIARALA
+MEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVFMADG
+EILEDTDPESFFTRPQHPRAQEFLGKILVH
+>MHAAABBN_01263
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>LFPAFLNI_01480
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000895.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d8a3f0715cf47ccfe7c89cd5d5ef78ef65cf09c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000895.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01373
+MDPDQHPRTDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARRPGDALPPAADLASTTS
+EAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFTVIT
+GGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKYAQG
+FVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMISPGD
+PEIFHVVETAEEAVDCVQRVCGPGAP
+>MOLHKGIG_01552
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRRPGDAARPAADVASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMISPE
+DPDLFHLVDTAEEAVACVLRSAGRADA
+>NAFOICDF_01264
+MTDKPDPARADRVDRHRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPSTSSTSD
+AWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWAVITG
+GGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRYAQGF
+VVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMISPGDA
+DLITVVDTAEEAVAHVSATCGGARA
+>MHAAABBN_01262
+MAPDEHPLDGDVAEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQPGDATQPAADIASTTS
+EAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVIT
+GGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQG
+FIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPED
+PDLVQLVDTAEEAVACVLRSAGRADA
+>LFPAFLNI_01479
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRRPGDATQPAADIASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPE
+DPDLVQLVDTAEEAVACVLRSAGRADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000897.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b1fce5ef33dca4c2a79fcaf8c864079fb935780
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000897.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01375
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG
+>MOLHKGIG_01550
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>NAFOICDF_01266
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA
+>MHAAABBN_01260
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>LFPAFLNI_01477
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000899.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d0ee0053d786fcb381b4a7c1e1893d04151eaca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000899.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_01378
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT
+>MOLHKGIG_01547
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT
+>NAFOICDF_01269
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT
+>MHAAABBN_01257
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT
+>LFPAFLNI_01474
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000906.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..944ab72d397036f3bad41d5c7f8e32aa310ffe18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000906.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01385
+MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV
+PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE
+LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI
+RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD
+LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG
+>MOLHKGIG_01540
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>NAFOICDF_01276
+MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL
+LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT
+WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR
+LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR
+HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG
+>MHAAABBN_01250
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>LFPAFLNI_01467
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000908.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5f3984d3c48127f4ad9e8e15c3f5355afbffb60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000908.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01388
+MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE
+INAKKSGPLGFAAS
+>MOLHKGIG_01537
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>NAFOICDF_01279
+MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE
+IGAKKSAPLGFAAV
+>MHAAABBN_01247
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>LFPAFLNI_01464
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000909.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43d66bb5300111c2bba93cc92d17896b422fdfd1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000909.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01389
+MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR
+GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS
+ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT
+DDDAL
+>MOLHKGIG_01536
+MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>NAFOICDF_01280
+MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL
+ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA
+GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP
+>MHAAABBN_01246
+MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>LFPAFLNI_01463
+MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000911.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89a9709d50aa3ed62436aec8cba35b06bc6c0342
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000911.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01391
+MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS
+LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA
+AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR
+LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN
+LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA
+>MOLHKGIG_01534
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+>NAFOICDF_01282
+MSAMTTPPGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRSLPEYRKA
+REGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVPGVGPVLD
+HPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYMVEGRPSR
+DHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLSAADYRKH
+VQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHRITLAEAH
+RRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVNLAHGVPP
+ETDPEVLTRVVELIHSIPVADGAEK
+>MHAAABBN_01244
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA
+>LFPAFLNI_01461
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000914.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2c110dc1b0ea01d1f4583c000d6d92ca5c0a54a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000914.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01394
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV
+YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD
+TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD
+CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES
+>MOLHKGIG_01531
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>NAFOICDF_01285
+MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF
+LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR
+NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT
+RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL
+REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI
+NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT
+PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA
+VDAPVRGLAEHRGEQDGADDAGAQDS
+>MHAAABBN_01241
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>LFPAFLNI_01458
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000916.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30e193aba1a4e5662d8b66f38077c0fb6651bd39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000916.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01396
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPGRSDGSRWLVLTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGGRAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDAAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFLAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>MOLHKGIG_01529
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>NAFOICDF_01287
+MDGRPLVLTRQPAQAGTLEADLAAAGRRVAFCPLTDFELPPTPGGLRAVVEAVVGGRCAW
+LLVTSPNAVRALQAAGWTGAVGAGVRVAVTGAGTARVLADAGCAVEPWMPESASAAGILA
+EFPAAPAETGDGARRVLLPQSALATAELEEALTRRGWAVDRVEAYRTVPYPADAARRLLT
+EEPGDAGTVVPVAELAGADVVLTSPSAARALAVHPALDDPELRRTWRLVALGAPTAREAR
+RLGLRLTGQAATPDATGILAALARPVG
+>MHAAABBN_01239
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAEVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>LFPAFLNI_01456
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAVGPVRSDGPRWLVVTSPNTVRALRAVGWGGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGKRVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000918.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35e9839f538ba17e0055a881c5ae3f3d00298773
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000918.fa
@@ -0,0 +1,38 @@
+>ACLBLIBL_01398
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS
+GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR
+GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI
+GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG
+>MOLHKGIG_01527
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
+>NAFOICDF_01289
+MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA
+TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR
+GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW
+ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG
+>MHAAABBN_01237
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA
+AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT
+KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV
+SLVRRRSRRAEG
+>LFPAFLNI_01454
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000921.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c7bba34b110c2d2ae5633887b5762d412d9e4cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000921.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01401
+MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL
+VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW
+DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV
+QRVLDALPAAAKAAAAATPQG
+>MOLHKGIG_01524
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>NAFOICDF_01300
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL
+VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT
+LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV
+ERVLAALPTAAKAAAAATPQG
+>MHAAABBN_01233
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>LFPAFLNI_01451
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000922.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11c3befe75875c1def3e5187f149393aa82f25c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000922.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01402
+MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR
+>MOLHKGIG_01523
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+>NAFOICDF_01301
+MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEAAAV
+HGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGVAPL
+EPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELVRRH
+PKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV
+>MHAAABBN_01232
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAAQY
+EQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER
+>LFPAFLNI_01450
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000924.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4032b31e4eeb0a3c4b93d86c538cdf993c8ca62a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000924.fa
@@ -0,0 +1,104 @@
+>ACLBLIBL_01404
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR
+>MOLHKGIG_01521
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>NAFOICDF_01303
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR
+>MHAAABBN_01230
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>LFPAFLNI_01448
+MTREHGEDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHGAVLVLGAPG
+TGRTTVAVEYAARRIEEGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPKHEVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGMPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000925.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5632c84a56756716a436355c467673405930511
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000925.fa
@@ -0,0 +1,105 @@
+>ACLBLIBL_01405
+MAPLTGGPAAPDADRPAGPDAVPADRPGTADAVHAPQDIAARLGLPAPTEEQAEVVTAPL
+APRLVLAGAGSGKTATMADRVVWLVANGVVRPDEVLGVTFTRKAAAELAERINGRVDALL
+RSGLRIPGFDGEPEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLMGGADAHRLMGSV
+VRSHPVVADTLGVAPSRLVSQALHLAGDMAEHLVTPEEVRTHLARVAQQGRDLPLPPRTK
+APTKEIAAFFTGLADRALMADLVARYDEVKREQDVMDFGDLLRHAARIASEVTAAGEQER
+ARFPVVLLDEFQDTSHAQMRIFAGLFGPRGPEDDAAGLGHCVTAVGDPHQSIYGFRGASA
+GQLFAFPHAFPRLETGPDGGRRRVNADVSHLTVAWRNEESILAVANTVAAPLNAHAAASG
+GAPVEVRTLRPRPGAGDGVVRVDRFLTPEEEAHDVVRRLAALAEADGAAPSRAVLCRTRA
+QFGPVLEALEAAGVPYEVLGLSGLLALPEVAEVLAVLHVLADPVRGDQLVRLLTGPRWRI
+GPADLEVLHERARFVARMRARRAAGEDAQDPEGTGGADPEATAAEDVSPEEEADSAALLE
+ALDSLPGEGTEWTGSRGRGFSAEGLARLRAAHAELRRLSARAGEDPADLIAEVVRETGLD
+VEVALRPGLSAAAARRHLNAFQDAARDFGAGTAGADLAAFLAWTESVMEHEDGLGVENAE
+PTPGLVQVLTAHASKGLEWDAVAVPGLQEGTFPSTRADRWTTPGSGALPWPLRGDRGSLP
+QWDGTWAQDQRDWVQSAGTKYSSKAAQEDNPDPYAAAVEAHAEREERRLAYVAVTRARRE
+LWLSTSAYKGTNKDPLPPSAFLEEAAGLAGRVPGVVAGHAPDEDGMPEANPAAGRTLVAW
+WPFDPLDGPEAFLADPEDPEDEGQWRPLPRRARARRDAVEAAAAAVRAAEPSALAAEPEL
+ARQVDWVLLRRRDVAGSGGDVALPDHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARR
+GTAFHAWLEERFGATGMLDIDSAEDAEDLWVDEALDLEPMQAWFRSSRWAERTPAFVEAP
+VETTVGGITLRGRVDAIYRSGGDPRNPVDPEADWELVDWKTGAVPRGRDLELKSLQLAVY
+RLAWSRLHGIPLERIGASFVYVAHGQERSFPDLPGEAELERRLAEALRRR
+>MOLHKGIG_01520
+MAPLTGDPAAPTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG
+KTSTMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAAAGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRAQRAAGGREDPAGAAPDAAPDRDVSPEEDADAAALLEALDSLPGEGTDWVG
+SRGRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAA
+RRHLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHAS
+KGLEWDVVAVPGLQEGTFPSTRADRWTSPGAGALPWPLRGDRASLPQWDGSWAQDQRDWV
+QSAGTKYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKE
+PLPASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAARTLVARWPFDPLDGPEAFVA
+DPEDPEDEERWQPLPHRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDV
+AGTGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGA
+TGMLDIGSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRV
+DAIYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLER
+IGASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>NAFOICDF_01304
+MASLSSPVPLRPAPVDAGPRVDVSRAVHSPQDIAARLGVFPPTDEQVEVIAAPLTPRLVV
+AGAGSGKTATMSDRVVWLVANGFVRPDQVLGVTFTRKAAGELAHRINAKVDALLRSGLPI
+PGFEGEPEDLGRASVSTYHSYAGALVRDYGLRIGVEPEARPLGEADAHRLMSAVAASHPI
+VADGLRVSASTLVAAALRLSGDLAEHLVEPAQVRAHLRERIAVGEALELPPRMKEPSDEI
+VEFFAGLETRVLMADLVERYTQAKAERGVMDFGDLLRHAARVAREIPAAGRAERERFPVV
+LLDEFQDTSHAQMEIFRGLFGPESTDLDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFTF
+PSAFPRLGELPGGAPGRVNADVSHLTVAWRNDEAILAAANAVVAELNAHAADAGTPLELK
+PLRPRPGAGTGEVRVDRHVSAQDEAEALVARLAALGEDPATADLSRAVLCRARTQFGPVL
+DALEAAGVPYEVLGLSGLLSLPEIAEVLSVLHVLADPGRSDHLVRVLAGPRYRIGPADLE
+LLHERARFVSRLRRRAAAHEPLDPATAVEAPDVSADEDADAPALLEALDSLPGESTVWTG
+SHGRPFSAEGLRRLRAANAELRRLSAWAGADPADLIGEVVREIGLDVELALRPGPSAASA
+RRHLDAFQDAARGFAAGDGAPADLPAFLAWTEAVEEHEKGLGIASADPAPGVVQVLTAHA
+SKGLEWDVVAVPGLQTGTFPTARPDRWTSGGTGMLPWALRGDAASLPQWDGSWAENRRDW
+VQSAGTGYSSKTAAATNPAPYGDAVADHAAREERRLAYVAFTRARSALWLSTSHWKGTAK
+KPVDPSPFLVEAAALAGEVPGVVLGEEPAPEELGEANPTAERTLVAWWPADPLEGPEAFE
+ADGEDLDDEAAWTPLPRRTRPRRARVENAARQVAAADPAALAEDTDLARALDWVLLRRRR
+VGAAADGVALPEHLSVSLYGELAADPQAVADQLRRPMPRPPAHAARRGTAFHAWLEQRFD
+ATGMLDIDESDDAADAWVEDALDLAPMQEWFLASRWADRVPAFVETAVETTLAGITLRGR
+IDAVFRTGARPGMPFDPEADWELVDWKTGRVPGGAELRRKALQLAVYRLAWSRLHGIPLE
+RIRASFVYVAAGQERVFDDLPGEEELEAIVTAAVAGPGATSSGEVSPPDAAR
+>MHAAABBN_01229
+MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTQEQAEVVTAPLTPRLVLAGAGSG
+KTATMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANTVAAPLNAHAAATGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR
+GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR
+HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG
+LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS
+AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL
+PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP
+EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLVRRRDVAG
+TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG
+MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA
+IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG
+ASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>LFPAFLNI_01447
+MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG
+KTATMADRVVWLVANGLVRPDEVLGVTFTRKASGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVSADEVREFLARLAEQGSALPLPPRAKTPSKEIQEFLTS
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAATGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGATPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR
+GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR
+HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG
+LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS
+AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL
+PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP
+EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDVAG
+TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG
+MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA
+IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG
+ASFVYVAHGQERSFPDLPGEEELERHITDALARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000926.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0302e2eb04e9c3861ce8784db3e8f96f89fc1e4e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000926.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_01406
+MEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIRLETELQVLAGLTPAVRAALPFRT
+PSVAGAVRLEGLRTFVYQDMPGRPVSLDELARLGEPAVQDVGRVLAAIHTLPDDVVDQAD
+LPSYSAEEIRQRHLHALDQAATSGRVPPLLLRRWEEAMEEEALWRFTPVPVHGDLHEDNL
+LLERGRVVGVTGWTDLHRGDPAADVAWLAAAEDPDLADRVLDAYESRRAAAGAADDGDTH
+LMRRAALLAEFALAQWLARGLDRHDAAMVTEAEAMLAELAADVRAAQEAEDRQDREQAAA
+DAAEDADAAADARDDAQRHAAVQEGSPPGGAEPGGASGRRRVTDA
+>MOLHKGIG_01519
+MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALSQWLTRGLDRHDEGMVAEAEAMLA
+ELEGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAVRSADPETGSLPAVEVVRP
+INGGPGRP
+>NAFOICDF_01305
+MHRQPLRLAALAAAAVPGLTPVSVEPSPDDSPDVAAALVVDDAGQRWLVRSPRSAEAGIR
+LETELQVLAGFDPHLRAGLPFRVPSVAGAVRIDGLRTFVYQALPGEPATLEQIGGLGDAA
+VQDLGRILAALHTLPLTVVEQADLPVYTADHVRERHLTELDRAAATGQVPPRLLRRWEET
+LEEADLWDFSPVPVHGDLHEDGLLVSRGRVVGVSGWTDLHVGDPAEDFAWLAAAEDPALP
+ERVLAAYAERLDSEGAAAPDAHLLRRGALLAEFALARWLLRGVDRHDAETTADARALLTE
+LAEAVGVAEATAPQAAPTADNVVGLHAAHDDRAPDWDEDDADGVVDVSDDDGRAGGTVSV
+LRPVD
+>MHAAABBN_01228
+MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRVLDRHDEAMVAEAEAMLA
+ELAGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAARTADPETGPLPAAEVVRP
+INGGPGRP
+>LFPAFLNI_01446
+MDRQPLRLAALAAAAVPGLAPVSAEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRGLDRHDAGMVAEAEAMLA
+ELEGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAARTADPETGPLPAVEVVRP
+INGGPGRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000928.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40f642cca9332b5174037af123869c2bf1a83167
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000928.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01408
+MSTPDEILRGLDPEQRRAATALQGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQGMRMSVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARGREMPAGWDATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPRIAATIRDQYRVFLVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERHPDATVVELVRDYRSSPQVVEAANRLL
+ADRTKAGQRDRTMPRWPDPLELVSQRPNGPDPVFAECTDDEAEAGWVADRIRALIDDGVA
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVPDRVRDVLASLGYSAQPPAATGAARERWESLHALVNLAEQLAGSRGAEFTLTELVA
+ELDERAQHQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRAREHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAPGAAKP
+RRRGATVATCRTCGKPLETGAERKVGRCLDCPATYDEAVLEQLRDWRSRTAAEMKMPAFV
+VFTDATLVAIAEAMPASPKELLAVPGLGRTKLEKHGEALLELLHGTPTA
+>MOLHKGIG_01517
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>NAFOICDF_01307
+MSTPDEILRGLDPEQRKAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVDGVQARTFHSAALRQLQYFWPQAVGGQMPTLVENKVRLLT
+EVAHRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARDREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPKIAATVREQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRQDLCVVGDSSQTIYSFTGATSRFLTGFRERYPEATMVKLVRDYRSSPQIVGAANTLL
+AERTQAGLRDRSLPFWPEPLALSSQRPSGPDVVFAECQDDEAEAGWVAQRIQGLLDDGVP
+AAEIAVLFRTNGQSEAFETALSAAGIGYQLRGGERFFSRREVREGVLQLRAAAREAQDLV
+GADVVQRVKDVLSSLGYSDTPPSASGAARERWESLHALVNLADQLAGTREDFTLVQLVAE
+LDERAQAQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFADTPAEVDEERRLL
+YVGITRARQHLHLTWTLARSGGGRANRRPSRFLRAIDPTLGGTREHAPAAAMPARRPRRG
+ATVAVCRTCGRPLETGAERKTGRCVDCPALYDEGVLDTLKDWRSRVAKTDKVPAFVVFTD
+ATLEAIAETMPATPAELIKVKGVGKSKLDRFGQDVLDLLHGTSAA
+>MHAAABBN_01226
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>LFPAFLNI_01444
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGSCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKTKLEKHGPELLELLHGTPTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000935.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4934c7acabef3c5fbd1d1a49e662854f29df243
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000935.fa
@@ -0,0 +1,66 @@
+>ACLBLIBL_01417
+MTAAGLGGVGLVLAAPGAGAGIAPPGVYVVDEAGVLSSADEQRLTQEITDLRRDTGQGLY
+VVFVDSFETNAQGLADDVARQRGLGTNDSVLAIAVEDRSYGLGSGGDASLQNQITRTYVG
+PQLSRIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEYDPEGALPAGSGAGAGT
+GAGSSQGSDEGSGVLTAVLGAGAVAAAVGGGVLVARNRRKKDGGAVERSGRDARPVERDP
+LDEMSLEDLRTRAGSKLVAADDAIRSSEQELGFAMASYGEDAVRTFREDIDQAKEHMRAS
+FQLQHQLDDHIPDTEEDQRSWLKEIIQRSDAVGAALASHQKDFDSLRDLENNVPEALERI
+DARLPEARARVQQAESSISALHGQYAESALAEVADNAAQARERLDFVETAEAKARQAWET
+QDRSTAALAVRAAEESLSQVDTLTEAVGKAEGSLRTIVGNLQTGLAQSEQDLAEAEALVA
+NGSHPELAGPVAGMKTTLAAVRRSLSGGRPDPLDLLHQLEAAHRQLNTPLSGVRDAREQA
+RQASQMLNSAIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRAAIDLSRTDPVT
+ALQQAQRASQLAERASELARQDVEGFGYGGSMYGPGMGGMYGGRQRSGAGASFGGGLGGA
+LLGGILMNSMFNSGGGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>MOLHKGIG_01485
+MTVLTRPADVGRLARAVTAAGLGGLGLLVAAPTAQAVAVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEERAYGLDS
+GGDANLQNQVTRTYVGPQLSKIGTDPGSAEWLAVGIAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTTGGGSTAQGASDGGGALTAVLGAGAVAAAVGGGVLVARSRRRTQGGAVER
+GRTEEARRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDI
+DQAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLE
+NQVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETA
+LAKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQ
+DVAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPL
+AGVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSA
+ISLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMGSRYGTRPRAGVGGSFGG
+GLGGALLGGILMNSILNSGHGDSWGGGGFGGFDGGGLGGGDFGDISGGGF
+>NAFOICDF_01317
+MAESVVRPSAPRLSRAAVLGGLGAITTTALLAPGAHAAVDVPPGTFVVDQAEVLSSAQES
+ELTQDITQLQSKAGQNLYVVYVDKFDSTPQATIDSVVQQRGLGNSDSVLAIAVENRNYGF
+DTGMSSTMQSDIRSAYILPALRKAAAGGDWEAPAVAAVQGLDDAANGTLDGRGRSGETYQ
+PDGTLPQAAEQDSSAQTSTSDSGNGASGALVGAGALAAVAGGAYVVSRRRRKSDGGAEPG
+AVATGPQASRDPLDELSVDELRKRAGATLVAADDAIRSSEQEVGFAMASYGEGAVGTFRQ
+DIEKAKEHMRASFQLQHQLDDEIPDTEADQRSWLKEIIARSEQVGATLAAHKKEFDSLRD
+LENSVPEAISALESRVPQAEGAVQAAERELVDLHGRYAESALTEVNDNATQARERLEFVK
+TAEAKARASLEAGDRSTAAVAVRAAEESLSQVGTLTEAVSKAGAALSTHVANLQMGISQS
+EQDLAEAQALLSAGRNPELAGPVGGMQQTLAAVRAELQSGRPDPLALLQRLESAHRQLNT
+PLSGVRDAREQARQAEQMLSAAISQAQAQIDGTADFIGARRGAVGSEARTRLAEADRSLQ
+TAMSLRSTDPVAALDHAQRASQLADRASERAQQDVADFGYGGMGGYGGLGGGYAGAGYRG
+GYGMPRSGAGGGFAGGLGGALLGGILMNSMFGGHHHDSGFGGGDWGGGGFGGFGGGGLDG
+GDFGGFGDADFGGF
+>MHAAABBN_01217
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFREDID
+RAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGAALAAHKKEFDSLRDLEN
+QVPEALERVDARLPEARSRVQESESAIAALHGQYAESALAEVADNATQARERLEFVETAV
+AKARSAWDAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSNPELAGPVAGMKNAVNAVRRALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>LFPAFLNI_01435
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDID
+QAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLEN
+QVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETAL
+AKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000936.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc12b726ac9d4ac8802f6e657f4bf82b1a0b4669
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000936.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01418
+MRSEDTVAHTPADQTPTDQTPTDQTPAPARPAAEARHPGRRAPRARAGLGLLAAAVLVTG
+LAGCGVAAEPGADASGSAPDSSTSSGSASADPGQDVADTAVGTAAKTALPSVVTISATSG
+QGSGSGSGTILDEEGHILTNTHVVTLGGQASDAELTVRTADGTVYAATVVGTDPLSDLAV
+IKIDAPDLTPIQMGRSADLKVGDDAIAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPRQ
+QESEQGQGPGQGSSSGPERFRFELPGAQQGPQGEVYINVLQTDAAINPGNSGGPLVDGQG
+RLVGVNVAIASAGQGQGEAGNIGVGFAIPVDYAQRVAQDLIEHGEATHAVLGVSVTPEPA
+EVQGGDAQARTVFSDGARVREVVADSPAAQAGLREGDVITAVGERAVIDTESLTAVVREH
+RVGDSAEITYLRDGAEQKAQVEFQEDTSQ
+>MOLHKGIG_01484
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGDAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGSDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGGENAQTVFSDGARVQQVV
+GGSAADAAGLKEGDVITAVGDRAVIDSESLTAVVREYRVGDSVDVTYLRDGAEQKTEVTF
+TEDTQS
+>NAFOICDF_01318
+MGRAAHRPDCTDGGADQKPAQTRSEATVEHPAPDTVTPEAAPVASSPRPASPRGRRRALG
+GALAATVLAGSLAACGVAGPGAGASASASASGSSSAAAAPAVGSTDQPVADNPVGAAAAK
+ALPSVVTISATSGSSAGSGSGSILDAEGHILTNTHVVTLGGTASDASITVRTSDGKVYAA
+KVVGTDPVSDLAVIKIDAQGLTPITIGSSKDVKVGDDAIAIGAPLGLSNTVTDGIISTLN
+RTIAIQSSAAPEGQTGSSGTERFRFQLPGEQGQSQQQDIYINVLQTDAAINPGNSGGALV
+NGAGELVGVNVAIASAGGSSASGAESGNIGVGFAIPVDYAKRVADDLIADGTASHGLLGV
+TVQPQPAQVQGAAGGSKSTEFSAGALVHTVSSGSPAEKAGLKEGDVITQVGERTVTDTES
+LTAAVREYRDGETTPVRFTRDGREQTADVTLTAMEASR
+>MHAAABBN_01216
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGTDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTVFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
+>LFPAFLNI_01434
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGAEQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTMFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000941.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7d2d49d651128671ec4a53340cd1f6a36b575a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000941.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01423
+MRRLAAVGPELSDEDLLALRRAPSTQDAPGPWVRAVFVSSLDGATALDGRSGTLGSPADR
+RQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLDP
+DGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGAR
+VVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLTQ
+DGDLYLRLLHERHAALLADAPGLDGRAGTGR
+>MOLHKGIG_01479
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>NAFOICDF_01323
+MRLLTATGPEIDDDALLALRRAPAPDLVPGPWVRAVFVSSLDGAATLDGRAGGLGSPADQ
+RQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLDP
+DGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGHR
+VLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLTE
+DGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP
+>MHAAABBN_01211
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>LFPAFLNI_01429
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000945.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1322b5f83e4b464b07506a64848a4020230736ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000945.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01427
+MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE
+LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD
+PAADSLPDGTRTDAGDDPRRGGADA
+>MOLHKGIG_01473
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>NAFOICDF_01329
+MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA
+LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE
+ASDAGSADA
+>MHAAABBN_01205
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>LFPAFLNI_01423
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GAGSGDADD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000950.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1acbdb98693428d438a7858ba137cbd3eeb5cf89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000950.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01433
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA
+>MOLHKGIG_01467
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>NAFOICDF_01335
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE
+>MHAAABBN_01199
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>LFPAFLNI_01417
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000966.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff649dfd9451b83c92dbaf32a00e5717ea44ef88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000966.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01450
+MVGLALLDDAAAPSRLLAARRSAPAVLRGLWEFPGGKVETGEGPREALAREVREELGVAV
+RLGAEVPSPDPEGWELANGARMRVLWGVLAEEGAEPAALEDHDLLAWVPLSGAGAHHLDW
+IPADRPIVSAVVAGAATAFAAAP
+>MOLHKGIG_01449
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR
+>NAFOICDF_01354
+MSPATPQTPPVPSAPRPVVGVALVDDAARPTALLAARRSAPASLAGLWEFPGGKVEPEEG
+ADAALHRELVEELGVRVRLGTEVAAPEGPGWELANGARMRVWFGVLREDSGAPAALQDHD
+RLEWTPLTAEALHALDWIPADRPIVDALLAAVEAGRLGL
+>MHAAABBN_01181
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR
+>LFPAFLNI_01399
+MTSATPARPAPAARPTTSPRDGARPRQVVGLALLDDVAAPTRLLAARRSAPAPLRGLWEF
+PGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEEG
+ATPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000969.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a81ec7f27c33ae68d1111c5818d4133df026d8cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000969.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01453
+MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG
+WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST
+WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR
+>MOLHKGIG_01446
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRASLALGGYIERPVVRGLRRRR
+>NAFOICDF_01357
+MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP
+GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP
+ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA
+>MHAAABBN_01178
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
+>LFPAFLNI_01396
+MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000977.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..280ca4f3637fe0aa1e13ed0b2cf0b76bca5174e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000977.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01462
+MSQSSSRQPDPVTTAAAPVLSAADRLDRAESKAEVLIEALPWIQRFAGSVMVIKYGGNAM
+VSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLDRLGIESEFRGGLRVTTEEAMDV
+VRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGV
+DPTAILDVVRSGRIPVVSSVAPEIDEHGEPTGQVLNVNADTAAAALASALGAAKLVLLTD
+VEGLYADWPDRESLISSLTAGQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRP
+HSMLLEVFTSAGVGTPVVPDADTAGRPAPTTVQEDA
+>MOLHKGIG_01436
+MTPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
+>NAFOICDF_01370
+MTGQPAPADPTTPSVPVLSTAQRLERAASKAEVLVEALPWVQRFAGATMVIKYGGNAMVS
+DELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLERLGIESEFRGGLRVTTPEAMEVVR
+MVLTGQVGRELVGLINSHGAYAVGSSGEDAGLFRARRTGAVVDGETVDLGLVGEVTAVNP
+EAIRDVIDAGRIPVVSSVAPEIGDDGEPTGEVLNVNADTAAAALAAGLGAAKLVLLTDVE
+GLYADWPDRDSLISSLTASQLRGLLPGLQSGMIPKMAACLHAVDSGVHRAHVVDGRRPHS
+MLLEVFTSDGVGTQVVPDPTPATRPASAPTTATAQEDA
+>MHAAABBN_01168
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
+>LFPAFLNI_01386
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEIDDDGQPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000982.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4dd5e2c9ad41f8e71fcff526017990a78649e306
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000982.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01468
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS
+>MOLHKGIG_01431
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND
+>NAFOICDF_01375
+MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND
+>MHAAABBN_01163
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
+>LFPAFLNI_01381
+MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY
+VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG
+KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV
+WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII
+EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK
+HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD
+FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000993.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d298e8894e5e9d04a49e81e5c5deaa0ddacee60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000993.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01483
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG
+>MOLHKGIG_01416
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>NAFOICDF_01390
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK
+>MHAAABBN_01147
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>LFPAFLNI_01366
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001003.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c5062231b2544e0e3aefafb66fa303a4019b09e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001003.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01512
+MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG
+EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA
+EGYASHTS
+>MOLHKGIG_01380
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>NAFOICDF_01407
+MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG
+EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA
+AGYAAHVG
+>MHAAABBN_01100
+MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>LFPAFLNI_01335
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001007.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91acd9763ed12fab0bb892eca283e30247aaf754
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001007.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01516
+MTPTAGSGRPPALGAQGTLFDEDVTPGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRGAAGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVIVAPEPGDELAGR
+RRARRSA
+>MOLHKGIG_01376
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
+>NAFOICDF_01411
+MTPHAGPGLPLGIDGRQGRLFDVDALAPGGDVGYRGPTACKAAGITYRQLDYWARTDLVV
+PTVRGASGSGTQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVAHLRERGVDDLAQITLM
+SDGASVYECTSPDEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPGEVLGDDHAPEDELS
+ARRRARRPARTAS
+>MHAAABBN_01096
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRAAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
+>LFPAFLNI_01331
+MTPTAGPGRPPALGTQGTLFDEGATRGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001008.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b601ea0ef279757bbe5977d76d8470fe66b8e345
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001008.fa
@@ -0,0 +1,105 @@
+>ACLBLIBL_01517
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVSQITPAIEAVRATGTAVAEAALCYTGNMTDP
+AEKLYTLDYYLGLARQMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFELPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRAAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKQFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALGEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQPVATIEAMKME
+AAITAQVAGTVRRVVTEGVTPVNGGDLLLVIE
+>MOLHKGIG_01375
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVSAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFLSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALGEAGQTRRGVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+AAITAQVAGTVRRVVTEGITPVNGGDLLLVIE
+>NAFOICDF_01412
+MSLPLDPDTTRNGAGRPAHAAAPAFSKVLVANRGEIAVRAFRACHELGARTVAVFPHEDR
+NSIHRQKADEAYRIGQEGHPVRAYLDVDEILRVAKDVGADAIYPGYGFLSENAGLARAAA
+EAGITFVGPPADVLELTGNKVEALRAAKRAGIPTLKSSDPSSDVEWLLGQAEEIGFPIFV
+KAVAGGGGRGMRRVERPEDLKDSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQVLADA
+EGNVVHLFERDCSLQRRHQKVIEMAPAPHLDEEIRQALHRDAVAFAKEMGYVNAGTVEFL
+VDTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVAAQLRIAAGATLEELGIRQEDLHV
+RGFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKL
+TCRGRDYETAVRRVRRALAEFRVRGVTTNIPFLMNVMDDPQFVAGDVATDFIDKHPELAM
+VNRSQDRGSKALQYLADVTVNKPHGERVDGIDPRDRLPGHPSDKRHEPDRSPFDGPSRNP
+GAVPPAGWRQVLAEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPA
+VAHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTP
+YPTEVTDAFVQEAAATGVDVFRIFDALNDVEQIIPAIAAVRATGTAVAEAALCYTGNMTD
+PAEELYTLEYYLGLARRMVDAGAHVLAIKDMAGLLRPAAAKELVGALRAEFDLPVHLHTH
+DTAGGQLATLLAASEAGVDAVDVAVASMAGTTSQAPMSALVAALEHTERDTGLTLEAAAA
+MEPYWESVRAIYAPFEAGLKAPTGRVYQHEIPGGQLSNLRTQAIALGLGERFEQVEAMYA
+AADDILGHLVKVTPSSKVVGDLALQLVGGGVDPDQFRERPEDFDIPDSVVGFLRGELGDP
+PGGWPEPFRTRALKGRREGSGMVQVSEEDAAALAEAGQGRRDVLNRLLFPGPTKEYEAHR
+EEFGDISTLHTRDFLYGLVPGREHVVSLGRGVRLIATLQSVSEPDEKGMRTAMLTLNGQL
+RQIQVRDRSVESSVRQAEKADAAVPGQVPAPFAGSVTVQAAVGDVVEQGAPVATIEAMKM
+EAAITAPVSGTVTRVVTQGVTPVQGGDLLLVIE
+>MHAAABBN_01095
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDIGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE
+>LFPAFLNI_01330
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLQAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYAMAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDAATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGSMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001014.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b6262ab9052c73cb209e15316cdd226e9e20db5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001014.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01525
+MPRSSVSHTPSRRLRHALAGGAVPLLLLTGLPAQAQAQEAPVHTVRPGDTLTAISAAHGV
+PLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQPDDGWWIIARRTGVSAAEL
+QRLNGMSASTMLHPGMVLTTAGKAAAPAPTPAPPRCSLAPATRDVVRYAVVSGDSMWGIS
+QRFEMSIPRLRELNGLTRSSMLHPGQVLVISDGTLEVEPVSDVQPIGDTFLGRTYPAHVT
+ASANENLRLLQSVPQPSPEQMREIVRETAVRMDVDPRLALGHAYTESRFRMASVSPANAI
+GAMQVIPITGEFASELVGRELNLLDPYDNAVAGVAYIKYVQDRTPTLDTGIGAYYQGLGG
+VLQGGLSAEGRTYVATVRAAMAMF
+>MOLHKGIG_01368
+MPRSAVPHTPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTTPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>NAFOICDF_01420
+MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT
+HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER
+GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTEAPARPTTPATPVAAAPAPVRQ
+AAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADGTEQAPVIDG
+PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELGVDPALALGHAY
+TESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAGVVLIKYLQEHT
+DTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF
+>MHAAABBN_01088
+MPRSAVSHTPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDTLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQPNDGWWIIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASAPASTAPAAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGIAFIKYVQDRTPTLDQ
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>LFPAFLNI_01323
+MPRSAVPHTPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTAPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001019.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f039462211a5c9cf425b39414a4e6c8738571d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001019.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01530
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF
+>MOLHKGIG_01363
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>NAFOICDF_01425
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL
+>MHAAABBN_01083
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>LFPAFLNI_01318
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001025.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5761b330bd338e43c9f60b9bb59c8c4b982568f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001025.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01536
+MSASENTALVPVRRPLADTGRTAALTSWDAEGWAGLRVVVAGLGVTGFSVADTLAELGAV
+VVVVDGNDGPENQARAETLRIVGVHEVLLDAEATQSLPEVDGAPAELVVTSPGWRPDQPL
+LMAAHAAGLPIWSDVELAWRVRERAGRPTADWVCLTGTNGKTTTVTMVEAILRADGRRAI
+ACGNVGTPVLDAIRDPEGYDVLALELSSFQLHWTHRVAPASSAVLNLAEDHVDWHGSMEE
+YAAAKGKVYENTRVACVFNEHDPVTRTLVERADVQDGCRAVGFTTDTPGLSDVGVVDGIL
+VDRAFTENRRHEAIALAERTDLGPVAPRHTMANAAAAAALTRAVGVAPAAVAEGLRSYDR
+GEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFTSVVWIAGGLPKGVTYEELVGAHAH
+RLRAVVLLGTDASALRSALAAHAPDVPVHAPLADADGTGPADGAAVMAEAVRVADGLARP
+GDTVLMAPAAASMDQFRSYAQRGEAFIDAVAALMREHGWDTDAGTAAP
+>MOLHKGIG_01356
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVEGDDGPENRARAETLRIVGVREVLLDRAATQALPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTVANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPEVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDIVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDAD
+>NAFOICDF_01432
+MSAPVMRPHADTDRTRGLRTWDDAGWAGLRVVVTGLGVSGFSAADTLAELGARVVVVDGR
+DSPENRAKADTLRIVGVADVLLSEDATHSLPEVDGERPDLVVTSPGWRPDQPLLMAAHEA
+GLPIWSDVELAWRLRERAGRRTADWVCLTGTNGKTTTVTMVEAILRADGRRALACGNVGT
+PVLDAVRDPEGFDTLAVELSSFQLHWTHSIVPASSAVLNLAEDHVDWHGSMEEYAAAKGK
+VYERTTVACVFNEADALTRTLVERADVAEGCRAVGFTTDTPGLSDVGVVDGIIVDRAFLE
+NRRHEAIALAERSDLGAVAPRHTVANACAAAALTRAVGVSPEAVAEGLRSYDRGEHRIQL
+VATSRDVMWVNDSKATNPHAADASLAAFSSVVWIAGGLPKGVTYDELVSAHAGRLREVIL
+LGTDTSELRRALAAHAPEVPVHAPLADADGHGSPDGRAVMAEAVRLADAHACPGDTVLMA
+PAAASMDQFRSYAERGDAFIAAVAELMREHGWDVDSEADAPA
+>MHAAABBN_01076
+MTGPASAAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGVTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPVTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD
+>LFPAFLNI_01311
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPEGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMTEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001029.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f1addafd9462d4c99a5d5db6b7b0a2ac2f634f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001029.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01540
+MTPGRGGRPPRPAGPAQPPAGSTVVPFPGRSVRRRRAVRWAVAGAVAALLGALAWVLLFS
+PVLAVDEVDVTGTRHVSAEAVQERLAPLHGVPLPRVGSSAVRELVGDLPGVAEVRVVAHP
+PTRVEAAVREHEARARRGGEAGVDLLLDDGTVLAGVPAERVEGESLPEFSEELSAGPRRD
+REEVAAVLAGLPAPVAERVESVDSSRAGQVRLGLRDGVVLVWGDAEDAELKGTVATAFLE
+GDQHGSRAGGVREVDVSVPTRPITR
+>MOLHKGIG_01352
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLGALGWVVFFSPVLA
+VDRVEVTGTRHVSAAEVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVVVREHETRARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRAQEERAEV
+AEVLAALPEAVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGPVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
+>NAFOICDF_01436
+MVAFPGRSARERRRRRAGMLAAVFAALALAAWAVFASPLLAVDRIDVTGTRLVDRAAVEE
+RVAPLRGVPLPRIGSSSAGDLLSGMPGVASARTVAVPPTALEVRIEELAPVARSAGGDRA
+QVLLEDGSVLGSVPVSALPGEGEEGGALPSAPEALLTAGPDVRASAATVLRALPDGVRDR
+VRGVDAGSPEQVRLDLGGGRTLVWGDASEPERKAAVAQALLDGLEDARGVREVDVSVPDR
+PVTR
+>MHAAABBN_01072
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTALGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLAPVYGVPLSRVGAGRVGELAGGLPGVAEVQTVPRLPTGL
+EVVVREHEARARRDGGDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRVQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEAGVAEIDISVPTRPITR
+>LFPAFLNI_01307
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTVLGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVAVREHEARARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELPQRAQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001039.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93e8b7133c791b0183adac401d870beaddb34750
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001039.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01550
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR
+>MOLHKGIG_01342
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>NAFOICDF_01446
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR
+>MHAAABBN_01062
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>LFPAFLNI_01297
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001040.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2698aaf07d3eedb1d11c31f241c77625b720d5b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001040.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01552
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP
+>MOLHKGIG_01340
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>NAFOICDF_01448
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP
+>MHAAABBN_01060
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>LFPAFLNI_01295
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001041.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1d693b1f0930abf4ed6e85e6d533ff1e0772cde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001041.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01553
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD
+>MOLHKGIG_01339
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS
+>NAFOICDF_01449
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS
+>MHAAABBN_01059
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
+>LFPAFLNI_01294
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001047.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3bddba2cba60c21adbe46a2a9e144faf21fc029
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001047.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01560
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>MOLHKGIG_01331
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>NAFOICDF_01456
+MAKNPSTSPSSSGSSSLKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVFAI
+TRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGERAM
+FDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASRVG
+KLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKRLS
+ALGTQKPPIPKGVDPMRARPDRRGMRGR
+>MHAAABBN_01052
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>LFPAFLNI_01287
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001048.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..025eaf0a6869c5039f2426c4e28400888cd7da21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001048.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01561
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS
+>MOLHKGIG_01330
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>NAFOICDF_01457
+MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA
+QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS
+>MHAAABBN_01051
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>LFPAFLNI_01286
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001052.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3d7966dea5a478fa935386e5ce8d165db8b6eda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001052.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01565
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL
+ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE
+ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST
+DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA
+SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE
+ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE
+QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV
+TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED
+IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS
+VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD
+AGRFLTTLRQRLEGGEFANELGL
+>MOLHKGIG_01326
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLRTLRQRLEGGEFANELGL
+>NAFOICDF_01461
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT
+EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR
+RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP
+AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK
+LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT
+LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG
+AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL
+GL
+>MHAAABBN_01047
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGEFANELGL
+>LFPAFLNI_01282
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK
+ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGQFADELGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001058.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f53bdfc0e181d708df3ae76d7694acdd281fbf37
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001058.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01571
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA
+>MOLHKGIG_01320
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>NAFOICDF_01467
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA
+>MHAAABBN_01041
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>LFPAFLNI_01276
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001060.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e20eab832d89fb664bd47d07f300ea2d36e14d21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001060.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01574
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR
+HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH
+HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR
+>MOLHKGIG_01318
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR
+>NAFOICDF_01470
+MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSGVPG
+AVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARRRGV
+HRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVLALR
+PHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHTHGE
+ALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRSSGR
+GSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR
+>MHAAABBN_01039
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
+>LFPAFLNI_01274
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001061.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3308c5fd5fa34628c3c77a4054c3d5be6a68dc99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001061.fa
@@ -0,0 +1,89 @@
+>ACLBLIBL_01575
+MEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLLAETVRRA
+RRGMAAWRVVAPDQLDMGFSERLAHPGHPAAASMGRDGDTYRSLGARIEDLDALLETLGL
+RDLAATGHPLITLGHDWGGVVSLGWAGRNPELVDGVATLNSAVHHPEGAPIPAPLQAALA
+GPVLPASTVLTDAFVSVTTSLAKPALASDVRAAYHLPYETADRRGGVGGFVADIPAEPSH
+GSHAELRRVWEGVSALGRAGTPALILWGADDPVFLDRYLDDLRDRLPQARVHRYEEAGHL
+LVDDRDVTAPLLQWAQLLRAGQLDDPGSGLPGPVPHAPAASPADEDGLHVDLGEHAAPAG
+DDVARLWDHLRDWGAPGSEHREYTALVDMAGAQTGRSLVGGARRPVAVSWGELQETVSAI
+ATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGGVAVVADQGLGIAGMTRAMKSARP
+RWIIGRTPGLTLARAQSWPGARISVTEPGAAQKRLLDVSDSIYAMIERHRDPAVGEPVDE
+HGSPLPEPALAADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFA
+PFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVASADGL
+DAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQR
+LRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQGHGVLGEIVVSAPHLKDRYD
+ALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPE
+KTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALA
+SAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVARWAEGVLAGGRAGAL
+>MOLHKGIG_01317
+MPQIPAAPAVLPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHTGSPSASS
+MGRADDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEGAGHLLVDDRDITAPLLQWAQLLRAGQLSDPASGLPGP
+VPHATADPGLEVDLGEEPGAREPGMVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSL
+VGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGAV
+AVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDV
+SDSLYAMVDRHRDPATGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGR
+LVAMISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAG
+QSTVLFASPAALANVVATADGLDAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEV
+HTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDP
+AQGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVW
+LEGRLQHVITTPEGPLGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRP
+ARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVAR
+WAEGVLAGGRAGAL
+>NAFOICDF_01471
+MPRIPAAPAALPPFDQLPGWDPDWSRLVTIRSAADLPGVERTLHVADNGPQLAALGAELA
+GTILAVHGNPTWSYLWRALLAETTRRARRGQQAWRVVAPDQLDMGYSERLEHPASPTPSE
+MGRARSTYRSLGDRLDDLDALTAALGLTDLAATGHPLITLGHDWGGVVSLGWAGRHRDVV
+AGVSTLNTAVHQPPQAKIPAPLQAALAGPVLPASTVSTDAFIAVTTSLAKPSLAPEVRAA
+YHLPYPSAERRGGVGGFVADIPVDASHGSHAALEEVSSGVSALGAQGTPALIQWGADDPV
+FLDRYLDDLRDRLPAARVHRYEEAGHLLIDDRDVVTPLLTWAQLLTAGLLADPASGLPGP
+RPHADDAAPRTSALPLLPEASRGVHVDIADHASEAGSPAGLPRLWDRLEDWGAPDSPMRE
+YTALVDMAGAETSRALFGGARRPVAVSWGEFQETVSAIATGLWEAGMRPGDRVSMLVPPG
+RDLSAALYAVLRVGAVAVVADQGLGVSGMTRAMKSARPRWVIGKTAGLTLARAQNWPGTR
+LSVSTLAAPQRALLDVSDSLYAMVDRHRAPELGVPRDAAGAPLPVPELGADAAVLFTSGS
+TGPAKGVVYTHERLGHLVRLIARTLDIRPGASLLAGFAPFALLGPALGAASVSPVMDVTK
+PATLTAAALADAAIAGQSSVLFASPAALANVVATAGDLSGEQRTALRQVRQVLSAGAPVH
+PALLRQVSALMPEAEVNTPYGMTEGLLLANIDGETIHALRRADDAGVCVGSPLPTVEFRI
+APLAEDGTPEEVTLDPAAGHGVLGEFVVSAPHLKDRYDALWFTDHQSKRDGLIRRDGRVW
+HRTADVGHFDAEGRVWIEGRAQHVLTTPDRPLAPGGPEGVVDALGPVARSAVVGVGPAGT
+QAVVVVVEAAVPAARPPRRAGHHRDGRPKQGLAPTALAASVRSALEPLPVAAVLVADHIP
+TDIRHNSKIDRPRVARWAEGVLAGGTVDGL
+>MHAAABBN_01038
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGYPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDAAARRGGVGGFVADIPADPGHGSHPELQRVGEDLASLGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPRARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATTDAAADPGLEVDLGEEPGARDPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPQREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGDEVQRLRTADDAGVCVGSALPTVSLAIAPLLEDGSADDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKAGAL
+>LFPAFLNI_01273
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVALHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGSPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATADAAADPGLEVDLGEEPGAREPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPRREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGAEVQRLRAADDEGVCVGSALPTVSLAIAPLLEDGSAEDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKVGAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001062.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fc305eb2301a61032565219df34865aaff33770
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001062.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01576
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMMASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW
+>MOLHKGIG_01316
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW
+>NAFOICDF_01472
+MVQVPHVSGNASFEFSRAALLSVTEVQAPLEVTSDDLDEQLADVLTRLRLPRHLLERVAG
+VKVRRAWDAQKDFQQAAAEAGTAALAAAGVAPGQVGLLVNTSVTRATLEPSVAVRIHDLM
+GLPTSATNFDITNACLGFVNGLMLASTMVDAGQIDYAVVVAAEDASKVQASTVANLHAET
+TVRGNFMEQFASLTLGSGAAAAVVGRTDEHPDAHRILRGITRAGTDHHQLCVGDHNGMFT
+DSNALLKDGLELVMDAWHDVPAEWGWDHAARYVTHQVSQMHTDAISESAGIPLEKLPTTF
+PVLGNVGPASLPITLVREQDSLRRGDAVVCLGVGSGLNTAMLEIQW
+>MHAAABBN_01037
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPQADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW
+>LFPAFLNI_01272
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPEADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001064.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d678bec177e03bc4d29a20b2aa60711f604cbb3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001064.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01580
+MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV
+WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC
+LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV
+VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM
+AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV
+>MOLHKGIG_01312
+MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV
+WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC
+LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV
+VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM
+AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV
+>NAFOICDF_01476
+MTEALPVYWFVIIAVLWLGYLALEGFDLGVGMLMQAWARDERRRRVLLNIIGPVWEGNEV
+WLITAIGAMFAAFPFWYAALLSTLYIPMLLLLFALILRAVSIEYRGKAQTDRVRGIWTWC
+LAVGSFLAAFIVGAMLALTTTGLPLDAHGDRVGGPSAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRVAAARFLRTWTPVAVLPMLVWALAVLVRGDRPGAWILLLLALAAVLVSV
+LAARAGREGVALAGLTGFAAATWSAVMVAQFPVLTPSAVDRAYDLTAQVSSSGSYTLGVM
+AVVSLVFVPIVLAYSAWSYWVFRHRVKETHIPESHIVEPV
+>MHAAABBN_01035
+MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV
+WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT
+LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA
+FIGLKTDGAPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV
+VAARAGREGLAFTSLTLVLVLAWTAIMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM
+AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL
+>LFPAFLNI_01270
+MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV
+WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT
+LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA
+FIGLKTDGVPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV
+VAARAGREGLAFTSLTLFLVLAWTALMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM
+AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001075.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31b1973231b72d119125c7be07c3c8d1f8e4eb1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001075.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01592
+MTEPRGPESPAPDVAGALPSRARVDEQGRLDALASVGGWRGIVEASLPTLVFMAGYVVSQ
+QVWPSGVAAVAVALVLGAVRLVQRQSPVQVLAGLAVVVLSVVVALTTGQARDYYLWGFVT
+NAAYGLAFALSVVVGWPAAGLVLGLVRGEGTHWRRSPRRRRAYATATWILVAVFTLRLAV
+QVPLYLADAVTALGVARLVMGLPLYALGLWLAWSVSAPAPGEDDGLRPAAEDEPAPGRA
+>MOLHKGIG_01300
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>NAFOICDF_01488
+MSAHPRPDHGPDAAPSAAEGLQALGARTRVDEDGRIDALATVGGVRGIVEASLPTLVFLV
+VFLLAGQVWTAGAAALGVAAVMTAARLAQRQSAAQALAGLLVVGVSVVLALTRGEARDFY
+LWGFVTNIAYGLALPLSAALGWPLAGLLFGMVRGEGLHWRADPARRRAYGIATLIVAAVS
+WLRLAVQAPLYLADAATALGVARVVMGLPLYALGLWLAWSVSTPRPGAPPLRRDPAAG
+>MHAAABBN_01023
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
+>LFPAFLNI_01258
+MTEPRGPVTAAPDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMVGYVATQ
+QVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYYLWGFVT
+NAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVFALRLAV
+QVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVSSPGQDDGVPADSAASERP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001077.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a23f4cd7863b4f253c5029b9651812aeb990a607
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001077.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01594
+MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL
+AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI
+QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR
+RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA
+>MOLHKGIG_01298
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVPDGTDEDEEGRA
+>NAFOICDF_01490
+MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR
+RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV
+EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR
+YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEAGDVRAGEDEDQEEDA
+>MHAAABBN_01021
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
+>LFPAFLNI_01256
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001078.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d25a66d32ce57c5123e38217cdcf70f66b075da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001078.fa
@@ -0,0 +1,61 @@
+>ACLBLIBL_01595
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT
+AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF
+VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA
+GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE
+DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS
+SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT
+MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV
+>MOLHKGIG_01297
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>NAFOICDF_01491
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT
+GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF
+VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV
+GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV
+EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA
+PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG
+WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML
+RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA
+VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL
+EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV
+FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA
+PGDVPEGVESS
+>MHAAABBN_01020
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>LFPAFLNI_01255
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001079.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69b9311923745b72df4b32ea94cfff1c26b1f31f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001079.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01596
+MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA
+RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE
+RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ
+LAAVPAIVEI
+>MOLHKGIG_01296
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>NAFOICDF_01492
+MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPGARF
+WRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVFRDT
+VARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNMPLG
+VHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQAAN
+ACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVHQHA
+PATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDARRN
+LLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIERIL
+ALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGEVEQ
+TTL
+>MHAAABBN_01019
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>LFPAFLNI_01254
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001081.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a0f5df80d071dcd09f1a44b1b72061ce40c7ac6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001081.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01598
+MEHLPPTSPGAPLLPQIASPADLADVSEEQLTALAAEIRDYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVLFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRAESEHDVV
+ESSHASSSLSWADGIARAWHQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGIADHLDGLRRGVLDKVRTHHRYEQTLDFLKRRLQEAGTAGEMVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLGELEEALEDAKAYGGPVIVHALTEK
+GHGYAPARAHEDDQFHAIGVIDPSTGEPVTSSTAQSWTSVFGEEMLAIAEERPDVVAITA
+AMRNPVGLAPMALAHPDRVFDVGIAEQHAVASAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDAETLREELREA
+VAVEDAPTVVRFAKGSVGEPVRAIERLADGTDVLARRGEAGARDGAERDVLIVAVGALAE
+LGLDVAERLERHGISSTVVDPRWVLPVAESVIEAAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRVTQDTVAQVLGAKVPYARPVPQ
+DEAARHPQEHA
+>MOLHKGIG_01287
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK
+GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGESVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
+>NAFOICDF_01494
+MSDTSRAPLGAPLLPGIHSPEDLALLSDAQLRALAAEIRAFLIQHVSQTGGHLGPNLGVV
+ELTLAIHRVFDSPRDAVVFDTGHQSYVHKLLTGRQDFSRLRQQGGLSGYGDRAESEHDVV
+ESSHASSSLSWADGISRAWKQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAADRDRRVVI
+VVNDNGRSYAPTVGGIADHLGGLRRGVLDKVRMHHRYEQTLDYLKRRLQEAGTAGEMVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDEHALEEALEDAKAYGGPVIVHAMTEK
+GHGYGPATSHEDDMFHAIGRIDPETGRPISSPTAQSWTSVFGEEILDIARERPDVVAITA
+AMQNPVGLGPMAAEFPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAFDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDADTLREELREA
+VAVDDAPTVLRFAKGSVGEPVRALERLSDGTDVLARLGAPTGADGAERDVLIVAVGSFAE
+LGLDVARRLGQHGITATVVDPRWVLPVARSVIELAGRHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHATRDQVLERVGLTAQRITQDTVAQVLGAKVPYARALPR
+DAEHPEASAHPAGAPTTSAQAARPEEQA
+>MHAAABBN_01006
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK
+GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
+>LFPAFLNI_01245
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLIAMEEALEDARAYGGPVIVHAMTEK
+GHGYPPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001083.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc26e81709721a3ee048a8fb18e84431ea8588c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001083.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_01601
+MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA
+MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG
+VAAPKGLAPRRRYGAERD
+>MOLHKGIG_01284
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>NAFOICDF_01497
+MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY
+PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED
+>MHAAABBN_01003
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>LFPAFLNI_01242
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001084.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1b9289e431a54e96f97408ebbf74db8432fcffa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001084.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_01602
+MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL
+SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT
+NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV
+KL
+>MOLHKGIG_01283
+MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL
+>NAFOICDF_01498
+MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA
+AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV
+VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL
+>MHAAABBN_01002
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
+>LFPAFLNI_01241
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001085.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72bac654cb88267c8a8f8af94db344c3316f1262
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001085.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01603
+MTDPAPVRPSLDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRARPEL
+PERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLLAVAA
+ADGPVVVAARLEESSPLQGGLRMPRAELRPADAGDGDVSVTVVADGAALGAHLVRDGAVV
+ASDWGGGTASTPVAGRAEATEGLDEHVVTFSGMPLV
+>MOLHKGIG_01282
+MTDPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAAR
+DGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>NAFOICDF_01499
+MSARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRERADLPQRYLA
+QARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLITAQRTPEHDG
+APYLRLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEGLRVEVVSEGHVL
+AVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFAQLPTD
+>MHAAABBN_01001
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>LFPAFLNI_01240
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001086.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b00ed42538240e79a2bed8445590b31b54d99c4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001086.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01604
+MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV
+LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD
+AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR
+LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD
+RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW
+LALVPALTWPEAAATSGTP
+>MOLHKGIG_00218
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV
+CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL
+EPAWLGLTPPMTWEEFARAPASSSLDDKVT
+>NAFOICDF_00616
+MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL
+VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA
+AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA
+DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT
+VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS
+>MHAAABBN_02212
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
+>LFPAFLNI_00219
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001092.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef4a6dd1136e3ffbed3d118759f1db583763688a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001092.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01611
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA
+>MOLHKGIG_01276
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>NAFOICDF_01506
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA
+>MHAAABBN_00995
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>LFPAFLNI_01234
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001094.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73a73829248764ce730e6c247cded33ae832d4cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001094.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01613
+MVDVDARRRAALVHVEVAGTPPTASLDQRLLRIDEAVSAVLTAHAPDRAAVERMFANTNT
+PTVLGTAQAAGVAIAAAARAGIPVGLHTPSEVKAAVTGYGDAGKEQVTTMITRILGLDAP
+PRPADAADALALAIAHGWRGTALGAAAGQTGLDTSDLASRAGRSQFAAGTRSRGGRRGEL
+TAAQRAWLDAERSAGGGCR
+>MOLHKGIG_01274
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARQRGQLTAAQRAWLDAERSAGGGRRR
+>NAFOICDF_01508
+MTDRPAGVVRVLGVDPGLTRCGIAVVDVDARRRAELVHVEVAGTAPEESLDARLLCIDRA
+VSAVLVRFRPERAAVERMFANNNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV
+TGNGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHAWRGTALGRAAGHTGLDTSG
+LASRTGASRGAAGARVRRAPKAALTPAQQAWLAAERSAGARPGRRSAG
+>MHAAABBN_00993
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR
+>LFPAFLNI_01232
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001096.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7163dcb3bea56bf2b77cfc80d7c576b4c55fa70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001096.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01616
+MPVATAATLPVIAQQAQGGGGSMLMLIAFAMLAVMLFLSFRKGKKVQQQQAEMRSTLAPG
+VEVMTGAGIFGTVVSVDAENQRVTIETAPGTRMDVHLQGVTNVVEPTAAAAATPADDEAR
+LDRAPGAEYGAQQPVVEPRADDAVDPRDRRGDLA
+>MOLHKGIG_01271
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETTAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>NAFOICDF_01511
+MPLTPLAPVLADDAAGGGNVLVLAMFAALAVMLFLSFRRGKKAQAEAADMRARLTPGQEV
+MTGAGIFGRVVAVDAAAQRVTLETAPGTRMDVHLQGIVKIEEPDVAPAADTAPAVGGAHA
+AETAPAADDTDRA
+>MHAAABBN_00990
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>LFPAFLNI_01229
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001100.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9cf5ef2abff5f5cc1453bb56df3ffcf04b64ff4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001100.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01620
+MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG
+WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED
+VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR
+RRLDVLLGALEAAG
+>MOLHKGIG_01267
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>NAFOICDF_01515
+MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL
+LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP
+TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS
+RRPGSVGARRRLRMLLDALGADG
+>MHAAABBN_00986
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>LFPAFLNI_01225
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001103.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a561f43030ef3bb1300e4a64aba7fcd21c51187
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001103.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01623
+MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALCNALST
+AQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPDDAAAA
+RLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADAFAGVA
+DSPVTGVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTAGLYVLLTAAL
+FAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTGISRTALAMAR
+ESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVLVYYAVANLAA
+ATLRGGEDGRDPALPRPLRVPRAVNVLGLVLCAVLAATLPPMAVVAMLAVFLVGVGGRAF
+VLAGRGRPGRRGAVAP
+>MOLHKGIG_01264
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTGISRTALAM
+AREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDHGHRPARPRPLRVPRAVNVLGLALCLLLAFSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGG
+>NAFOICDF_01520
+MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC
+NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD
+SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLAGGRAAADTP
+VSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTVVLYALLAA
+ALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAGISRTGMAM
+AREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVLVYYAVANL
+SALTLRPEQRTLRVPRAVNVLGLGLCLVIAFTLPPASVAAMVGVFLIGLGGRWFVRSRRP
+DRIG
+>MHAAABBN_00983
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDD
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGV
+GGRAFVRAGRRGR
+>LFPAFLNI_01222
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001105.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..342a6407203d125fd421e322ae1d6bf3dba2d66d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001105.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01626
+MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA
+SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV
+FGAQMDVTLVNDGPFTLVVDTADLTGPRRG
+>MOLHKGIG_01262
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>NAFOICDF_01522
+MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER
+SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV
+FRADMDVALTNAGPFTLVVDTADLAGPRRG
+>MHAAABBN_00981
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>LFPAFLNI_01220
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001107.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc70aefd3dbacada3c09fa4f163478140f806822
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001107.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01628
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE
+>MOLHKGIG_01259
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>NAFOICDF_01526
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD
+>MHAAABBN_00978
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>LFPAFLNI_01217
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001111.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecfb9ba8e9e8d566738c12bcd56f1e309b870046
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001111.fa
@@ -0,0 +1,85 @@
+>ACLBLIBL_01633
+MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML
+LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG
+DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE
+ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES
+VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ
+DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA
+RAA
+>MOLHKGIG_01255
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR
+DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV
+RAA
+>NAFOICDF_01530
+MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP
+EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV
+KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE
+KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ
+DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV
+RDA
+>MHAAABBN_00974
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
+>LFPAFLNI_01213
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001113.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18ccc6a0563e12205cbb2bdff1e3fc7a6a1a5da9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001113.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01636
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG
+>MOLHKGIG_01252
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>NAFOICDF_01533
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR
+>MHAAABBN_00971
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>LFPAFLNI_01210
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001114.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e815272b3fb9a5fc4f78aa5706206f99f9f1a680
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001114.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01637
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ
+>MOLHKGIG_01251
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP
+>NAFOICDF_01534
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ
+>MHAAABBN_00970
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
+>LFPAFLNI_01209
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001115.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d9a3cddd26e0dd847f8fd0ff123b2dddb38e742
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001115.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01638
+MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP
+FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR
+RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV
+DTTGLTAAEAAWRIVEGVHRPRRSESHP
+>MOLHKGIG_01250
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR
+RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>NAFOICDF_01535
+MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV
+FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR
+ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL
+DGTGHRPGDIASRIVEAIPTLPRRHTRP
+>MHAAABBN_00969
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>LFPAFLNI_01208
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001116.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30ab9ed2c2567471f996750d501fec610d5c9ab5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001116.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01639
+MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP
+EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS
+EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ
+NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE
+>MOLHKGIG_01249
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDL
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>NAFOICDF_01536
+MTEHQPDQSDPIAEHSAAAPEQDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLPAVLGPQ
+VRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVLGQNDFT
+RSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEGKNLV
+GAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQNPHSAV
+LRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVSVGLVFA
+AELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQLRFVLLD
+GLARPTTVDIPDASLLFAAYQEIAE
+>MHAAABBN_00968
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>LFPAFLNI_01207
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001117.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97ab554498b342f49433df5d69feca8730b49efc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001117.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01640
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND
+>MOLHKGIG_01248
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>NAFOICDF_01537
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND
+>MHAAABBN_00967
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>LFPAFLNI_01206
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001118.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e847d590efe1f2872937cf0addcc853d0c5386a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001118.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01641
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>MOLHKGIG_01247
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>NAFOICDF_01538
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA
+>MHAAABBN_00966
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>LFPAFLNI_01205
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001119.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b442e891acef955126c469c10e6f6591df7d0fa5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001119.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01642
+MGADPAAPRAARTVLSASEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAV
+LARIEPAFDPEAAVGEVDVTLYRDDLRRSAARTPMPTRLPAVPLDGAVVVLVDDVLFSGR
+TVRAALDAISELGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTSERVQVRLVEVDGP
+EGTGEVSEDAVSIADQADRPEQREA
+>MOLHKGIG_01246
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
+>NAFOICDF_01539
+MGGIPAAPRAARTVLTAPEIDRALTRIAHEILESNKGPEGLVLMGIPRRGVPLARRLAAV
+LHRIDPAFDPVSAVGEVDVTLYRDDLRRGTARTPAPTRLPDHPLDGAVVVLVDDVLFSGR
+TIRAALDALADLGRPAAVRLAVLVDRGHRELPIRADFVGKNLPTSTAERVQVRLTEVDGP
+DGSGEVPEDAVRIVDAPAETPREA
+>MHAAABBN_00965
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
+>LFPAFLNI_01204
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001120.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b6ff6f35f15b90bd20598bab1d5bb227474c401
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001120.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01643
+MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR
+SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>MOLHKGIG_01245
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>NAFOICDF_01540
+MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV
+DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR
+SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG
+AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV
+LEQVANGVSVRMAVLHLVLNQDPALAPQEARP
+>MHAAABBN_00964
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>LFPAFLNI_01203
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001123.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5ea3cc921c2cc098d93f3473700b2102633bb19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001123.fa
@@ -0,0 +1,100 @@
+>ACLBLIBL_01647
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL
+RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV
+TSLQEHDARLQQAVEASA
+>MOLHKGIG_01241
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>NAFOICDF_01544
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL
+ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI
+AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL
+ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ
+LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV
+TSLQEHEERLAQAVAAEASA
+>MHAAABBN_00960
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>LFPAFLNI_01199
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001124.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a85f0f93358dc5bb20a1ae04263f611ada177401
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001124.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01648
+MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE
+RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP
+YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA
+ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW
+PQVLATSSRGILAGGPTVAALVERIERDRADLG
+>MOLHKGIG_01240
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>NAFOICDF_01545
+MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA
+AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY
+AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA
+SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP
+GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR
+HAAGRDA
+>MHAAABBN_00959
+MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>LFPAFLNI_01198
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001126.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30f7564edd26569fb6ec0e7945267743ab487296
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001126.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01650
+MTDAFDHGPAPAVPVARTAAQERRPGPGVTVLAGPTAVGKGTVSAYVREHYPQAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVAADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRESLPEATFVFLAPPSWEELVSRLVGRGTEGPEEQRRRLDTARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPEHSSPEA
+>MOLHKGIG_01238
+MTDTFDPGPAPAVPVARTVVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>NAFOICDF_01547
+MSDLSDLGPAPSVPGERAPSRPPAPGAGVTVLAGPTAVGKGTVSAYIREHYPQAWLSVSA
+TTRAPRPGEEDGVHYFFTTPEEFDELVAGDQMLEWAVVHGRNRYGTRRDRVAEAVAAGRH
+VLLEIDLQGARQVRRTLPEATFVFLAPPSWDELVSRLVGRGTEGPEEQRRRLETARLELA
+AEPEFDAVVVNDAVERAAAELVKLMGIDPHDAPASA
+>MHAAABBN_00957
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>LFPAFLNI_01196
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001128.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44492075792897e0afa76d835f0d4b09dddf3197
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001128.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01652
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGTATWEALSGRPVRTGTF
+EAVDEVNHVRLGRQADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVEPAVGRLTGADSGARRLPEPDEIWELAQAAAADPAARR
+PRATTSRPGPAAAGAAPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGVALARAALA
+AGARVRFIAGSMSVPVPEGVERAVHVESTAELLTAVLEQAADADVLVMAAAVADFRPAEA
+SESKMKKGDDGSSPVIVLERTEDVLATAVRTRAAGGPMAPLIVGFAAETGDAESSVLEYG
+RAKLARKGCEMLVVNEVGRDKVFGRDETAVTILFADGSPAVEAAGSKDEAAAAVVGAVVD
+RLAASAPGSASAR
+>MOLHKGIG_01236
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRHADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATAANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSGTEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGAIV
+RFIAGSMSVPAPEGVERVVQVESTQDLLEAVLAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDPTSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDQAAAAVVQAIVDDLAGR
+DPAGASGR
+>NAFOICDF_01549
+MEVVLGVGGGIAAYKAALLLRLMKEAGHGVTVVPTDNALRFVGAPTWEALSGRPVRTDTF
+TDVPEVSHVRLGREADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWRHPATVANVALLRERGVHVIEPDSGRLTGADSGPGRLPEPARIWAEAQDAAARAGGRA
+GREAAVTAAEPGAASPLAGRTVVISAGGTREALDPVRFLGNRSSGKQGTALAEAVLAAGA
+RVRFIAGPMSVAPPAGTEVTAVESTQELLEAVLSEAADADVLIMAAAVADFRPAQVATSK
+IKKTDDGGAPTIVLERTPDVLATAVQTRDAGGPMAPVIVGFAAETGDEHTTPLEYGRAKL
+ARKGCDLLVVNEVGDGKVFGQDATEVTVLSADGAEPVTRTGSKAEAAAAVVEALERVLAS
+REAGGAPGR
+>MHAAABBN_00955
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVQAIVDDLAGR
+DPVGASGR
+>LFPAFLNI_01194
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVRAIVDDLAGR
+DPVGASGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001131.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65de0f9e4a8deee70935bc4dcec35d190233a688
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001131.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01655
+MHGFRGDHHGLALLADALPERAITSIELPGFGDSEPFPDAEHTVAHHADAVAAVLAAMPP
+SQRPVLVAHSYGTVVGAELVARDPGRWDRLALLNPIAEPALDASASWTSRGLAALARGYY
+ELAARLPERAGRLVLGAAPVVWVTTLAMSRTPDRRVLAYTHDQHRRYFSRFASARMLSES
+YRASSTGTVADAADRLRLPVLLVAGREDPLGSVPAQEALAAAIEAGGGRAELHVLDGVGH
+LLHYERPGECAALLRAWAARGR
+>MOLHKGIG_01233
+MPVPTPPAAPGPPVRLRDLLRPPAAPADPRVLTGHVARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPEAAPGSRGAPEGDPAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+DSEPFPHAEHTVAHHADAVAAGVAALGLPAAPVLVAHSYGTTVAAELAVRDPSRWARLVL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERPARLLLGAPPVVWVTTLATTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQKALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
+>NAFOICDF_01552
+MPAPHDADPASPAGPRPIRPWHRLRIPAPTTPPRALTGHDVRVPRRRDVAVPDPISGAPL
+SVAVWQHDAAPSSGASVAGAARPHLVFVHGFRGDHHGLQLLADCLPEFGVSSVELPGFGA
+SDPFPDAEHTVAHHADALAAAVAALGLDAPPVLVAHSYGTVVAAHLVQRDSGAWPALALL
+NPIAEPALDASGSRADRLLAGVAEAYYEAAARLPERVSRLLLGAPPVVWVTTQAMSRTRD
+RDVLAYTHDQHRRFFSGFASARMLSESYRASSTGTVAQAADRLDLPVLLVAGREDPLGSV
+AAQEALAARIAAAGGVPELHVLDGVGHLLHYERPAACARLLREWLAAGA
+>MHAAABBN_00952
+MPVPTPPAPPGPPVRLRDLLRPPAAPADPRVLTGHPARTPRRRTLAVPDPVRRTPSSVAV
+WEYAPVPVAAPGSPGALEGDAAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPRAEHTVAHHADAVAAAVVALGLPAAPVLVAHSYGTTVAAELVAREPSRWGRLVL
+LNPIAEPALQASASATSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWATTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAAGGTAELHVLDGVGHLLHYERPAACAALIRDWFRRAGR
+>LFPAFLNI_01191
+MPAPTPPAAPGPPVRLRDLLRPPAAPADPRVLTDHPARTPRRRTLAVPDPVSGTPSSVAV
+WEYAPVPEAAPGSPSGLKGDTAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG
+ASEPFPHAEHTVAHHADAVAAVVAALGLPAAPVLVAHSYGTTVAAELVARDPSRWGRLAL
+LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWVTTLAMTRTR
+DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS
+VPAQEALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001133.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75791799f3ea294ebcca8bfa29201a824a68690a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001133.fa
@@ -0,0 +1,75 @@
+>ACLBLIBL_01657
+MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE
+WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC
+PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA
+MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE
+LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA
+VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR
+AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL
+NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV
+FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG
+GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL
+ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI
+DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT
+VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI
+R
+>MOLHKGIG_01231
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK
+SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR
+>NAFOICDF_01554
+MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS
+GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV
+LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE
+ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA
+PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV
+KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA
+AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA
+DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV
+KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR
+>MHAAABBN_00950
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
+>LFPAFLNI_01189
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001136.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbf3b8f25c9899fdfe3e060bf463b6b05edef4a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001136.fa
@@ -0,0 +1,79 @@
+>ACLBLIBL_01660
+MVSAPAGSRPPEAPGARTDPAARRGDVPGPLDARWVPALLACLTLGIVSDGWEAATRTTV
+ALACLGAAAAAVLLAARAPTPAWIRGTGTAVALAGVAVALMLQHSAVPAAALERTGWADV
+VREQAAVRVELAVTGAAVETAGTFGPRWSAPVRVRAFGHPARAPEAAVAARLSGPGTVPS
+ALGAAPDSEPAPGGRVVGPPAATVLCVVVTPDAGDGTVFLTAAAAPTPGPCPAADAAHGA
+ASVEDEPPPRREALRAAFRAAAAGTAGTAPELIPGLVLGDRSAQGRPLDAAMKASGLSHL
+SAVSGANVALLLGFTAVALRSLRVHRAVVIAAGLGLLAVFVVVVGPEPSVLRAAVMGALG
+AVAVFLGRGRQAFALLAVGGTALLVAVPSLSVEPAFHLSLAATAGIVLAGSWGDRTLHGP
+LRRVLPDAAARWLSASLAVTLAALLACQPVLLAMTGELSAYAVLANLVAAPAVAPVTVLG
+TLAAALVLPAPAVAAALVWLVQWPSAWIGVVAHAAAGLPGALRPWPSGALGVGLGALLTA
+ATLAGFAAVLVLERRRHARVRRVGEGAPLPPERTPALVLLAAVLVAAAVGGVGAVLVPRP
+AGAAPPDWAVAFCDVGQGDMAVFRSGPRAGVVVDVGREPEAARRCLEDLGVDRVEAVLLT
+HLHADHAGGLAGVADRAVPGAVRYATRDAAGVGRSGATAGEAPGVAPPAGGARLVTGERG
+AAGQARWEVLLADARAAEENDASAQLLVTVDAPAGPVTTLVTGDMEEEASGVWAAGRRSD
+AAGPPSVDVLKVAHHGARNGGTAVPRAVRARLHVVSVGAENTYGHPHPATLDALHRLGPV
+ARTDLHGTVALVAEGPDGAAGAGEIGVYTVRPPSAVRTAP
+>MOLHKGIG_01228
+MNPAPGPPNDPVDRRARHREVPGPLEARWVPALLGCLTLGILGVGWDAPARSAAALTGLA
+VAAAAILGAARSTGRIRGVATATALAGVAAALMLQHSAGPAAAASGSGWTGAVHAGSPLR
+LELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIVAPEGG
+TWAPDGGPGSRVCVVARPSRSGSTVFLAAASAPQPGPCPGGTQTAGGATGGDPGPPRREA
+LRAAFRQSAEGTVGAAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMILG
+AVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQAF
+GLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLAGAPLDRALHAGLGRMLPDVVARWL
+SASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPGI
+AAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLLE
+RRRTAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRSSGSAPPDWAVAFC
+DVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHAGGLAGV
+VDRASRGAVHYATRDAPAQGREGRGGEADGVDPLADAARLRTGATGTAGPVRWHVLLADA
+RAPEENDASAQVLVTVESGAGPVTTLVTGDMEEDASAAWVAGRRSDAAAPPRVDVLKVAH
+HGARNGGTAVPRAAGARLHVVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTAA
+DGPDPDGAPEIAVHTVRPPSSVRTGP
+>NAFOICDF_01557
+MSLGCAALAAVTLTLRLRIRRTGSSRVRTGAATAVVLAGLCGAVLVQHIAVERSGREQVG
+WIETVDTGGPVRLEVTAQGPATAGDSRFGPSWTRPVTVQRFGHPLRPLTPPAEATLTGTG
+SLDAAANGAEVLCVVAEPRPADGALFLAARAAPESDGCGEGSTAASSGPTGRDVLRARFR
+EAAADGVGLAPELVPGLVLGDRTAQSEQTDQAMKDAGLSHLSAVSGANCALLLGTVALVL
+RSLRCPRGVVLGAGLAVLGVFVLVVGPEPSVLRAAVMGALGALAVFLGRGRQAFGLLCAG
+GTLLLVSVPDLAGEIAFHLSLAATAGIVLVAAPVDRWLHGRLGRVLPDLAARGLSSSLAV
+TLAAHLACQPILLVMTGTVSLWAVPANLMAAPAVAPVTVLGTLAAALVVPAPWAAAPLLW
+TVQWPAAWIGVTATAASAAPGAVRPWPEGALGVALGALLTAATLAGFHAVLVLERRPTAP
+VRRVGRSARDARVRVPAGVVLAAVLAASATGAAAAVLVPRPPGTVPEGWAVAVCDVGQGD
+MTVFRSGPGSAVVADAGPDPAAASRCLDDLRIERVDALLLTHLHADHAAGAPGLSGPRAA
+AAVRHGAWSGSGGGGGEEPGLDAPAGSAPLTTGDEGRAGDVAWRVLLADPRAAEQNDSSA
+QLLVTVTTPAGPVTTLVTGDMEQEASAAWAAGTRSDAAPPPRVDLLKVAHHGARNGGLDV
+PRRVRARLQAISVGADNTYGHPAAATVAGLEELGPVLRTDRHGTVALVPGPDARLTPYTV
+RPPT
+>MHAAABBN_00947
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP
+>LFPAFLNI_01186
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGVGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001137.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c401b4705fcdc2a35522ff2ac87ec5e79873b19a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001137.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01661
+MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH
+SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL
+RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT
+GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH
+AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG
+IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>MOLHKGIG_01227
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>NAFOICDF_01558
+MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET
+HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL
+LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA
+TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR
+HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA
+GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR
+>MHAAABBN_00946
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>LFPAFLNI_01185
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001142.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b893b9cea6304024ad19b92d51cf4774df04a8af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001142.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01667
+MDWSSWGPAGHEEMTRRPGRPARDVPAAPGTVVEDVASGFTGAVIRVERAGGVHTVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPHVASAPRPPARTASGSRRVEGVRARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIAAFDPGPRRRLGILVDHLVPGSKE
+ERIAAEAMRVPGAAGNVLILGHPYVDVWQVIKPAVLGIPTWPVVPKGQDWKTGVLQGLGW
+PHGTKEATGLGWKRLLSHVGSYADLEPSLLGRVEELIDFLTAEPER
+>MOLHKGIG_01221
+MDWSSWGPAGHDDLTRRPARTVPDVPAAPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>NAFOICDF_01564
+MDWSSWGPGAHEDLARPAGRTAGEAPATPGTVVEDVASGFVGAVVRVERSGGTHVVVLED
+RRGVRRGFPLGPGFWVDGSPVVLVPPRSAAPAAAARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLPGAIRDFAPGPGRRLGILVDHLVAGSKE
+ERLAAEAMAVPGAAGNVLILGHPYVDVWQVIKPAVLGIDAWPVVPRGQDWKTGVLRGLGW
+PAGTKEATGLGWKRLLSHVRTYADLEPALLGRVEELIDFLTAPGA
+>MHAAABBN_00940
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVSGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVFGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>LFPAFLNI_01179
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPWRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001143.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5072ca1a61b07095b7b65555a2e7338e38701d19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001143.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01668
+MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ
+VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL
+LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA
+RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT
+>MOLHKGIG_01220
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>NAFOICDF_01565
+MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ
+VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV
+LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA
+RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>MHAAABBN_00939
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>LFPAFLNI_01178
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001145.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70ce61b976ac07ef2464c2416e129c41b76e69d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001145.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01670
+MTAPLFHLEPGALTGAVPGAEVSFGGPEARHAAASMRLAPGESVLLADGSGVRGHGTVLA
+AAPDAVTVRLDAVDEEPAAVPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAEKARQKWADTARAAAKQARRARVPEVRGHVSGTGVAGLASAPDDGARLVLVLH
+EDAERGLSEVPVERLREAAEIAVVVGPEGGVGPAELEACTAAGAVPVRLGPHVLRASTAG
+PAALAVLAHRLGRW
+>MOLHKGIG_01218
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLARDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>NAFOICDF_01567
+MTAPLFLLDAGALAGVAPGAEVAFTGAEARHAAASMRLGAGESVLVADGSGARASCVVVD
+AAPSAVTVRVESLEHDAAPRPALVLVQALAKGDRDLMAVQASTELGVDAVVPWEAERSIV
+RWKGAKAAKAHQKWEDTVRAAAKQARRARVPEVRPVVSGTAVAALAGPDRLLLVLHEDAD
+LGLGGLPDADLEAAAEVALVVGPEGGVSPAELDACTAAGAVPVRLGPHVLRASTAGPAAL
+AVLQHRLGRW
+>MHAAABBN_00937
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARRKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
+>LFPAFLNI_01176
+MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA
+AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV
+RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE
+DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP
+AALAVLQHRLGRW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001146.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4995b1fba9b519e205f1c92b7e9252e2a584757c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001146.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01671
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR
+>MOLHKGIG_01217
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>NAFOICDF_01568
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+>MHAAABBN_00936
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>LFPAFLNI_01174
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001149.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f85680e8e8d1a241776e1ecdf01fe0738f578f87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001149.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01674
+MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL
+AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM
+ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>MOLHKGIG_01214
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>NAFOICDF_01571
+MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR
+PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA
+ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV
+EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN
+PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL
+RVKVAKDWQRDPKHLNRLGM
+>MHAAABBN_00933
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>LFPAFLNI_01171
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001152.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3d3b762972a59f4c3de1ede646e76c2af4a8082
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001152.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_01677
+MSIKPAEQPIPADESEPSRPPEGGPTDEDTRPLLDDPPGLGWVEDGMAGFERLTLGLDTD
+EQGQNLVTVVRPQATGPRDRTRRAILSVHGWSDYFYNAPLARAFEEAGYAFHAVDLRHYG
+RSLREGQTPGWTDDLARYDADLEAALATIAEDHPLPPVLMGHSTGGLIASLWAHRNPGRI
+SALVLNSPWLEMQGSAGVRLLAKTIVDPVSALKPYAMLTLPRIDYYWRTLSDQAEGEWDL
+HPLWRPTHAFEVPAAWLSAVLKGHRTVARRLQVSAPILVLVSARGHRGTSYDEAMLASDI
+VLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEA
+ESGAPDDGAG
+>MOLHKGIG_01210
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRAGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYATLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLHVSVPILVLVSARGHRGTSYGEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG
+>NAFOICDF_01575
+MTLFPHVRGPWPRHGLGLPADDAAAPPTPVDPEAGWTPDVLDGFERRSLALNADRQGRNV
+VTVVRRRAASRHRDPCRRPFVAVHGWSDYFYNTPLAEAVESAGYAFHAVDLRHHGRSLRP
+GQTPGFVDRLDRHHEDLDAALALIAEDHPATPVVEAHSTGGLTTALWAADRPEAASALVL
+NSPWLQTHGGPLARAVAAPAVRRIARRDPYEILPLPRVDHYWRSLSAEADGEWDLEPAWR
+DRWAFAVPAGWLAAVLDGHTTVARGLDLPVPVLVLVSDRGGLPLATRRRAASSDVILSPR
+AQARAARRLGPGVVVHRCPGALHDVFASAPPVRRAALDATLSWLAETAPPRIAG
+>MHAAABBN_00929
+MARDPLQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAARDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLARYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAMLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVTVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEAG
+APDDGAG
+>LFPAFLNI_01167
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAVLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVSVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001159.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dbebb2f9bf92cf6e320aab116fcb024943a7a21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001159.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01684
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL
+GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF
+GWVYEFSRGKYAH
+>MOLHKGIG_01203
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF
+GWVYEFSRGKFAH
+>NAFOICDF_01582
+MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL
+GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF
+GWVYEFSRGKYAH
+>MHAAABBN_00922
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV
+GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF
+GWVYEFSRGKYAH
+>LFPAFLNI_01160
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF
+GWVYEFSRGKFAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001160.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..370d454992ea32db951fdd4678ae385b54b50acd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001160.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01686
+MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALL
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWYCVMWAAASSDLIATHFRLSL
+NDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ
+LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARA
+HGHHGVEDGGHHELGADPSSHNPKIDG
+>MOLHKGIG_01201
+MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP
+LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEART
+HGQHGHEEHPVELGHGSDAPRLER
+>NAFOICDF_01583
+MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSHVTYDGAYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALL
+FVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAGFTGYSLPDDVLSGNGLRIID
+GILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVS
+AGTQPDWYIGPFDGALRLMPGMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGM
+ISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMWCTMWAAASSDLIATHFHLSL
+NDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ
+LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEART
+HGHGEHVGAVQGGSHSAELGH
+>MHAAABBN_00921
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFRLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEEHPVELEHGSHAPHLDR
+>LFPAFLNI_01155
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEDGGHHELGADPSSHNPKIDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001164.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3fdd5178018af47abb7327ecb3cb578aace8fd9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001164.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01690
+MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT
+SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV
+LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS
+>MOLHKGIG_01197
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>NAFOICDF_01587
+MRETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAKGETVPE
+LRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVKHGNRGA
+SSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQLGVPTV
+FNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITTSGPSTI
+MEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAVLLNAAA
+GLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS
+>MHAAABBN_00917
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
+>LFPAFLNI_01151
+MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK
+GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK
+HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ
+LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT
+SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV
+LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001170.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee815a3e124f1275816b07b52fcaee326b8bd89f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001170.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01697
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS
+>MOLHKGIG_01191
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
+>NAFOICDF_01596
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD
+>MHAAABBN_00910
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA
+>LFPAFLNI_01141
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001171.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3deaa108064f24fc09449baf7c26bfdb37729ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001171.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01698
+METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG
+ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE
+ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH
+>MOLHKGIG_01190
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>NAFOICDF_01597
+MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT
+SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD
+EALQTPPEAEPAPVRREPGMP
+>MHAAABBN_00909
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR
+RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>LFPAFLNI_01140
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001173.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65533753bd75af88af78e8ac5b9e6c30e68c2913
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001173.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01700
+MRVLTIIPTYNEIESLPLTLGRLRDAVPTSDVLVVDDASPDGTGQWADARAAQDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLDAVRTADLVIGSRRV
+PGGKMVNWPASRKMISWAGSLYPRIMLGLRLTDVTAGYRAYRAETLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRSR
+LGL
+>MOLHKGIG_01188
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>NAFOICDF_01599
+MRVLTIIPTYNEIESLPLTLGRLRDAVPDSDVLVVDDASPDGTGAWADARAAEDDHVHVL
+HRAEKNGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPASRKLISAAGSLYPRIMLGLKLTDITAGYRAYRADTLRRIDLGAVQSKGYG
+FQVDMTFRVARLGLRIVEVPITFVERELGESKMSGGIVGEAVVNVTKWGLQARWETLTGR
+GPQRG
+>MHAAABBN_00907
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>LFPAFLNI_01138
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001175.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bea412d04d3e17f0b6621bf25829695660805ca9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001175.fa
@@ -0,0 +1,90 @@
+>ACLBLIBL_01702
+MSHAPASATPPEEPQLSPAERFARAKAARHHAGSELGRFASRLGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLSRVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGQEAERRSERPDWGRPGRHRGRGGRDGGQRGRGGRGG
+DGRKGGRDADRRGRHGSHAMDREQPATGRVRGQEDGERRGPRLSTSRPEMIRALDREGLL
+PCITFIFSRTGCDAAVEQCLRAGLDLTTAHEKALVAERVEQAARLLPVEDLEILGYWAWR
+DGLSRGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFN
+GENHVDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLKSSFRP
+TYNMSANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEKAMQCHLG
+DFSEYLALRKELASAEKSGSQGRRRAQLAAVKESLADLAVGDVVELDAGRSLGRAVVVFP
+AGNPQNPRVGVVTDKAQLRRITVDDVTGPVEPVAGAALPQVLQVKTPTQRKDVAALMREA
+VRTGRPPAGGGRRTSGFRLREDPAAPRVEELRRALQRHPCHACQDREEHARWGDRWWGMR
+REVSVLRERIAGRTNTIARTFDRVVGLLRSYGYVHEDASSPRQALTARGEALRRIYGERD
+LFTSLVLQDPTVQGLTPEEWAAVAALLVYQGKGEAGHGVVPMPTARLAEVADAAERIEER
+LRADEAQARLEPTPPTDPGLVGPMHRWVRGASLRRTLEGADLAAGDFVRWARQVIDVLDQ
+LANVPGDARRSRACRKAADLVSRGVVATSLPAATAREADED
+>MOLHKGIG_01186
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>NAFOICDF_01601
+MAPHTHHDLPPEEPALSPAERFARSRASASRPGTELSRFAARLGFPLDEFQLEACREVEA
+GHGVLVAAPTGAGKTVVGEFAVHLGLARGRKAFYTTPIKALSNQKYADLAAVHGADRVGL
+LTGDTSVNPDAPVLVMTTEVLRNMLYADSEALTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVVVSEHRPVPLWQHVMAGGRLYDLFAE
+DVAFEAAADADGTPLLNPELQRMAQEASRRVERPDWGRTGHRGRGRGGPGGRGAGRGRGK
+GGPRGGREGASSGWDRERPHRADASPGDGERRALGLSTSRPEMIRALDREGLLPCITFIF
+SRAGCDGAVEQCLRAGLDLTDRREKALIAERVEQAAAALPPEDLEILGFWAWRDGLSRGF
+AAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGVNMPARSVVLEKLVKFNGESHVDV
+TPGEYTQLTGRAGRRGIDVEGHAVVLWRPGLDPSAVAALASRRTYPLRSSFRPTYNMSVN
+LLAQVGAERARGILESSFAQFQADRSVVGLAREVRAKQSSLEKYADAMACDRGDFAEYLS
+LRKELAAAEKSGSRGRRREHLRAVKESLADLAVGDVVELHDGRALGRVVVVAAAGNPQNP
+RVAVVTDKAQLRKVAVEDLVDPVEPVAGAALPQTVQVKTPSQRKDVAAAMREAVRAHRPP
+TGGTRRGTGFRLREEVASPRLEELRRALQAHPCHACPDREDHARWGERWWDMRREVSLLR
+ERIAGRTNTIARTFDRVVELLGRLGYVGDDPDAPSRALTERGQTLRRIYGERDLLTSLVL
+HDPSTRSLTPEEWACVAALLVYQGKGDTQGLPVAMPTARLQALAEAVDRIEGGLREDETA
+ARLEPTPPTDPGLVAPLHRWVRGASLRDSLHGADLAPGDFVRWARQVIDVLGQIAQVPGD
+ARRTRACRKAADLVGRGVVAASLPAAAAGADGVEGEEPDRVDR
+>MHAAABBN_00905
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHIMAGGRLYDLFAE
+DIAFEDAADRDGEALLNPELKRLGEEAERRFQRADWGRPGRQQHRDGRGGGTKGRARGGR
+HTGRDGGRGRTGSSALDRERPVSGRPGGHDGGPRRGPRLSTSRPEMIRVLDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFTAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVARLASRRTYPLRSSFRPTYNM
+SANLLAQVGAEQARGILESSFAQFQADRSVVGLARELRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRSLGRAVVVFPAGNP
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRSTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVHEDAPSPRAALTERGEALRRIYGERDLFTSL
+VLQDPAMDGLTPEEWAAVAALLVYQGKGETEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>LFPAFLNI_01136
+MAHHPASATPHDEPELSPAGRYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001176.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f5da0e509a089ef464f5e762fe38f4742e829fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001176.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01703
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI
+>MOLHKGIG_01185
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
+>NAFOICDF_01602
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL
+>MHAAABBN_00904
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI
+>LFPAFLNI_01135
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001177.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cce11976f378c1c153dc7233e856fb148f0d449
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001177.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01704
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR
+SGSGSTAADEPVEGRVVERDETDVRPRDER
+>MOLHKGIG_01184
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>NAFOICDF_01603
+MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA
+DAPSQGAGSTAAEPVEGRVVDRDVRDDR
+>MHAAABBN_00903
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
+>LFPAFLNI_01134
+MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA
+GSTAADEPVEGRVVERDETDPRDPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001178.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71980b58ac1a5ef3f42885d98f3abecdd786521b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001178.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01705
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR
+>MOLHKGIG_01183
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
+>NAFOICDF_01604
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA
+>MHAAABBN_00902
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR
+>LFPAFLNI_01133
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001179.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba3b86a2e0d62321b69379d9d0cfaf9f20b7660b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001179.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01706
+MSFGQRDYDRTKPEIDFPGENPPAELVVEDLIAGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMQVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>MOLHKGIG_01182
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>NAFOICDF_01605
+MSFGQRDYDRTKPEIDFPGDTPPTELVVEDLIEGSGPAVEPGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGIGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>MHAAABBN_00901
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>LFPAFLNI_01132
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001180.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c475945eabfbf155a6ebb50ec76162f22543416f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001180.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01709
+MTDADRARRIFGLETEYGVQHWNPEGRPLSPEEVVRYLFRPVVEWGHSSNVFVSNGSRLY
+LDVGSHPEYATAECSTLDELIASDAAGDLILHDLVTRAQERMAADGISGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGDGAAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTSLSEHTHLLRFGATDL
+MLRMIEAGFPLGDRVLAHPTLAVRQISHDLTGTARVALRDGDASALELQEHYLERARAFV
+AAEGAHHERVEEILTLWEDVLEAVRTGDRSRIEDRIDWAIKLRMLEDYRARQNLDWGSAR
+LAQLDLAFHDIDPDRGLFRLLLRRGAAARLLPEDAGRLAVDAAPPTTRARVRADFIARAR
+QRGLGYAVDWTTLKLTDHPLHAIAAKDPFDASSDAVDRLFERIG
+>MOLHKGIG_01180
+MTDADRARRIFGLETEYGVQHWNPEGRALSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMATDGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARTFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFGRIA
+>NAFOICDF_01607
+MTTDARRIFGLETEYGVQHWNPQARPLSPEEVVRYLFRPVLEWGRSSNVFVRNGSRLYLD
+VGSHPEYATAECSTLDELIASDAAGDLMLLDLIARAEEAMAADGIGGRIYLYRNNADSSG
+SSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVIPAGVWPEGEGRAHFAFSQR
+ADFVQEGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEATTLLRFGATDLML
+RMIEAGYPLGDHRVAHPTLAIRQISHDLTGTVRVNLREGTASALDLQDHYLSRARAFVAS
+EGAHHDRVEDVLDLWGTVVDAVRSQDFGPIEETIDWAIKLKLLRGYRDRYGLDWDAPRLA
+QLDLAFHDIAPGRGLFPLLRERGGVRRVLPEGAARAAVDAAPPSTRATVRAEFIARARAA
+GMDYAVDWTTLKLNDHPIHAISTKDPFSTDATPVDRLFERVG
+>MHAAABBN_00899
+MTDADRARRIFGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVEAAPPTTRARVRADFVSRAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA
+>LFPAFLNI_01130
+MTDADRARRILGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001182.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c839d3649d3ebc5c0bba51fca06c21fa8ee13b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001182.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01711
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPTVGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWADTPVPDVHPLFTIVPGPVASWERA
+>MOLHKGIG_01178
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA
+>NAFOICDF_01609
+MRLWTLHPRHLDRQGLTGGWREALLAQAVLARRTKGYRDHPQLERFRGHGDPAAAIGAFL
+SGIALEASARGYRFDVSKIDRPLLPADGAGELVLPFRIAPIEVTTGQVAHEWGHLRAKLA
+ARSPGWLERWADVQTPDVHPLFEVVDGPIASWERP
+>MHAAABBN_00897
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA
+>LFPAFLNI_01128
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLEQWSDTPVPDVHPLFTIVPGPVASWERA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001184.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2813525ad48a0e96bbf277cf72b623f668ebcbba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001184.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01713
+MSAFGRGTADGFARAVAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFDELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLALAEAGTAPRLVLDDPVAALQTISHDPGLRATVP
+LLEHTADGPVRRHWTGLQILRSYLDAAHAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARAGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA
+>MOLHKGIG_01176
+MSAFGRGAADGFARAAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLAPLFGARA
+>NAFOICDF_01611
+MPGGIGGAPEAVAGTPAFAGQRRLFPADLTAPPGGRDAAGWGVHRVMGTESEFGIHAPAN
+PGAHHSVLSVELVNSYADLITHSGGAVAGTEWDYAGESPLVDARGWRMPRSAAHPSQLTD
+QALVGPDGEPVHLLLSTVLPNGARWYVDHAHPEYSSPEVASPREAVVWDAAGDRVAQAAA
+EHIAAAEGAPEVLVYKNNTDGKGQSYGSHENYLVARALPFDELAEVLLPFFAARQVLVGA
+GRVGVGLRGERPGFQLSQRADFFEEQVGLETTIRRPIVNTRDEPHARGDAYRRLHVIIGD
+ANLSQHATWLRMGMTALVLALAEAGTAPRIVLDDPVAALQTISHDPTLRAAVPGRERGAD
+GVWTRREWTGLQILGAYLDAAREHCARCGVDDAETAAVLDAWGTDLADAAADPLALADRA
+DWAAKLRVLEGLRARGGLDWSDPRLAMVDLQYADLRPAKSLHRRLVAAGAMRVLVEDAEV
+EAAVVAPPRSTRAWTRGNLVRHHARQVSGAAWDSVLVRAAEEAPLHRLRLEEPLVGAAED
+LPGWWDDTPGSAAPAPEPNELVTRLGELLRR
+>MHAAABBN_00895
+MSAFGRGAADGFARVAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA
+>LFPAFLNI_01126
+MSAFGRGAADGFARAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEFGI
+HAPANPGAHHSVLSVELVNAYADLATRSGSAVAGTEWDYTGESPLVDARGWRLPRSAAHP
+SQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGDLV
+AQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAARQ
+VLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRRLH
+VIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVPLL
+ERTADGPVRRHWTGLQILRSYLDAARAHCAAFGAADPQTREVLDAWAVDLDDATADPLSL
+SDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTLAD
+EAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLVGA
+AVDLPGWWEDAAAPRPDDEALVATLAPLFGARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001189.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2844460b2a92996645e3502c39b53ada82410eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001189.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01718
+MTDASSADQPDDALGPLRTHLTATVDDLEAGLRAPTVLLLAFEGWNDAGDAASGALDALR
+EQWDAAEAGRICDGEFYDYQVTRPVVRRDADGLGTLEWPAVRLHEAQLDAQGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWQAFAEELFAAAAARQVDAVVTLGALLADVPHSRPLRARPTS
+PLVDVRVAVGADRPAYEGPTGIVGVIADEAARRGLPSVSLWGAVPHYVAQAPSPKTLLGL
+VEAIEDLLHVSVSTCELEDDAQAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+AIAREFERYLRGRGGR
+>MOLHKGIG_01171
+MTDATSEDQPDDALGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEAFLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADAHDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>NAFOICDF_01616
+MDEQTDPGSLDGAPSPEDRLGALRAHLTATVPEVEDGSRPPAVLLLAFEGWNDAGEAATG
+ALAELSAQWEAAPAGVVCDGEYYDYQVTRPVVHRDADGLGTLEWPALRVHEARLDAHGAP
+VPDGEAVPADGLRVLLASGVEPNVRWRAYVEELLRWAEAEGVDAVLTLGALLADVPHSRP
+LRARPTSPLVAVRVAVDAGLPAYEGPTGIVGVVTDEAARRGTASLSLWGAVPHYVAQAPS
+PKTLLGLVEAVEDLLHVELLTHALRDDAQAWQRGVDELAREDPEVASYVRRLEESQDAQE
+LPEASGEAIAREFERYLRGRGRD
+>MHAAABBN_00890
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
+>LFPAFLNI_01121
+MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR
+EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA
+PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS
+PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL
+VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE
+SIAREFERYLRGRGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001190.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7df7c0f6b3c39bce6d74c60e3071be1d05ea98a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001190.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01719
+MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY
+VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE
+VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG
+QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE
+CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH
+AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL
+RLR
+>MOLHKGIG_01170
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
+>NAFOICDF_01617
+MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY
+VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN
+VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG
+SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE
+CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS
+KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH
+ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL
+R
+>MHAAABBN_00889
+MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR
+LR
+>LFPAFLNI_01120
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001192.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..666ab0ce88e2dbd34b7e4ff3b744f2fc438a2f22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001192.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01721
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLEVFDDEEDDEA
+>MOLHKGIG_01168
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
+>NAFOICDF_01619
+MSSDARVALEALTSALNEHLVAAQNRRGEDDPAVEAAFFAVADAFDAYEEALYAETEEVT
+PLELFDDEDDLDEED
+>MHAAABBN_00887
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
+>LFPAFLNI_01118
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001203.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f07a19f436738f5214a503cea7563f1e878c227
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001203.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01736
+MTTHHGEYKVIGGKLVAADLTIDDGRIAAASINGDFFLEPDEALEDLNAAVTGLSADAEH
+RVIQAAVEAGLREDAELFGVDAHAIATAVRRALGKATTWEDHEWEIIPPEPLPIALTVAL
+DEVLTRQVAEGRRRPTMRLWQWNEPAVVIGAFQSLANEVDPEGASRHGINVVRRISGGGA
+MFMEADNCVTYSLHVPRSLVDGLETAESYPFLDEWTMDALSRLGVQAFYQPLNDIATDQG
+KIGGAAQKRVGQDGLLHHVTMSYDIDADKMLEVLRIGREKLKGKGVASAKKRVDPLRRQT
+GVARPEIWETMMATFEERYGARRVELDDATRAEAEELARTKFGTQEWTARVP
+>MOLHKGIG_01154
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
+>NAFOICDF_01632
+MSTQTTHHGEFKVLGGKLVAADLEVQDGVIVRASVNGDFFLEPDDALEDINAALTGLPAD
+TEHHVLAERVRAGLRPEARLFGFDAEAVATAVRRAVGLATTWESHRWEILPPEPLPIEMN
+TALDQILTEDVAAGRRNPVMRLWQWTEPAVVIGAFQSLANEVDPDGVTRHGIHVVRRVSG
+GGAMFMEADNCVTFALSAPASLVDGIDTAESYPFLDEWVMEALRELGVQAFYQPLNDIAT
+DQGKIGGAAQKRFGATGLLHHVTMSYDIDADKMTEVLRIGREKLRGKGVASAKKRVDPLR
+RQTGVPREQIWETMMAVFERRYGARRVELDADTRARAEELARTKFSSPEWTARVP
+>MHAAABBN_00873
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
+>LFPAFLNI_01104
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001205.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d287af765812c2ec75cde485c31854a73dd24388
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001205.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01741
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG
+>MOLHKGIG_01151
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>NAFOICDF_01635
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA
+>MHAAABBN_00870
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>LFPAFLNI_01101
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001210.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..478cd9f81155726729ef5cefcb40c261ff3f8fd9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001210.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01747
+MTAPAPATGFRRDPGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRVQV
+QHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAGRP
+GYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDRDA
+PEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAIQW
+YLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDEEA
+EDALFD
+>MOLHKGIG_01144
+MSIPAPMTDPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>NAFOICDF_01642
+MTPAPAPTDTPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRVQV
+MHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAGAP
+GYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDRDA
+PEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAIQW
+YIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDEEV
+EDALQEDVLRDRPGQASEIRSR
+>MHAAABBN_00863
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>LFPAFLNI_01094
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001212.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f91cab8e223c34499f8f099228d8d646c52df4ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001212.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01749
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI
+>MOLHKGIG_01142
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI
+>NAFOICDF_01644
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI
+>MHAAABBN_00861
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
+>LFPAFLNI_01092
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001215.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70e7e4ee2700e258e653c4f84a3d518e3ab588cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001215.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01753
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL
+>MOLHKGIG_01139
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>NAFOICDF_01647
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL
+>MHAAABBN_00858
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>LFPAFLNI_01089
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001217.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6c54186d42001e296ac2035644487f5a0b67162
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001217.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01755
+MVYSDLPSHRAAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDA
+LVEVKRVTSARGAGRPSRRYVVTSHAQEHLPKDHLAVALHSLARLEELGGDEEVRRTARR
+AFRDVEERFAAAVDGRDTELQERTRILASVLDDAGFAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPQFCEEETELFARLLQVDVRRLSTLAAGAHVCTTHVPLGRD
+>MOLHKGIG_01137
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>NAFOICDF_01649
+MYSDSADPAAPAPGTRERVLERVLSHGPVSAAEIGGALGLTAAAVRRHLDALEEEGFVEV
+KVVSAARGAGRPSRRYVVAPQAQRRLGGDHLGIALQAVDRLVEVGGEGEVRRLAADALQP
+VEEAFQAAVAGREMGLEERTRVLADLLDDAGYAASIRHVGAGLAPTLRAEQLCQGHCPLQ
+GLPARHPEFCEEETALFARLLGVDVRRLSTLAAGGHVCTTHIPLGRA
+>MHAAABBN_00856
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>LFPAFLNI_01087
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001221.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6d17b22429300ebe99daa3b2f51b44ba7405171
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001221.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01759
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA
+>MOLHKGIG_01133
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>NAFOICDF_01653
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS
+>MHAAABBN_00852
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>LFPAFLNI_01083
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001222.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d070c9ef83edc1e9fbf7303714ba9934bc09c13d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001222.fa
@@ -0,0 +1,69 @@
+>ACLBLIBL_01760
+MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPV
+AWQMYQNVMHLDPQDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSK
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ
+EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVH
+GSKLGAEELAGLKEGLGFDPAESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHP
+ENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+RSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLENRDRPAGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGS
+GAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA
+RGLL
+>MOLHKGIG_01132
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>NAFOICDF_01654
+MTDTASTALDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQL
+YQNVMHLDPSDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGH
+PEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLASDGD
+IQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQEVDW
+SNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKL
+GGDEVVGLKEALGFDPQKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENAR
+LYDRLASRELPAGFEDAFPSWDADEKGVATRAASGKVLTALAPVMPELWGGSADLAGSNN
+TTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGTFLTF
+SDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADAN
+ETAWAWRTILQHRDRPAGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAA
+PARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDGPGAP
+VRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTARGLL
+>MHAAABBN_00851
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>LFPAFLNI_01082
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001226.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9d47217e8fded2647fafafb38ba4c49a6df0c46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001226.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01764
+MKIRMHDTTTSQVAKRITQLREKGGVVALGRVLTLVISTDDAGIEAAVEAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVA
+WWPGVPPAVPSETALGRLAHRRITDTASAARAEPALWTLRQGHRDGDTDLAWTRLTLWRI
+QVAGIFDTLDVAALRSVTVDGAPDSPSTMLLAAWLTLALKVPVTIAHSKAGHGIRAVRLR
+CQDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTDQDCLAEELRRLDPDEVFGAVLHRGL
+PRTDLSPVQASER
+>MOLHKGIG_01128
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>NAFOICDF_01658
+MKIRMHDTTTSQVAKRLTALRESAGVSALGRVLTLVIVTDDAGIEAALGAANAASLEHPC
+RIVVLALGDPLAPTRLDAEIRVGGDAGASDVVVLWCQGEDAVADEPLVSGLLLPDAPIVV
+WWPGEPPAEPATTALGRLAHRRITDSATCRDAKETLQRLAAGLHDGDTDLAWTRLTLWRS
+QVAAILDNLDLADVRSVTVDGAPDSPSTLLLAAWLTWGLDRPVTIAHSKAGHGIRAVRLR
+GPEGDVVLSRSQSEVARLYQQGRPVQRISLPRRSDQDCLAEELRRLDPDEVYGDVLRVGL
+PRTDLAPVDASDR
+>MHAAABBN_00847
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>LFPAFLNI_01078
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001230.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51326e7d6748a3e61018518f5c5f11c9e7353112
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001230.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01769
+MTKIAINGYGRIGRNIVRVLRDRGYENLELVAVNDLADNEDLFWLTQYDTILGRYPGELE
+LTETGFRIDGRDVAFFSEPDPAKLPWGELGVDIVIECTGFFTTGPKAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEKNYDSATMDIVSNASCTTNCLAPMAKILNDEFGIVDGIMTTIH
+AYTGDQNLHDSVHKKDRRRARAAAQNMVPTDTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLVDFADLIGSKL
+>MOLHKGIG_01124
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAESMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
+>NAFOICDF_01662
+MTKIAINGYGRIGRNAVRVLLEQGHDDLELVAVNDLAATEDLFWLTKYDTILGRFPGELE
+LTDKGFSINGKDVAFFAETDPANLPWGELGVDIVVECTGRFTTGPAAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEGDYDSSTMHIVSNASCTTNCLAPMVKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEAEEVNEAFRRAAESGPLVGRLVYSTDPIVSSDIVTAPAACTFDAP
+LTKSIGQTVKVIGWYDNEYGYTCQLMDMASHMASKL
+>MHAAABBN_00843
+MTKIAINGYGRIGRNIVRVLRDRGHEGLELVAVNDLADPEDLFWLTKYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
+>LFPAFLNI_01074
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001234.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d42317e1dcfcb98d1e8cb133b8fa5ba8fb5769d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001234.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01773
+MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS
+PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP
+LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM
+LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE
+>MOLHKGIG_01120
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>NAFOICDF_01666
+MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR
+SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH
+PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV
+MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA
+ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE
+>MHAAABBN_00839
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
+>LFPAFLNI_01070
+MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS
+PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP
+MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM
+SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM
+LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001236.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c99e1c312a287126f01afe63729e7f0b8b359747
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001236.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01777
+MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA
+AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH
+HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW
+>MOLHKGIG_01116
+MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW
+>NAFOICDF_01670
+MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA
+AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA
+HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF
+ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW
+>MHAAABBN_00835
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
+>LFPAFLNI_01066
+MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA
+ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR
+HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF
+RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001240.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3da8514e8cf965a0378027b34152e4c9aa2bae8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001240.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01782
+MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG
+GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA
+LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME
+RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA
+LVWVGLGAPALS
+>MOLHKGIG_01110
+MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG
+GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA
+LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>NAFOICDF_01675
+MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL
+ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET
+ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ
+AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL
+AGG
+>MHAAABBN_00829
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>LFPAFLNI_01059
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001241.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4470797175705a22bd3a2e2c336aba30c9855ce1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001241.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01783
+MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG
+VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA
+RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI
+TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG
+>MOLHKGIG_01109
+MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER
+AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQAVARSGIDRLLELDAELAAAATEVAP
+>NAFOICDF_01676
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE
+ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE
+TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP
+>MHAAABBN_00828
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
+>LFPAFLNI_01058
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001243.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ba7d5416825d412caad832411a509383fe37a7a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001243.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01786
+MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV
+QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA
+DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD
+>MOLHKGIG_01107
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>NAFOICDF_01678
+MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA
+VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV
+VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV
+ADVVIVNDGDLDRLREITRRVWEGMAA
+>MHAAABBN_00826
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>LFPAFLNI_01056
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001249.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b67c904a8c9dc1700f28dce3e5d1abe871fb55f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001249.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01796
+MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP
+SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+TPDAS
+>MOLHKGIG_01099
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>NAFOICDF_01686
+MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP
+SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR
+HPED
+>MHAAABBN_00818
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>LFPAFLNI_01048
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR
+LPDMD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001252.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b491a7285e7dd54fd9d47bb0ab80ceee57a6cfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001252.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01799
+MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGD
+VLATSVGGWPGGIGIGFAADMLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLM
+AGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+VVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST
+SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVR
+LVLSWQMVSGIGGILVGLGLSTQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLA
+DLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVTAGVEAGRLVTVAVVLVGSLV
+SLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTGPSGRGSSTDHERTESWT
+STQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAA
+QGLLDPARYIEAVLAP
+>MOLHKGIG_01096
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
+>NAFOICDF_01689
+MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGS
+VAAAGVGGWPDGIAIAFAADMLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLM
+AGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARMYVTLNLLTSTIL
+VTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST
+SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGAR
+AVLSWQMVSGIGGIMVGLGLATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLA
+DLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVLAGVAAGRTVTVVLVLVASLI
+SLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE
+RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWS
+VTDQAARGLADPTAYIEAVLGR
+>MHAAABBN_00815
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
+>LFPAFLNI_01045
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001253.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6204cf2546e5a07c2cc3a3e29b01599f5a05e0a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001253.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01800
+MTIAITVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGRGDV
+ETQADALPQAFVLTAIVIAFAITVLLLTLAVTGRDDDAVADGHEAPDPLEQSAADARFPR
+EELRAAAARLGREAEARDGGRA
+>MOLHKGIG_01095
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>NAFOICDF_01690
+MTVALTVGLLMAGAVYLFSKRELLRVILGMVLLGHAANLAILATGGTDRRALPFVDGGPA
+PAGAADPLPQAFVLTAIVISFAVTVLLLVLAVTGRADDAVAAPGERPDVREAAAADARFP
+LAERHAAARTLTGSLPAAPEAGATPEREERA
+>MHAAABBN_00814
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>LFPAFLNI_01044
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001255.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14ab5e219fd4bc02b55b26886ec8c6fb7fbf6ce2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001255.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01804
+MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV
+VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV
+PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVR
+>MOLHKGIG_01092
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>NAFOICDF_01693
+MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD
+IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD
+LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT
+SMDRRLTMREVAQTVVDQIGA
+>MHAAABBN_00811
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>LFPAFLNI_01041
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001256.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4dace523fbc7627345f750fb0a1da39ca7b30d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001256.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01805
+MRHAKIIATFGPATASDETTRSIIRAGADVVRLNMSHGDHEVHAASFERVRRLSVEERRP
+VAIFADLQGPKIRLGRFADGPHHLETGDRFTITTRDVEGTAELVGTTHAGLPGDVRPGDT
+LLVDDGKVRLRAVEVTDTDVVTEVEVGGDVSDSKGINLPGVAVDVPALSEKDEEDLRWAL
+RTGVDMVALSFVRDAADIERVHAIMDEEERRIPVIAKIEKPQAVDNLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGRYPVETVQTMARIIESTETHGLEMIHPLGSRPRTRGGAITRAAVE
+VADQLDIPFLATFTESGDSARRLSRLRPRQPIYAFTHREHTHNILCLTWGVYPKMVSFQD
+STDKMTLQVEESLTSEGIAERGDLVVIAAGSPPGMVGSTNTLRVHRVGDDAGGGSSPARP
+VQKEPVGFWPARSPL
+>MOLHKGIG_01091
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEESRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGTVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPLGFWPARSPL
+>NAFOICDF_01694
+MRHAKIIATFGPATQTDETTRALIRAGADVVRLNMSHGDHEVHASSYERVRRLSVEEKRP
+VAIFADLQGPKIRLARFSDGPHELAVGDRFTITTREVTGSREIVGTTHKGLPGDVSVGDP
+LLVDDGKVRLRAVEVTDTDVVTEVVVPGKVSDNKGINLPGVAVNVPALSEKDEEDLRWAL
+ETGVDMVALSFVRDAADVTRVHEVMDEVGRRIPVIAKIEKPQAVDNLEAIVDAFDAIMVA
+RGDLGVELPLEDVPIVQKRAIELARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVQTVETMARIIESTETHGLDMIHPLGSRPRTRGGAITRAAVE
+VAGQLDIPFLATFTESGDTARRLSRLRPSQPIYAFTHEEHTHNILCLTWGVYPKMVPFAD
+STDKMTMQVEESLTSEGIAEQGDLVVIAAGSPPGKVGSTNTLRVHRVGDGVAADSSPVAP
+EDREPVGFWAAHSPM
+>MHAAABBN_00810
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAIMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGGDAAGGSSAASP
+QTREPVGFWPARSPL
+>LFPAFLNI_01040
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSNNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPVGFWPARSPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001257.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee4346244afb2ec56d0d46ba3ae79c4fc1241fab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001257.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01806
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGEPEPISAQGRHVVILGGGDTGADCIGTA
+HRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDAE
+GRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERGL
+VVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSDH
+GFVLR
+>MOLHKGIG_01090
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>NAFOICDF_01695
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>MHAAABBN_00809
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>LFPAFLNI_01039
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001259.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7683954ab2387d619dfcda20ee9856dc6bb1f21d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001259.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01808
+MKIYAYALSIILGIVLALWLAERRWKARGGPEGRVLDVALWAIPFGFVGGRLYHVFSSPD
+RYFGPGFDGTGDPVQILHVWNGGLGIWGAIALGAVGAWIACRRYGLRLSAFGDVVAPGIL
+LAQAVGRWGNWFNQELFGRPTTAPWGLRVDADHPNFPDGVAPDTLFHPTFLYESLWCLLG
+VAVLLLADRRWRLRRGAMVWAYVAWYTAGRVWIETLRIDDAELVTLFGLTQRLNVWTSIV
+MLLLALVMLAVILVKHGPAAAGPRSDDSVWLPGRGPALEAGAGAPVDAAVAGQGPDDGAG
+STAAGVREDR
+>MOLHKGIG_01088
+MTALASLASPAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG
+GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA
+IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV
+DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG
+RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV
+WRAGHAPEGDDGVAVAAGRSGSHAVGAAEDDAVRR
+>NAFOICDF_01697
+MGSGALTPLAAFPAPVWDGFELGPMKIHAYALCIIAGIVVALWLSGRRWADRGGPEGRVL
+DIALWAIPFGFVGGRLYHVFSSPDLYFGPGYDGTGDPIKILYVWNGGLGIWGAIALGAVG
+AWIACRRYGLRLTAFADVVAPGVLLAQAIGRWGNWFNQELFGGPTTLPWGLTVDPASPNF
+PAQYAPGTLFHPTFLYESLWNLLGVAVLLLVDRRLHLRHGAMLWSYVAWYTAGRTWIEMM
+RIDDAELVTLFGVTQRLNVWTSLLMFAIALAFLIGILLRHRGAAAGPHARQSVWRDGHGP
+VGEDVEGAGPAAAPAVRTTQGGSGSHAWDDVGA
+>MHAAABBN_00807
+MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD
+IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA
+WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP
+AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR
+IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE
+GDDGAAVAAGRSGSHAVGAAEDDAVRR
+>LFPAFLNI_01037
+MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD
+IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA
+WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP
+AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR
+IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE
+GDDGAAVAAGRSGSHAVGAAEDDAVRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001267.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08989876d8f85d34e06bcb37513e6adc74b46d18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001267.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_01818
+MVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTADRATTYDVVTRTAEEVFIP
+LTVGGGVRTEEDVDRLLRVGADKASVNTAAVARPELITEITRRFGSQVLVLSLDARRTQD
+PGCASGYEVTTHGGRRGTGIDAVAWCREASERGAGEILLNSIDADGTRNGFDLEMIRDVR
+AVTRVPLIASGGAGVPEHFPPAVEAGADAVLAASMFHFGPDDMLARVKDALRQAGHTVR
+>MOLHKGIG_01080
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADELTFLDVTASTSDR
+ATTYEVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDAVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
+>NAFOICDF_01705
+MTVAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELAARYGAQGADELTFLDVTATTGDR
+ATMFDVVTRAAEQIFIPLTVGGGVRSVEDVDRLLRTGADKASVNSAAVARPELIGEIARR
+FGNQVLVLSLDARRTRDPGCASGYEVTTHGGRKGTGIDAVAWCREATERGVGEILLNSID
+ADGTRDGFDLEMIRDVRAVTTVPLIASGGAGLPEHFPPAVDAGADAVLAASMFHFGPDDM
+IGQVKDALRAAGHVVR
+>MHAAABBN_00799
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
+>LFPAFLNI_01029
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001268.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d189fbefba3910108536ff031ba61223cd6e9bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001268.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01819
+MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG
+LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE
+AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL
+RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL
+>MOLHKGIG_01079
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>NAFOICDF_01706
+MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG
+LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE
+AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL
+RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL
+>MHAAABBN_00798
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>LFPAFLNI_01028
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001269.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe0867fe6b4a71620915535dacd4f0f1628ec1d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001269.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01820
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGIALEDVYRHL
+>MOLHKGIG_01078
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>NAFOICDF_01707
+MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE
+EISQLLYHVQTMMIAKGIGLKDVYRHL
+>MHAAABBN_00797
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>LFPAFLNI_01027
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001270.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b3711467d2ad7ddf6433ef5072ef0e34cdd6604
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001270.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01821
+MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG
+VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR
+ESLEAAVLTELALRDVQA
+>MOLHKGIG_01066
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>NAFOICDF_01710
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG
+>MHAAABBN_00785
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>LFPAFLNI_01013
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001271.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0340a9287fb1f551d2339a9ad0ac42a676ab08a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001271.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_01823
+MSGAPDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWE
+AARAADPALAALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGG
+GAARLAAHGVRVSGPTGEPAALALTERWRRARDAGRPWITGHLAQSLDGHAAAADGTSRW
+ITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVPVVQGRTPIPA
+GAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLV
+DELMVYTAPLLLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAP
+APEGPDPQEDCMFTGIVTHLGTVLALEPDPAADTARLVLDAGGALEGLPAGGSLAVDGVC
+LTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPTDHLDGHVVQGHVDG
+VGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGL
+IPATLEATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP
+>MOLHKGIG_01063
+MNAAETPSADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDAL
+TRWRAARAADPALATLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>NAFOICDF_01713
+MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAH
+AEVDALNRWAAARAADPSLHVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAV
+ADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRRVRDAGRPWITVHLAQSLDGRA
+AAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVPV
+VMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVL
+GAWLAAGLVDEVFAYTAPVLLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVL
+THLAPVTDPAD
+>MHAAABBN_00782
+MSAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTG
+HDGGGAARLAAHGVRVTGPTGEVAALALTARWREARDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>LFPAFLNI_01010
+MNAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVPVVQGHR
+PVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001272.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24cd50086d0b8c252db70e86ab58de0706d49fab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001272.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01824
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL
+VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR
+>MOLHKGIG_01062
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>NAFOICDF_01714
+MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL
+ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL
+AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR
+>MHAAABBN_00781
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>LFPAFLNI_01009
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001273.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..754289e2e2fd1dcd0722ae9843308935e48c97ae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001273.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01825
+MSPRAPRLHPSILSADFAHLAEELGRIRGADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDIHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGARAGMALKPAT
+PVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGAAAPLALQVDGGVN
+AETIERAAEAGADVFVAGSAVFGAEDPDAAVDGLRRAAARACC
+>MOLHKGIG_01061
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
+>NAFOICDF_01715
+MSAHPCIHPSILSADFARLADELARIPGSDAVHVDVMDGHFVPNLTLGLPVVEAIRAATD
+LPLDIHLMIEDADRWAPAYADAGAESVTFHAEAARAPIVLARSLRAAGAQAGLAVRPATP
+IEPYLDLLPELDMLLIMTVEPGFGGQSFLDVTLPKIRRARQALDGAPVPVRLQVDGGVNR
+ETILRAAEAGADVFVAGSAVFGADDPGAAIAGLRDLAAGVAPACHTR
+>MHAAABBN_00780
+MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAADPDAALVGLRTAAARACH
+>LFPAFLNI_01008
+MTARALRLHPSILSADFARLADELARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT
+DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT
+AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN
+RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001275.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bfca8e9007c06447b18081e1abdcfee66bfbf92
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001275.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01827
+MTATTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPIGRRRVLTPSPVAVVAEE
+AGVPVVKADRLRGPAGEPALEAVRALEPDVAVVVAYGALVPAEALALPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGEPEIAADVFQLEEGLDTGPVHARLTRAVAPDETAGQILADLAER
+GGPLVLELLGRIADGTAAPRPQEGEPSHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTVGEGGEPARFKLDGVAPATPADADWPADLDAAPPGALRTAGRAAWLRTADGAVR
+LGRVQPAGKKLMPAADWARGAADGAALLAGEALAAHTARLGQEAAARAARREAARETEAH
+A
+>MOLHKGIG_01059
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGTVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVRAGDDGWPSVLDAAVPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRDAAARAAARQAARNATEQ
+DEEARA
+>NAFOICDF_01717
+MSIPETALSPDAGSAPARSLRVLFAGTPEAAVPVLRALVGSAHEVAGVLTRTDAPVGRKR
+VLTPSAVARAAAESAPDVPVLKADRLRGPEAAEVLEAIRALEADVAVVVAYGALVPAEAL
+TIPAHGWLNLHFSHLPAYRGAAPVQRALMDGVERTGADVFQLEEGLDTGPVFARIGRDVA
+PEDTAGDLLAALAEDGGPLVLEVLDALAAGEARSVPQTGEPTHAPKLTAADGLVDAAAGT
+REVAARINGTTPEPGAWGWLVPAGEADAAPARLKLGGVVPTHPGEDGWPEAAEAAAPGAI
+VAAGGTAWLRTAGGAVRLDQVQPAGKKPMSAADWARGLTAPVRLLAGDELAAHLAALDAE
+AARRAAQQAAARAAQAGEGA
+>MHAAABBN_00778
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKIDGVAPVRPGDDGWPTALDAAAPGQILVAAKAAWLRTTDGAVR
+LSRVQPAGRKLMPAADWARGAAPGAALLAGEALAHHEDQARQEAAARAAARQAARNATAQ
+DEEARA
+>LFPAFLNI_01006
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+AGLPVLKADRLRGPEGADALQAIRVLEADVAVVVAYGALVPVEALQIPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVSAGDDGWPSALDAAAPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARREAAARAAAREAARNATAQ
+DEEARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001276.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7766078b1d8bc9db052daa75f94687c8ef997edc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001276.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01828
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPRGGTR
+>MOLHKGIG_01058
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR
+>NAFOICDF_01718
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GARPSVSPSAARTTPRRGAQ
+>MHAAABBN_00777
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
+>LFPAFLNI_01005
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001277.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cba71fb0113a6e1f6b1809396f1802c2ce19995
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001277.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01829
+MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE
+SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE
+HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG
+RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA
+NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG
+>MOLHKGIG_01057
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS
+SRPASAEGGDRVTA
+>NAFOICDF_01719
+MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ
+SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW
+DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA
+LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD
+RLQP
+>MHAAABBN_00776
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS
+SRPASAEGGDRVTA
+>LFPAFLNI_01004
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS
+SRPASAAEGGDRVTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001284.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1abdfd9fb21798558093b3f77d17e2d3e84b5db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001284.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01842
+MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVD
+ITEQDGLDVLRHSTAHVMAQAVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLE
+KMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKKNDAATAGEGASVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW
+PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYY
+LKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA
+SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGI
+RARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRFRDGSQDNGVPVDEAIER
+IVRAVREREATP
+>MOLHKGIG_01046
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>NAFOICDF_01730
+MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVD
+ITEQDGLNVLRHSTAHVMAQAVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLE
+KMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKKDDAEAAGEGATVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+KRHAAAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGI
+RVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRYRDGSQDNGVPVDEAVAR
+IVKAVREREVTP
+>MHAAABBN_00759
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>LFPAFLNI_00987
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001285.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41379e84f854e21ac9dbfc0da7151ea3bea76361
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001285.fa
@@ -0,0 +1,109 @@
+>ACLBLIBL_01844
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER
+>MOLHKGIG_01045
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>NAFOICDF_01731
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES
+>MHAAABBN_00758
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>LFPAFLNI_00986
+MSQAAAAGRTAAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDENAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALRRWEAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001288.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa9681c24e484a4ba29bd00d1a0d5afe4b2f4021
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001288.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01847
+MPQKVRGVVARAKDAPVTLETIVIPDPGPGEAVVDVKTCGVCHTDLHYVQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAQELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETVALDEVNEAFETMKAGDVLRS
+VVVL
+>MOLHKGIG_01037
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>NAFOICDF_01737
+MSQKVRGVVAMAKDAPVSIETIVIPDPGPGEAVVDIKTCGVCHTDLHYVQGGIGDDYPYL
+LGHEATGVVSAIGEGVTHVEVGDTVILNWRAVCGECRACKKGEPKYCFNTHNASQKMTLE
+DGTELSPALGIGAFAEKTLVHAKQCTKVDGVDSTEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRALTGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>MHAAABBN_00750
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLPEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>LFPAFLNI_00979
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001290.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3071bae7a438bdca4cbc6317732dd49fec289fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001290.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01849
+MILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA
+>MOLHKGIG_01035
+MTILPASPPPSVILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPDGVIVAE
+GIFAERMPAALDRAEVHYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAMAAGFTPRRKREIIADLT
+>NAFOICDF_01739
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA
+>MHAAABBN_00748
+MILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA
+>LFPAFLNI_00977
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001291.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bc94d7bc32920526b65714c59e57d39b2cd5615
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001291.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01850
+MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+KVVDEHLAVLAAGTSG
+>MOLHKGIG_01032
+MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
+>NAFOICDF_01740
+MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF
+ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL
+EVVDEQLAVLGAGTSG
+>MHAAABBN_00747
+MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR
+DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAGLE
+VVDEQLAVLTAGTAG
+>LFPAFLNI_00976
+MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR
+DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF
+ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV
+VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI
+EVVAEQLAVLGARTSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001292.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff949a76f0d21950e6bc3764c23574581f0d8835
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001292.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01851
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>MOLHKGIG_01031
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>NAFOICDF_01741
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>MHAAABBN_00746
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL
+>LFPAFLNI_00975
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001294.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce2f9ce7c8cf32edf044fb92bf3c0a0550cc83d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001294.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_01859
+MTLTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVQRVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLTYSHI
+GQDISCNLGSMNIAKTMDSPDFGQSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGL
+GQMNLHGYLARERVHYGSEEGVDFTNMYFYAVLFHALRASNKIAIETGERFGGFEDSKYA
+SGEFFDKYTDQEWTPATERVAGLFSDAGITLPTQEDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>MOLHKGIG_01026
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>NAFOICDF_01749
+MTVTEADLIQQAKHMPEAWQDLGYHELNAMLNLYGSDGKIQFEADHAAARQYFLQHVNTN
+TVFFHDLEEKLEYLQEKHYYEPETFAQYAPEFVKATFDRAYKAKFRFPTFLGAFKFYTSY
+ALKTFDGKRYLERYEDRVAVVALHLAAGDEALATHLVDEMISGRFQPATPTFLNAGKAQR
+GELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNVREQGAPIKHIQNQSSGVL
+PVMKLLEDSFSYANQLGARQGAGAVYLHAHHPDIHRFLDTKRENADEKIRIKTLSLGVVI
+PDITFELAKRNEDMYLFSPYDVERVYGKAFSEISVTEKYYEMVDDARIKKTKINAREFFQ
+TLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHVGQD
+ISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGLGQM
+NLHGYLAREHVHYGSEEGVDFTNIYFYTVLFHALRASNLIAQETGQKFGGFEDSTYASGE
+FFAKYTEQEWTPATARVAELFETAGIDIPTQDDWRELQAKVMEHGLFNRNLQAVPPTGSI
+SYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDTYAA
+ATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGCVSC
+ML
+>MHAAABBN_00741
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>LFPAFLNI_00970
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKISARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEYGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001310.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02e2465ddd9403fa88bda256adfc762819a3db6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001310.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01888
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGNGGNGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHRAGKHGESLVIPVPDGTVVKDEQGNIVADLVGEGASYTAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAAIS
+AARPKIADYPFTTLVPNLGVVQAGEVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGTLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLVALNKTDLP
+DGAAMAEMVRAELEGRGLRVFDISALARDGLEALKYAMAGLVTEARERVPEPEPAAPVEV
+PRRHRRKGEHAEFTVRREERNLEPLFRIRGEKPERWVAQTDFQNDEAVGYLADRLQRVGV
+EDALFKAGATPGDAVVIGDDASGVLFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDQRRAARAATRAEMEAERRSGLWTETYDRED
+>MOLHKGIG_01002
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>NAFOICDF_01816
+MAAFVDRVVLHLTAGNGGHGCVSVKREKFKPLGGPDGGNGGNGGDITLVVDHQTTTLLNY
+HHAPHRSADNGQPGMGDHRAGRHGEDVVLPVPAGTVVKDADGNILADLVGEGASFVAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGEERELILEVKSVADIALVGYPSAGKSSLIAAIS
+AARPKVADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGKGLGLEFLRHVERCAAL
+VHVLDCATLDPERDPLSDFEAIEAELEAYAVEPVFSQGGAGVVPLNERPRLVALNKTDLP
+DGREMADLVRAQLEERGLRVFDISALAHDGLESLKFAMAGLVEEARAREPEPEEAPVVEV
+PRRRRRGDQADFTVRREERNLEPLFRIRGDKPEKWVAQTDFQNDEAIGYLADRLQRAGVE
+DALFKAGARPGDAVVIGDDATGVVFDWEPTLSAGAELLAGPRGSDLRLEERTRATRAEKR
+AEQDQRRAARAATRAEMEAERRSGLWTGDPVEEEELD
+>MHAAABBN_00716
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>LFPAFLNI_00945
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001313.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b320099218300cd866d8e3feb6c6203d9a5c1db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001313.fa
@@ -0,0 +1,96 @@
+>ACLBLIBL_01891
+MAANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPER
+TAEAADIEDEAETDTAAEPEPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARD
+ERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDEAVETAEGEQDAETAERGEGAV
+VSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKRQ
+RRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQ
+DSLIGNVYVGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSG
+DTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDH
+LPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIKT
+VRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQ
+LHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQ
+LRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMG
+TGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRRRRRKGAGEGEQAQPAE
+STTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAE
+DQAAEAVEAARQDAAEETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAEAAEA
+ASEDGSRDADAAPAGQAPAADEEEAPAADPVAQAEAAVTAVAEAEADAESGGEEREAEPA
+GDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQEPAQADAGAAGDRARAS
+RAGRVGAARAARVRPGRGRGGRRAASRPAPPPFAPRFERRCRAPGRGPGRRPGVVRPGDP
+VPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRARPAAR
+PELRARRPPSPGAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRAPRRP
+>MOLHKGIG_00999
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
+>NAFOICDF_01819
+MAADESTTQDTHETAEGSTTPVEATEEETAAEVAESPAGEAAEATAAPDVRFDPTNPFAV
+PEGLLPLIEAETVERRRRRPAADPVPEGAADDAHADDEDDEDRPAVSRRRRRRRRGTVDM
+ELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKRQRRRESRSGGRRRTVI
+TEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNV
+LPSMEAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHK
+GARLTSQISLPGRYLVYVPGGTMTGISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEG
+TSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQ
+GEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGG
+SLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFI
+DMVLESNQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCG
+GRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPAEPTAAELTEEERLRAE
+RAAAARTALMSIAKASGKAADEEPSEEAAPRAEDAPEEAADEVRPSPAGDAEEQGESESG
+GRRRKRRGRRRGRGRGGDDAARSAEEQDAPAEHPAEAAGEPAPAEAGAPDPAETATEDAD
+ADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPEEP
+AGAAEAEEALAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATSDGVSAPRPSGMDALE
+AAVDRRAEDAAAAAQRSPATPAATPTAAPEPAPAPVAGEGPAAAAPRRRSRRAVSADGAT
+VQVQEGAAAGGGRFTAQAAQAAPAGETAAPVMLGVGVKAADIVRGE
+>MHAAABBN_00713
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
+>LFPAFLNI_00942
+MAANNEDTTRADERVEETAEQAVTQTAADTAAGAVQPERTPASDDAADAPEEPSAPTLQV
+DPTDPFAVPANLIEVLRTETTSRQRSEDEDDPDTSGRSRRRRRPSREDDRAEEGAADASA
+DAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVST
+ASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQ
+IAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNW
+DAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGI
+SRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASG
+TKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHW
+VPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGN
+LEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRTKH
+QVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEG
+RRRRRRRGNGEGEHAHAAAATTTGAEHADSEDERQRRERAEAARVALHSIAKASGKVAED
+ETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAEAGQPAAADEEETPRRRRRRGRRRSRG
+RAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAAAPEHQDPVVQAEE
+AVAAVAEAEADAEAESPEDAAEQGDRPRRSRRRRGGRGRSRRGGEAASTEADADAEDHGA
+ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVPAEDAPAPRRRRSRRASSDGVVR
+PAAGADASAERTADRTDAAPVEATEPSPEESTDATEVHEQPAAPAAVEEAVMVEPAATEP
+TAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGR
+FTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001316.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c35869f796e0d327ba76667599b57d610c0b5a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001316.fa
@@ -0,0 +1,53 @@
+>ACLBLIBL_01894
+MSGAPAPQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTS
+TARMIEAVLRSYGLRTGRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAE
+LEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGITDATNVADGAVSVVTPISLD
+HTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVEFGVL
+ERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLR
+EGLAQVASPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDA
+PAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLARMAVDAGWPEADVFAAESVPDALEW
+AVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLDPADL
+PRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDES
+WRPERETRAQRAWRPGTRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWF
+IAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVLSGFWEYSMFVVGALFALTWAYAVI
+KGGGMDVENAERDRLQAEWEAEHGQ
+>MOLHKGIG_00995
+MRGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>NAFOICDF_01841
+MSAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNG
+KTSTARMIEAVLRAYGLRTGRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTV
+DAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVGLGGITDATNVADGAVSVVTPI
+SLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVEF
+GVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVE
+LLREGLAQVTSPGRLEVLRTAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQE
+KDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAALAVDAGWPEDDLFITESVPDA
+LEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMDP
+ADLLAAVGLEDDDADAVDPEVLELLDDREEHTR
+>MHAAABBN_00709
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>LFPAFLNI_00938
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+AMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVRMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001320.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b6cb4674c61c96afaa47d753486548deb4dcbd4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001320.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01900
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KAPRQGAAFMFQDAALFPWLTARGNIELALRFAGVPAAERRGRAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFGALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>MOLHKGIG_00989
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>NAFOICDF_01847
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVPAAGRRERAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAAHHDAPAAAALTAAITARLGQEIRRHA
+H
+>MHAAABBN_00703
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNIIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>LFPAFLNI_00932
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001321.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67106496d5c0adf85e0d1adc4750691dc6115469
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001321.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01901
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>MOLHKGIG_00988
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>NAFOICDF_01848
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>MHAAABBN_00702
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>LFPAFLNI_00931
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001325.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fdf4cbb5e1846a45b1109a4cd19c0249068ce25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001325.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01905
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>MOLHKGIG_00984
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+>NAFOICDF_01852
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>MHAAABBN_00698
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>LFPAFLNI_00927
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001334.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23bb9b7823f53c264ee0b93985e665c7d550534c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001334.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01916
+MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD
+LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED
+ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA
+AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA
+VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV
+FAPDGAAR
+>MOLHKGIG_00974
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>NAFOICDF_01863
+MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA
+AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF
+EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA
+ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL
+PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR
+>MHAAABBN_00688
+MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL
+QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE
+EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG
+FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA
+GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR
+>LFPAFLNI_00917
+MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD
+LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT
+EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV
+GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE
+AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001341.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c43617fc862b04dc2dba355d410845c9da8c18d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001341.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01928
+MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV
+AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV
+TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS
+SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN
+VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA
+STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL
+TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV
+LRHPDRAVSPTCTQYLQHR
+>MOLHKGIG_00960
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY
+PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>NAFOICDF_01879
+MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA
+KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII
+MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV
+WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT
+SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL
+LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR
+VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE
+AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER
+VWSQGDVVVLHHPTRPVSATCTDYLRHR
+>MHAAABBN_00673
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>LFPAFLNI_00906
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001342.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce03fa91e65a9e9109926eaecfedfee167d69149
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001342.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01929
+MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS
+TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL
+MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL
+LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL
+LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA
+FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA
+AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR
+EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA
+AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF
+PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV
+VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT
+LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD
+QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR
+MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA
+RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT
+IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS
+>MOLHKGIG_00959
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR
+>NAFOICDF_01880
+MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV
+HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE
+RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA
+ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW
+LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG
+VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA
+EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV
+RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR
+>MHAAABBN_00672
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR
+>LFPAFLNI_00905
+MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001343.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a194303e83b4d4f8aeee3111c7d8092fd2f7300a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001343.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01930
+MSVTTPRPSGSTAGRPAHIGVGGLRADPKVAGGNTWPILVGTLGSLLLVAGSFSVGWLAS
+ASPINRWQWLIPWRTQETGVIVGTILLTLGCWVMFWAWLRLGQTVRPFGRGSLRTVNLAT
+ALWCLPQVFALPIFSRDIFAYVGQGRLMVAGQDPYEDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAVSGDMNPDLAIFLFRLVAVAGVVLIMVFVPLLARRLRVNGAWAQWV
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQSAARSAAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTAGWIRRFVLWFLTAGISFGIMAVVGALNGFGFGWVAV
+MVGTGTGTVPWGPIGILSLLTVGISELVGQGADQQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVLTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDDWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLAIADQVKAISLIVSAVCLAWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RRAPRTPEPGE
+>MOLHKGIG_00957
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGAALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRMGVNDAWAQWI
+SVANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
+>NAFOICDF_01882
+MGVPAAGPSGSTAFRPEYIGVGGLRADPQVAGRPLWPILVGLLGSLMLVAGSFSVGWLAS
+ASPINRWQWLIPWRTQESGVMTGTVLLTLGCWVMFWAWLRLGQTVRPFGPGALRTVNVAT
+ALWCLPMVFALPIFSRDIFAYVGQGRLMVNGQDPYTDAISSLNNWFQLGADATWAGSETP
+YGPVFLWIEEVVVRISGDMNPDLAIFLFRLVAVVGVVLTMVFVPLLARRLSVNGAWAQWV
+SAANPLFTVSFVASGHNDALMVGLALAGTWCALRAGHPRGGQSTASHVGWGVAAVVLVTA
+SLGVKPITLVLLPFIGLLWAGPRAGWSRKFVYWAVTGGLSLALMVLVGRLNGFGFGWLEV
+MAGTGSGTSPWAPVGMMSIATRVLMEVLQLGPDLQAIEGFYKSVCRLLSVLIVLALMFLG
+RQDRVFTRMTWAFTTLVVLSPIVQPWYLLWLLPFFAVIGLRDNWQIKWVVFTVGYFLAFG
+AMDQLFTWQFLDIAEEVRAASLLVSGVSLVWILAVDRKTSRFIKDHWHVRPALREGVRRL
+RRRPTGGAAAPHTRPHPVERLGESGSEDAAARGAR
+>MHAAABBN_00670
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGTVLLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMVAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNDAWAQWI
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
+>LFPAFLNI_00903
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGTALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNGARAQWI
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRALSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLNIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001345.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b62b41cc592b4524902265a9d9886d7d73ee1e96
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001345.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01990
+MSVVKINAITVPEGAGPELEKRFAVRKHAVDAEPGFEGFQLLRPTAGEDRYFVVTTWATE
+EDFQNWKGGRMPAAHAAESEGRPAPVATGAELLEFEVVDLD
+>MOLHKGIG_00947
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFRRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>NAFOICDF_01891
+MSVVKINAISVPEGAGPELEKRFAVRKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHADEQGGRPTPVATGADLLELEVVDLG
+>MHAAABBN_00666
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>LFPAFLNI_00895
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFKGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001346.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf0f98d1477b948a203d3b935cf963ad08d7486e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001346.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01994
+MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL
+NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA
+CRRCEQACADLLAALG
+>MOLHKGIG_00637
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>NAFOICDF_02191
+MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>LFPAFLNI_00594
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>LFPAFLNI_00894
+MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL
+NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES
+CRRCEQACADLLASLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001349.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa2758824f3eb1722230c5152ecfaaab403d7de6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001349.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01997
+MTLEWPRDRRRPTPAKVVAIAESYGYRLLEKRERDHVIELDFERIRDDEGF
+>MOLHKGIG_00941
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>NAFOICDF_01895
+MQTIPVMGWVFPVVLLVIAAAFWLGVRSSGGARGDSDLERRLRERTFTGAPRARLEWPRD
+RRRPTLAQLVRIGASHGYRLVSRTEAEHVYILDFQRVEDDDL
+>MHAAABBN_00660
+MTAMNVFGVVYPFVLLVIAAAVWLGVRSSGRERTHASALEHRLRERTFTGQDRVTLEWPR
+DRRHPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
+>LFPAFLNI_00890
+MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR
+DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001353.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f188ef8591656edb9b605168b5c013e70d873f21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001353.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02002
+MDRMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRDLAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+FAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+VVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAVSGDGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>MOLHKGIG_00937
+MAGMTVSRPAVPASPEHALAPPTLGQVLEVVEGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAKGRLLHTLIEHRIALL
+AAHTNADAVVGGVSDVLARAVGVTGALSPLTASAAGTGAEGIGRVGDLPEETDLAAFARA
+VHAALPATAGGVRVAGGPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASEA
+RETAASGDGRPALVDVSHWASESLWLEHGARALEAALVERGLGVTTLFSDHRSDPWDFLV
+GGERADEGSRA
+>NAFOICDF_01899
+MTVPDHPLQGAGEGACGRAVATDAVASDVPRLSDVLAAVERLWPARLAESWDAVGPVVGR
+AGRPVRHVLWAVDPVQDVVDEAVRIGADLVVTHHPLMLRGTTSVAAVGHGGAFKGEVVHT
+LIEHGIALVAAHTNADSAVGGVSDAIAWRLGLTDVSPLQPSAGGSGAEGIGRVGELPAPV
+PLVEFARTVAALLPATAGGVRVAGDADLPVRRVAVCGGAGDSLFDAVRAADADVYVTSDL
+RHHPASEAREAARHAGGRPALVDTAHFAGEWLWLADGAAALAEELARGGHRARMTVSELV
+TDPWDLHLPSGLAERTTS
+>MHAAABBN_00656
+MAGMTVSRPTVPASPEHALAPPTLGQVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRVAL
+LAAHTNADAVVGGVSDVLARAVGVIGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAAPGEGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>LFPAFLNI_00886
+MAGMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+LAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGVEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+AQETAVSGGGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001355.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfd884be5678409c3762f51ea907efc770434db1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001355.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02004
+MAHILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEASG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQQIVASTPNSIWAQQFANQANVQAHYTGTGPEIWDATEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTELYDD
+VYAASLEESIETSRTLATQEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>MOLHKGIG_00935
+MARILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELSPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANVQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>NAFOICDF_01901
+MAKILDNITQAVGGTPLVRLNSLTEGLPGDVAVKVEFYNPANSVKDRIGVAIVDAAEKSG
+QLTPGGTIVEGTSGNTGIALAMVGAARGYKVILTMPETMSAERRVMLRAFGAEIVLTPGA
+DGMRGAVERAQQIVRDTPNSIWAQQFANEANVRAHYTTTGPEIWDATGGAVDTFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPSDSPILSGGQAGPHKIQGIGANFVPEILDTELYDE
+VYAATFEESIATSRALGAREGILGGISTGAIVSAALKEAAKPESEGKLIVAVVCDFGERY
+ISTALFEDVRG
+>MHAAABBN_00654
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>LFPAFLNI_00884
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001359.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc7878f631a083bc98a82b87afec57b5fc17e050
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001359.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02009
+MLFLQDGQWSILGLFQDELAGKATARTLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAG
+YDREFEEADVAESRDVEPHGRIWILPATDGATVGLKLPGHRRYHDAVAQFADVDAARAAV
+AAIDELLGVGPRG
+>MOLHKGIG_00931
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>NAFOICDF_01907
+MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR
+TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP
+ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD
+>MHAAABBN_00650
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>LFPAFLNI_00880
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001360.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f13444e88273595af2812f4785c36966b60f485
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001360.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02010
+MATTPSVGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGGR
+NVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRRG
+LRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRDW
+ARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLRR
+LNPDLVPEALAVGAPVRLP
+>MOLHKGIG_00930
+MGLLRDLLTRRSARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRAWA
+ERLGEPAPPPVRPG
+>NAFOICDF_01908
+MDPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGGRNVFGNDVGGVFSSPGAPD
+VEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAEGLDLADPEDNMTLGLSLLR
+DSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAAWERRLTARG
+>MHAAABBN_00649
+MGLLRDLLTRRSARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRAWA
+ERLGESAPPPVRPG
+>LFPAFLNI_00878
+MGLLRDLLTRRSARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGF
+RLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRVWA
+ERLGELAPPPVRPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001365.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c02c2f4c994780fb30b8a4737dcb113ebe8f7574
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001365.fa
@@ -0,0 +1,85 @@
+>ACLBLIBL_02017
+MSAAEESSQILSGLTQQFPDKDPQETAEWIESLDGLIEERGTERAQFIMRSLLQRAGAKS
+VGVPMVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAAAIVQRAQKEGIGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALSSYPHPRMMPDFWQFPTVSMGLGPMNAIFQAQTNRYLHNHGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSATKE
+MVADMSDEEIWGLKRGGHDYRKVYAAYKSAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKMTVEDIKVFRDRHRIPVTDEQIERDPYDIPYYHPGKDAPEIKYLMERRKELGGFV
+PERRAKHHSIPVPPEAAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGSRIVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAVG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVIAGTNPAVKHYDPAYSYEIAHIVRQGFEDMYGEHDRGEDVRNVIYYLTVYNEPIH
+HIDEPEDLDVEGLLKGIYRLSEGQGDGPKVQLMGSGVSLPWAVEAQGILAEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSAAPRVPYVTQKLEGAEGPVVATSDFATSWTNQIRPF
+IPNRFAALGADEFGFADTRSAARRYFLIDSHSMVVRALQLLEEEGSVEKGTAAKAHEKYR
+LDDVNAGTTGNAGGDA
+>MOLHKGIG_00924
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDGVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHGLPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHIAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
+>NAFOICDF_01916
+MSAAEESSQIVSGLTSQRPDKDPQETAEWIESFDGLVDERGTERAEYIMRSLMQRAGAKS
+VALPHVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVVNCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVREHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSTYHQIPLPPESVYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHEDGDARRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGGVERGTAAKAHEKYR
+LDDVTAGTTGIAGGDA
+>MHAAABBN_00643
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSASPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
+>LFPAFLNI_00872
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001367.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0073095355048d5daa080efd2d6f9a7bf896d846
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001367.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02019
+MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR
+ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV
+DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHTA
+>MOLHKGIG_00922
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV
+DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>NAFOICDF_01918
+MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ
+PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA
+EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR
+ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV
+NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA
+FIAEHTA
+>MHAAABBN_00641
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>LFPAFLNI_00870
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001370.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02b2d13b55dde1fc83ccc7a91d8175819afe268c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001370.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02022
+MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA
+DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD
+ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH
+VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>MOLHKGIG_00919
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>NAFOICDF_01921
+MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS
+EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD
+ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT
+GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV
+VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH
+VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH
+GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV
+>MHAAABBN_00638
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>LFPAFLNI_00867
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001371.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..323c00e3aeb2952eb04110ddb37d4d470217e995
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001371.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02023
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG
+>MOLHKGIG_00918
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>NAFOICDF_01922
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG
+>MHAAABBN_00637
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>LFPAFLNI_00866
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001372.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaa4beb75993d61cf57a17e7a9a9f082feabfc45
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001372.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02024
+MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS
+GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT
+FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH
+ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL
+DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA
+ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA
+>MOLHKGIG_00917
+MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA
+ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>NAFOICDF_01923
+MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD
+GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA
+PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA
+EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL
+LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS
+SLQTTQRYTHVSVDRLRDGYRRAHPRA
+>MHAAABBN_00636
+MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA
+GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>LFPAFLNI_00865
+MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA
+GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001380.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dceb4641081e36c5f891d030b38c2009f771c15d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001380.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02033
+MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>MOLHKGIG_00909
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>NAFOICDF_01931
+MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>MHAAABBN_00628
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>LFPAFLNI_00857
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001381.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc20fab16b63c58e1e01fba2a8ce569386f3211a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001381.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_02034
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQAPADAGERPVLLVPTPSGERFSQGLARELAQREHVAIACGRYEG
+IDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNPASLVEESHED
+GLLEYPVYTKPADWRGREVPPVLLSGDHGKVAAWRRAQQEERTRARRPDLWEALGRDG
+>MOLHKGIG_00908
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
+>NAFOICDF_01932
+MRIDVVSIFPEYMAVLDVSLLGKARREGLVDVHVHDLRDVTTDRHRTVDDTPYGGGAGMV
+MKPEPWALSLEAVAAASPMAAPAKPILMVPTPSGTPFTQATARELAQAEHLAFACGRYEG
+IDERVFGWAEDLFDVRLFSLGDYVLNGGEVAALAVIEAVGRLVPGVVGNPESLVEESHED
+GLLEYPVYTKPSMWRDREVPPVLLSGDHGRIAAWRRDQQEERTRIRRPDLWAAHHAGSAA
+ED
+>MHAAABBN_00627
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTVDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
+>LFPAFLNI_00856
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001383.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80a45ab5ec2abf1efe2ea0af59a32e1cc6f2eb0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001383.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02036
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRR
+>MOLHKGIG_00906
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
+>NAFOICDF_01934
+MLAEALEHLVRGIVDTPDAVRVASRPQRRGEMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRAR
+>MHAAABBN_00625
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
+>LFPAFLNI_00854
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001390.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7ebed78ba5d4c4e63366d328315134fdf5c79fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001390.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_02043
+MSGTGMAASGPVNTVVVDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANAVN
+TLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSKAV
+SSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVPLL
+ILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFDGQPIVQTAMHL
+NPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEER
+>MOLHKGIG_00896
+MSDTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADFPPMMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEER
+>NAFOICDF_01941
+MTDRVEATSPPVELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNRRHR
+LGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSRSLT
+ARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPVVVA
+LQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFVSQPNVLAVLQLN
+PMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR
+>MHAAABBN_00618
+MADTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADIPPLMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEER
+>LFPAFLNI_00847
+MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTRTIASNLSLTRAFR
+FPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPGVLGLHVILNFGIM
+LLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAIIQLNPLYVLITMY
+RQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001391.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0eb25025c29bd17bd1e3aafbb158e21bce67ab31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001391.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02044
+MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI
+IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL
+RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA
+VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA
+HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL
+VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT
+VSAIAELLGVGERLPAFDGA
+>MOLHKGIG_00897
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE
+AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERLPAFDGGDPA
+>NAFOICDF_01942
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA
+>MHAAABBN_00619
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE
+AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERMPEFAPDDRG
+>LFPAFLNI_00848
+MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP
+RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF
+DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH
+QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN
+PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR
+ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA
+IAELLGVGERLPAFDGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001395.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebc486e0aa737ebb39bbaeca06edab99a74ddbe0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001395.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_02055
+MPELPEAEVVRRGLARWATDAVAGALQVHDPRSLRRSPGGAEALRARLEGARLAEPARRG
+KFLWLPLADADEAVVVHLGMSGQILVDEPGAPDQRHLRLRLPVTAADGAARELRFVDQRI
+FGGWWLDALHPDFAAGGEPIPATAAHIALDPLHPLFDADAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTRRLMAAVQDVMRRALAVGGTSFDALYV
+NVDGRSGYFARSLDAYGRTGQPCRRCAAEGVESRIVREPFMNRASHRCPRCQPTPRRRRT
+ATPADGPARP
+>MOLHKGIG_00880
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAVDGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AAADA
+>NAFOICDF_01949
+MPELPEAEVVRRGMARWASGARAADLDVLDARSVRRSPGGAEALRERLSGAVLAEPARRG
+KFLWLPLEDADDAVVVHLGMSGQVRVDEPGAPDQRHLRLRLPITAADGSDRELRFVDQRL
+FGGWWLDPVVVGPETGDAVPASAAHIALDPLHPDFDPDAVHRRLVRRRSTLKRSLLDQTL
+VSGIGNIYADEALWAARLHPERPTQRMARAQTRAVLAAVQDVMRRALAVGGTSFDALYVN
+VDGRSGYFARSLEAYGRTGQPCRRCTAEGRRTLIVREPFMGRASHRCPVCQPVPRRSPSR
+>MHAAABBN_00602
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGAQLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLMAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGIDSRIVREPFMNRASHLCPRCQPRPRRRRA
+VAADA
+>LFPAFLNI_00839
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDGPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPVAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AVADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001396.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29dbb507cace4b6cdd4021010e562413664c3a86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001396.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_02056
+MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVHPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGADKDSILADTLEALIGAVHVDHGLV
+AASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>MOLHKGIG_00879
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>NAFOICDF_01950
+MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS
+VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA
+DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR
+HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP
+AAGS
+>MHAAABBN_00601
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
+>LFPAFLNI_00838
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001403.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8d5072ea41d90b5f4caa971388c3a9a99df8570
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001403.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_02063
+MGAEVRVTDLPLSEVLDGRLPARLDKELGLATVGDLLDHVPRRWIERGELTPIAALPWDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPAADGAPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTAYRGRITLNNPDFALLDDDVAPGDVDVRPVPLYRATGKLPSWTVRSAVARVL
+ADVDLTRIPELLTPRLRAEAAAALDLDAPLPDTARAYRDLHAPEEVEATGPARTALALRE
+ALVVQAALAWRRDRERAVPAVPRPPRAGGLLDALDARLPFALTPGQAEVGEQLAAELTRD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLALMGPLAEA
+GTLGAGDGPATKVVLVTGSLKTQARREALLALASGEAGIAVGTHALLSDKVGFAELALAV
+VDEQHRFGVDQREALRRSNPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVA
+THVARMDHGPRVIGRVWELIAEHAAAGRQAFVVCPRIDPDDADPGHANVEEMAPRLRSLP
+ALAGLRIEAVHGRMDQAEQDAAMQAFARGETDVLVATTVIEVGVDVPNATVMAVLDADDF
+GLSTLHQLRGRVGRGPDAAVCLLATRLPDEHPSLRRLEVLAQEQDGMRIAQEDLATRGVG
+DVLGAAQSGLASGLRHVDVLRDAPLIAVAADAVGRIMAEGPGLSAHPALAAEVARWESEH
+LTAADYLEKG
+>MOLHKGIG_00872
+MAAEAPVTDLPLSEVLGGKLPARLERELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDVPLPGTAQAYRDLHAPNDVAATGPARTALALRE
+ALLVQAALAWRRNRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRIALVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
+>NAFOICDF_01957
+MAADGVLDLPLGEVLSGRLPGRLEKELGLATVGGLLDHVPRRWVERGELTPIAALPVDAE
+VTVVARVEHVATRRMRSRAGFIVDVTVADPSVAGTAGASLSMAFFNGHDAQRRLAPGVTA
+MFQGKTSLYRGAVTLNNPDFALLDDDVAPGEVDTRPVPIYRATGRMPSWTVRSAVRRVLE
+TVDLDAIPELLTEPIRARATLALGLPETLPGTAEAYRRLHAPDAVEQTGPARTALSLREA
+LVVQGALAWRRSREKAVPAVPRPRRAGGLLEALDARLPFELTPGQRAVGEELAAELSGPH
+PMSRLLQGDVGAGKTLVALRAMAQAVDAGGQAAFVAPTEVLAAQHHRALLALLGPLAREA
+GTLGAAAQEGPGTDVVLVTGSQRSAQRRAALLKLASGEAGIAVGTHALLAERVQFAELAL
+AVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRTP
+VATHVARMAHGPRVIARVWEVVAEHCAAGRQAFVVCPRIDPDDADPAHANVTEMAERLRA
+LPVLGGLRIGEVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAVLDAD
+DFGLSTLHQLRGRVGRGQDAAICLLATRLADGHPSLRRLEVLEATRDGMRIAQADLAQRG
+VGDVLGAAQSGLASGLTHVDVIGDADVIGVAADVVADLMAAAPGLSAHPALAAEVSRWEA
+AHLTAADYLEKG
+>MHAAABBN_00594
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPHDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRPGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRVALVTGSLKTTARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRSLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLRHVDVIADAPLIAVAADAVTRVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
+>LFPAFLNI_00831
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARE
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+CTLGAGDGPATRVVLVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVAQMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQVEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001406.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d43c02738374d51ff09a10af099c46b67035d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001406.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02066
+MESRPLRPLRRLVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGDAAL
+RPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGRDPA
+VEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG
+>MOLHKGIG_00869
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG
+>NAFOICDF_01960
+MPRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGGQDRRE
+TDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGRTPAVE
+AVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG
+>MHAAABBN_00591
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG
+>LFPAFLNI_00828
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001410.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e510a9f4c0f2d525a228eb842eace478070f854
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001410.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02070
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNTPSVLRSIPEIKDVDVVSSLLEI
+HGVSVEWDKESGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVTEMRGYNHEALPDRNE
+SASWASAALATGGDIFVRGASQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEIDIPDLRGGFSHLIAALAAEGTSTATGLEIINRG
+YEHFMDKLQGLGADVELSDRTR
+>MOLHKGIG_00865
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVELTERDR
+>NAFOICDF_01964
+MAKLLTIHGGKPLQGEVTVRGAKNLVPKAMVAALLGTGPSVLRSIPEIKDVDVVSSLLEI
+HGVTVDWDKESGTITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIHVLQKMGAIITVQTDRTIRIEGVPELRGYNHVAIPDRNE
+SASWASAALATKGDIFVRGASQRDLTAFLNTYRKIGGEFEVTDEGIRFWHGGGELNPLVL
+ETDVHPGFMTDWQQPLVVALTQATGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVDFDVPDLRGGFSHLIAALAAEGTSHATGLEIINRG
+YEHFMAKLQGLGADVELSERPR
+>MHAAABBN_00587
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPKPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVELTERDR
+>LFPAFLNI_00824
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVEPTERDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001415.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c022dae7e11175b1bb97ae416e800267b2cc104
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001415.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02075
+MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT
+LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA
+ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA
+AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT
+GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA
+LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG
+>MOLHKGIG_00860
+MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARAPAGHRPLPGSGWDPFAG
+>NAFOICDF_01969
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL
+TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL
+ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA
+LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG
+>MHAAABBN_00582
+MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
+>LFPAFLNI_00819
+MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001416.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dc5f86c7f4a1cf2ccf9c8b95535bd78abe9afdf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001416.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_02076
+MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSV
+RDRDTVLASLRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADV
+AARARDLDAASGEGEPAGVGPGDEQRLGRDLATAGGVPAVVRAVEGSYRLRSAKQTSWPV
+LRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQKAVVDGAVRTL
+VTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLAL
+LTAVVGAGWLGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRIT
+AASRGRRARRRLEEGTTDVGRRLVVDPVRAEVDRFHAFRDAVARAAGATARRGRR
+>MOLHKGIG_00859
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHAR
+RRLEEATTDVGRRLVVDPVRAEVDRFRAFRDALARASGAPVRRGRR
+>NAFOICDF_01970
+MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGA
+TGSGKSSLFNALTGRELAGVAATRPTTSEPLAAVWGVGRGENLDGEGGGAAALLDWLGVR
+RRHLLDDAPVLDGGRPVFLGLGHREGADATGLILLDLPDIDSVQRSHRDVTARLAGHVDV
+LVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLASLRRMLSGHG
+MGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAG
+AGDDDAVRLGRDLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLL
+PERAVARRDRDPVDRDPALHRTSLPERTQTQRAVVEGAVRTLVTSASAGASEPWAASVRR
+AGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGWLGAYALAAW
+LQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVR
+VGRELVVDPVNAEAARHREFRSALAAAQGSGVRSRSRR
+>MHAAABBN_00581
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGTGAS
+EPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVERFHAFRDALARASGVPVRRGRR
+>LFPAFLNI_00818
+MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGA
+TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA
+ALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATGLILLDLPDIDSVERGNREIT
+SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS
+LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA
+ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA
+DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS
+EPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW
+LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR
+RRLEEATTDVGRRLVVDPVRAEVDRFHAFRDALARASGVPVRRGRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001417.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..891468e9ca87746eaabb2a7fd41282584d83ee1c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001417.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02081
+MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ
+LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR
+HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG
+TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY
+MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP
+EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE
+REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD
+ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR
+DSALARLDRFAAEQGLDQGLPTDA
+>MOLHKGIG_00853
+MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA
+>NAFOICDF_01976
+MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH
+TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE
+VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW
+RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE
+DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI
+PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE
+PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE
+IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG
+PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA
+>MHAAABBN_00575
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
+>LFPAFLNI_00812
+MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG
+TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE
+KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR
+MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL
+SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG
+LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD
+FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT
+AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR
+VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001423.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a93a2c126077faa46b34ec6817cfe2b8e5884ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001423.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_02088
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD
+VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL
+EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH
+VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL
+PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA
+VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM
+PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE
+A
+>MOLHKGIG_00847
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>NAFOICDF_01988
+MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA
+QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD
+VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL
+ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV
+WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV
+MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK
+NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF
+HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS
+SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG
+>MHAAABBN_00569
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>LFPAFLNI_00806
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001427.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1423b42734bc33c120303bd2e9a40d7a65702214
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001427.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02093
+MSTTPRDARAAVPPVPTPASRPEEQARPQERRPAVRPDTVEPRVPGEGNRVKPTLMTGSE
+GIIRALEELGVTDVFGLPGGAILPTYDPLMDSDQIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGSDAFQEADIVGITMPITKH
+SRLVTRPEDIPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRVDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDA
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPCARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLAAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRISALSGPEAAYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>MOLHKGIG_00831
+MSTTPRDARAAVPQVPTPASRPTESARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAVADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAERTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGDVKEIIPDLVAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>NAFOICDF_01992
+MSTTPRATAPAASAGRDQRGPTRTETVEPRVPGPAAVVEPTVMNGAQGIIRSLEELGVED
+VFGLPGGAILPTYDPLMDSSRIRHILVRHEQGAGHAAQGYHLAGGRVGVAIATSGPGATN
+LVTAIADAHMDSQSVVFITGQVSSAAIGSDAFQEADIVGITIPITKHSRLVTRAEDIPAA
+LAEAFHIASTGRPGPVLVDVTKDAQQSEFEFSWPPRLDLPGYRPVLRGHPRQIREAARLI
+REARRPVLYVGGGVARGEAHEELRALAALTGAPVVTTLTARGVFPDSHPQHLGMPGMHGG
+VPAVAALQQADLLITLGARFDDRVTGHLPSFAPGAKVIHADVDPAEISKNRLADVPIVGS
+VKEIIPDLVAELGAGADLPDLAPWWATLERLRETYPLGFTAPDDGLMAPQQVISRISALS
+GPEAVYVAGVGQHQMWASQFVEYERPRQWLNSAGLGTMGFSVPAAMGAKVAQPQRTVWAI
+DGDGCFQMTNQELATCVINGIPIKVAVINNSSLGMVRQWQTLFYDQRYSNTDLNTGHGTA
+RIPDFVKLADAYGAAGLRCEREEDLDDVIRQALEIEDRPVVVDFVVSRDAMVWPMVPAGV
+SNDAIQIARGMTPDWDHED
+>MHAAABBN_00563
+MSTTPRDARAAVPQVPTPASRPTETARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLVREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGTEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGYDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>LFPAFLNI_00801
+MSTTPRDARAAVPQVPTPASRPTETARAQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001429.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7ed797056fee0729345bd248232ed849856ca14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001429.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_02095
+MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW
+FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD
+LHAR
+>MOLHKGIG_00827
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ
+VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE
+TDATDVTPPDLHGV
+>NAFOICDF_01994
+MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV
+AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD
+AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV
+>MHAAABBN_00559
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH
+GV
+>LFPAFLNI_00796
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR
+GV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001433.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2da02029dd1a4f46722c3a9552ee78d8ba219482
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001433.fa
@@ -0,0 +1,98 @@
+>ACLBLIBL_02109
+MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE
+EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR
+GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV
+SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD
+QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY
+SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS
+VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP
+ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA
+LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA
+GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD
+IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE
+EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA
+SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE
+QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG
+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL
+AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE
+QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG
+RLRARLGGLVGRARRA
+>MOLHKGIG_00821
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM
+TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA
+>NAFOICDF_02000
+MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV
+DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL
+PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE
+EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE
+QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA
+PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG
+LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR
+VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE
+LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL
+ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS
+LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA
+LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG
+VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR
+LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA
+DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN
+SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR
+RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA
+SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA
+GPAAAAHPAPAGRLSRRRGWRGWIRRATS
+>MHAAABBN_00553
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
+>LFPAFLNI_00790
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRAPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001435.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0efe172b4c439e595a6db50a0df34fdd748543b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001435.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02111
+MLLLHTSDWHLGRSFHGTGLLEGQRQVLDALVDTVRERGVDAVLLAGDVYDRALPSADAV
+ALLDATLARLREAGAQVVLTSGNHDSAVRLGFGAGLLSAAGVHVLTDPARLDEPVLLEDA
+AGERAAVYGVPYLEPRHLGQAWEVDPTHTGVMTEAVRRIRADLEDRRAGSPTPLAGVVLA
+HLFAAGGDASDSERDIGAGGSSWPASPAPADPAGRDAGCGAEPEGLVGTLGQVPVTVFDG
+LDYAALGHLHGRQTMAEHVRYSGSPLPYSFSEAKHVKGGWLVHVHGGAVTEVEPVDWRAG
+RRLAVLADRIGPLLDSPEYAFAENRWVQATVTDPERPEKALERLRSRFPHLLVFRHEPEG
+GRPERVRTYAQALRQAPTDLALTTGFVDHVRGRPASAEESALLDDALTASRTREAQA
+>MOLHKGIG_00819
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAVELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA
+>NAFOICDF_02002
+MLLLHTSDWHLGRSFHGTGLLDSQRRVLAQLVDTVRERGVDAVLLAGDVYDRALPAADAV
+TLLDETLAALRAAGSQVVLTSGNHDSAIRLGFGSALMAAGGVHVRTDPERLAEPVLLEDA
+AGERAAVYGIPYLEPRHLGEAWGVDPHHTAVMTEAVRRVLADLEERRAADGPLAGVVLAH
+LFAAGAEGTESERDIGEGPHTDAHGTAPEGLVGTLGQVPVSVFSGLDYAALGHLHGRQTM
+APHVRYSGSPLPYSFSEARHTKGGWLVHVAGGAVTEVESVDWDAGRRLAVLEDRIQPLLD
+SPGYAWAEDRFVQATVTDPERPEKALERLRSRFPHLLVFRHEPEGGHAARERTYAQALRQ
+APDDLALTTGFVDHVRGRPASEAERELLDEALTASRIGEAQA
+>MHAAABBN_00551
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFAEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASEAEQDLLRDALEAARAAEVRA
+>LFPAFLNI_00788
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001436.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12cb975e2ef6c486c29903607dc3c76f9031616c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001436.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02112
+MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL
+AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP
+DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG
+MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS
+LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR
+HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA
+EREVVAEAARRWSAATT
+>MOLHKGIG_00818
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>NAFOICDF_02003
+MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA
+VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG
+APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV
+PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG
+EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR
+AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE
+VVAEAARRWIAATT
+>MHAAABBN_00550
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>LFPAFLNI_00787
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR
+AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA
+SVPGWVAEREVVLEAARRWSAATT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001438.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..714a3882093c57886e1d7f91880b5640bdb46f80
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001438.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02114
+MSGAATGVPEGARVVLATHNAGKVRELRQLLEGAVPGLDASVAVVDAGAVGAPDIVEDGV
+TFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLELLLA
+QLADVPDAHRGAEFVCAAALAVPSSADARGTHAIHVEHVEHGRLRGTLLRAPVGDGGFGY
+DPILRPDGRDESTAQLSAADKNAISHRGHAFRALLPYLVDALDARA
+>MOLHKGIG_00816
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLEVETAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
+>NAFOICDF_02005
+MSTPTAPVAPAGARVVLATHNAGKVRELRSLLAEALPALDVETAVVDAGAVGAPDVVEDG
+VTFEQNALKKARAVAAHTGLIAVADDSGLAVDVLGGAPGIFSARWAGRHGDDKANLELLL
+AQLGDVPDEHRGAAFVCAAALATPRGGDHVELGRMPGMLLREPVGDGGFGYDPILRPAGE
+DRSTAQLSSAEKNAISHRGQAFRALLPHLVAALSADS
+>MHAAABBN_00548
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
+>LFPAFLNI_00785
+MSAPASSSAGLPEGARIVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001439.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02dfa6b88c5c9f109c49373a592ece612bed0838
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001439.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02115
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA
+>MOLHKGIG_00815
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
+>NAFOICDF_02006
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA
+>MHAAABBN_00547
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA
+>LFPAFLNI_00784
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001443.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e60d14bbe0ddd0a7bbfd0afbc1308053273afcc2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001443.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02119
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+>MOLHKGIG_00811
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>NAFOICDF_02010
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED
+>MHAAABBN_00543
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>LFPAFLNI_00780
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001446.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83c116263158fb40b912403785ef93737ca7d798
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001446.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02123
+MAERRSSASGTPDGAVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALEKYLETGPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGSEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGDGIREA
+FEPAARRLALTGTPFRSDTSTIPFVEYVDGPDGLSRSKADYTYGYGPALRDHVVRPVLFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPKGEWIPAVLRAADRRLSEVRR
+GVPDAGGLVIATDHEDARAYAAQLEALTGQRPALILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLANE
+MELERDHALDRREGGVDVEDLEDAPEEDLLAQANREESGSDALLRGKFEAMESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQVQRRPKAPAKEPADVV
+DHRRMKELRSELSKTVSAWSARSGTPHGVIHNRLREVSGGPAVAQASRDQLEKRLSTLRG
+WFVGRT
+>MOLHKGIG_00807
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLTVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGADGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIASDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWATRSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
+>NAFOICDF_02016
+MAEGRSETSGAPTPDGIQPDLFHVGEDLPPALPERAAWGTAPKLRQWQQEALEKYLREAP
+QDFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGLAIDPN
+FKNADGRHGPEYRGVALTYAQVANKPVLHRNRTEAARTLVILDEIHHGGDARSWGEGIRE
+AFEPASRRLSLTGTPFRSDDAYIPFVRYERGEDGFERSRADYTYGYGPALRDHVVRPVIF
+LAYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEIR
+RGIPDAGGLVIASDHEDARAYAAQLQAVTGQAPAVILSDDKGASDRIEEFAASDERWMVA
+VRMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLAN
+EMELERDHALDRREGAVTVEELEDLSQAPEEDLIAEANRAERGSETLTRASFEALESRAS
+FDKVLFDGGEFGLGGDVGSEEELDFLGIPGLLDAEQVSELLRQRQNEQIRRKPAAAPKES
+RDVVDHRRMKELRAELSTTVSAWSARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLE
+TLRGWFVGRR
+>MHAAABBN_00538
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
+>LFPAFLNI_00774
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVDVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAVEPADVV
+DHRRMKELRAELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001447.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..584c9fbc514fc8e9a54054f3a0ffbac8671a8ee9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001447.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02124
+MSVTGEPDLTDPFSPAGGGTSVLEREQQLQDVEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPQKFPVCPTCQEIYEGLREPQDGDDAGAGGGRRGGWFGGRGRG
+>MOLHKGIG_00806
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>NAFOICDF_02017
+MSISDPFQNDPLSPSGGGTSVLEREEQLQDVEPGDHERFAHYVRKEKIMESALSGEPVIA
+LCGKVWVPGRDPNKFPVCPLCQEIYDGLRDPQDGDDAGSGGGRRGGFFGRGRG
+>MHAAABBN_00537
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG
+>LFPAFLNI_00773
+MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI
+ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGKRGGWFGGRGRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001448.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd7e8f8e95b41ce01f5aeebd45fc9516f4afe0ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001448.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02125
+MALTLVRLRWALTLNQWRRSTFTLVLAVLGALYVLGLAVFVVVMLVTFLPDAWVVDRGTV
+TVIVASALALGWLLIPPFITGVDATLDPHSFVLFPVRARTLIAGLTLSAFTTPSGLATLI
+VMLGTGLSWWDIPAALAAALVGGALTAVTAVASGYGLAGLMAAYAGRRRVREVLSIALLI
+PVMLSGVIVAQTLDSLGDLFDVAPRVAAVAAWTPFGAGPAAAWAVAEGQGLRAAAHLLVA
+AAWCLAALALWHLAVRRTVEPVAVGGGSAREAGRADGAPLRWLGRPATGPRTAIAARAQR
+YWLRDPRYAAGLVMIPVLAAVLWFASTAGGDAGPGLGMLTMLGPVSAWALAYSISADIAY
+DHTAFHLHVVSGVRGADDRWGRVMGLAGWGVPALVVLTVATTAAADRWDLLPALLGLTLG
+LFGVTAAMSAFVSARFVYPVPKPGESPFKTPQGATMRIMLVQGAAMLVVVPLAVPVVVPF
+VVALVTQSAVWGWATLAVGLAWGAVALWLGVRMGAAWYDRAQAETYQAVAAF
+>MOLHKGIG_00805
+MALTLVRLRWTLTLNQWRRSPFTLVVSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLVAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPAGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSRAVASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAAALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGGSRRVGAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVVLWFTGGLASGGGLGPGLLLILGPMTAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFLSARFVYPVPKPGDSPFKTPQGAAMRTMLVQGASMLVSLALAVPFLVP
+FIVRLATGAAVWGWVTVALGFAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
+>NAFOICDF_02018
+MALTLTRLRWALTLNGWRRSTLTLVLSVLGALYFFGMAAMAVAALVVGLPEAELPVRGAV
+TVLVAAVVVLLWTILPPLVTGVDATLDPSSFVLFPVPARTLVAGLLLSTFTTPIGALTLL
+GLLGVAASWWDTPAALAAAAVGAVLSAVTAVCLGYGVTGLMSSFTGRRRVREAISLLVLI
+PLMLGGVALSRVMQSIDDLLWLGPVLANAAVWTPFGAGLGAGWAAAEGRWGLAGLRLLVA
+LAWAVAAAALWMLAIRRTVEPAAVGSTDSAAPRGDRATDLRWLGRPATSARTAIAARAQL
+YWFKDPRYMASLVTVPLMFVLLWFMGTSGPEGATAILLAAGPVTAWALGYSLSADIAYDH
+TAFHLHVLAGVKGIDDRLGRVMGLLGWALPVVAGVTLATVAMHGDWSVLPAILGVSLGVL
+GACLGLSALVSARWVYPVPKPGDSPLKTPQGAAMRIMLVQGTSLLVTLVLLVPMAVPFVV
+LLVTGAAVWSWVTLAVGLAWGALALWLGVRAGAAWYDRAQAETLQAVQSW
+>MHAAABBN_00536
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSQAIASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPMPLRWLGRRATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAAEGGPGLGLLLILGPITAWSLAYSISADIA
+YDHTAFHLQVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWVTVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
+>LFPAFLNI_00772
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAVGLVGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGLALSRAIASFEDFLAIAPQIARGAAWTPFGAGPAAAWAVAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAGEGGPGLGLLLVLGPITAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWITVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001451.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc3c12a9a7b744db6bd60bd6394d8a9507c69b1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001451.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_02128
+MEPVDPTAAPASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEH
+PEPEPTGEPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGL
+DPLVRRVESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMT
+SAWFIELDQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTL
+YFLASLPHMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAV
+AGTPFAVLLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYV
+VSPRVMARAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR
+>MOLHKGIG_00802
+MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIPVEPAGAAAAPPSHGPTPAGRRRRL
+RLGSVLRRRRPFLEEDRVDPEPDPADGAEDPAVAAVALESPVLTGFLLAVGVTLAIGIVS
+VLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPRWVGVLTAALGLAAVAGAFVALLVP
+TVIEQSTQLVQDLPAIIDGVMRAEWFVQLDEEFHLQEAVRAQTERLAADGVAITDLFGGL
+LGLGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAYRLAPRSRRPRIEALSEQITSSVGH
+YVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAAFMAFIPLVGAAIGGTLLTLVSLLT
+SWQTAAVFAAIYFVYLQIEAYVISPRVMARAVPVPAAVAVIAVIAGGALLGVLGALMAIP
+LAAALALLVREVFIPRQDAR
+>NAFOICDF_02021
+MDHIEDSPAPSGPSRGARRLRLGSLVRRREAFLPNERVDPLPPGSPDAAPAEPEVPELAL
+RAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLVERWGAPRWV
+GVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREVDRQLQIQHA
+VQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLPHLKYWGYRL
+APRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPVLLAFVAAVM
+AFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMARAVAVPAAV
+GVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR
+>MHAAABBN_00533
+MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR
+>LFPAFLNI_00769
+MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP
+VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV
+ALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRVESWGAPR
+WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ
+EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY
+RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA
+FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA
+AVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001461.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c0dc54dbf6e7c17f3392e4c71e915a4cee9ccb3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001461.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02138
+MISNGLILAAGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGGLA
+KAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISEQA
+QAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSAGV
+AE
+>MOLHKGIG_00793
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>NAFOICDF_02031
+MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG
+LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE
+QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA
+GVSE
+>MHAAABBN_00524
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
+>LFPAFLNI_00760
+MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG
+LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE
+QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA
+GVAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001462.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bc52e35cd701dc17a928183a9bad8b4832cc73a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001462.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02139
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>MOLHKGIG_00792
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>NAFOICDF_02032
+MEISGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIN
+>MHAAABBN_00523
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>LFPAFLNI_00759
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001465.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b209ad34bdad2c186684eed3506c78763de5d2af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001465.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02142
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEEGA
+>MOLHKGIG_00789
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>NAFOICDF_02035
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA
+RAARPASRPDAQPKDQP
+>MHAAABBN_00520
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>LFPAFLNI_00756
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDAAAHPDERGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001467.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36580bb8a8aa979bdc44afabc0746dae377188e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001467.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02144
+MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA
+AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV
+FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER
+RLAALGGDA
+>MOLHKGIG_00786
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>NAFOICDF_02038
+MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD
+ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE
+AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH
+EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV
+NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ
+VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG
+EEAR
+>MHAAABBN_00517
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>LFPAFLNI_00753
+MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001469.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34814a88e7d48f16da5bfd00322e132de9d8d240
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001469.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02146
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG
+>MOLHKGIG_00784
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>NAFOICDF_02040
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG
+>MHAAABBN_00515
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>LFPAFLNI_00751
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001470.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..905a8407911f4847bf35f7957400b042c3990301
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001470.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02147
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA
+>MOLHKGIG_00783
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>NAFOICDF_02041
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT
+>MHAAABBN_00514
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>LFPAFLNI_00750
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001472.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92c55dc9a071e447e1f53df3b4a33acbded768bd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001472.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02149
+MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV
+RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF
+AREADPRLGR
+>MOLHKGIG_00781
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+ARETDPRLAR
+>NAFOICDF_02043
+MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP
+ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA
+AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE
+FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP
+AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL
+GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS
+VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV
+GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE
+IVRRETLDDLLRREVDPQNPA
+>MHAAABBN_00512
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF
+AREADPRLAR
+>LFPAFLNI_00748
+MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+AREADPRLAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001473.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e07a4c407901e461f7d6689a423995d21c4b43d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001473.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02150
+MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA
+ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>MOLHKGIG_00780
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>NAFOICDF_02044
+MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ
+AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV
+FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ
+DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD
+RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS
+QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS
+AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV
+LRNGLGLLGVSAPETM
+>MHAAABBN_00511
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVSAPEKM
+>LFPAFLNI_00747
+MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK
+AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND
+ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV
+FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ
+DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD
+RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN
+IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS
+TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA
+AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV
+LANGLGLLGVTAPEKM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001476.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea165d23eeea44ec561e6f90aec0b89acb018f47
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001476.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02153
+MSTLTLTLNGEPAELAAATVRDVVAHVTGRAIGDDGAAADARRLGVAVAVGGEVVPRSAW
+ATRELTAGDEVDVVTAVQGG
+>MOLHKGIG_00777
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGEDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRELAAGDEVDVVTAVQGG
+>NAFOICDF_02048
+MSALPLTLNGEPAELDGPTVRDVVEHVTGRTVRDDGAAADGRRLGVAVAVDGEVVPRSAW
+AARTLAGGEAVEVVTAVQGG
+>MHAAABBN_00508
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG
+>LFPAFLNI_00744
+MSTLPLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001477.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0ddc3cf5b5af28daa69663db790ce153afdf01a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001477.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02154
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVGLLAVFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAAFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPAGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTCAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>MOLHKGIG_00776
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>NAFOICDF_02049
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDALAPLLHAGWKGWPLLVDLLAGFSDVGTGFRTEGSWIVAADPSDVLAWEHVLAHAS
+ALGRRVEPVAVRALRRAEPALAPGLAAGFDAPDDHQVDPRRAAAACLAALVAEAGPDGGP
+LPAGAGPAARLVSGTVTSADPVGSGVGLTLADGGILTADGAVLAAGLGHRGIGGAATAEV
+PLRPVHGDVLRLRVRPEQLLPGEDHLITRTVRGLVHGRQVYLVPRADGTLVVGASAREDG
+LAGTSAGSVLDLLADAAAILPAVRECELAEVTTAARPGTPDDAPRVEVVPGAPVVVATGF
+HRHGILLAPWAAGRVLDLLTALPKETA
+>MHAAABBN_00507
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>LFPAFLNI_00743
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPTGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHAHLKEIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001478.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88bd95b4961e976305bbb94518c0532cb49a7d3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001478.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02155
+MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG
+QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART
+LRAGLPG
+>MOLHKGIG_00775
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>NAFOICDF_02050
+MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE
+LRAGLPA
+>MHAAABBN_00506
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>LFPAFLNI_00742
+MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001485.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cab216e7d05cea786f6b2d4968c7eda5b3bb981d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001485.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02164
+MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL
+MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD
+DAAARLRAALRELGHGEVVPQD
+>MOLHKGIG_00765
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>NAFOICDF_02060
+MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL
+TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD
+EAAAAIRAGLREDGHGDVVPQD
+>MHAAABBN_00495
+MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
+>LFPAFLNI_00729
+MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL
+TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD
+DAAARLRAALRDLGHGEVVPQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001489.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0c5475a847d223f787ff788f3e57f006fcd2908
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001489.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02170
+MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG
+ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV
+APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR
+AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF
+AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG
+GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE
+>MOLHKGIG_00760
+MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV
+IEVYESGVGPKDTPEADYAEAMLANARTLADALEG
+>NAFOICDF_02065
+MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ
+LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL
+DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA
+ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS
+AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG
+GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG
+>MHAAABBN_00490
+MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG
+>LFPAFLNI_00724
+MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ
+LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001494.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a184cd47d08d535a593de1b461a099f20c0bb11d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001494.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02175
+MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER
+WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT
+PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>MOLHKGIG_00755
+MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>NAFOICDF_02070
+MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER
+WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV
+PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL
+IAWLVLHRGWYQWLGVPEPTA
+>MHAAABBN_00485
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
+>LFPAFLNI_00719
+MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER
+WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT
+PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL
+IAWLVLHRGWYQWLGLPEPTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001499.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56825bbc0deb464151515c0ae661b42e928ebabb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001499.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02180
+MERPENPANRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLVDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRISVSGVDDVADASLSFSSIEGWRER
+GAIREFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHEDVLARLRPSGGGED
+>MOLHKGIG_00750
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGVVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEDSA
+>NAFOICDF_02075
+MDQTWNAARDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVSDADRAAEESI
+RSTLSRARARDLILGEEFGGNLSRTGRQWVVDPIDGTKNFVRGVPVWATLIALLIDGEPV
+VGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRIQVSDVDRVEDASLSFSSIEGWRERGAV
+REFLQLTSDVWRVRGFGDFWSYMLLAEGAVDVATEPELALHDMAALVPIVREAGGRFTSL
+DGEEGPFGGHALATNGLLHDEVLRRLTPGQD
+>MHAAABBN_00480
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFMRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGEEAEGGA
+>LFPAFLNI_00714
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEGGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001501.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38a6d396bade924d9944db459797594dec4da216
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001501.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02185
+MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL
+GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD
+>MOLHKGIG_00744
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD
+>NAFOICDF_02083
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG
+DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>MHAAABBN_00475
+MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>LFPAFLNI_00709
+MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001510.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2885b2bf87db2d7b98e8dfed68c0303384a6d457
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001510.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02196
+MVSVVGGRVDYSVVGLQNPMRISEMPGKTAKITVSGRMPNTRGSITRTGYSYSMTSKRAV
+IYTRISRDDRGVEAGVTRQEEDCRAKAAGLGFEVVRVYTDNDIGASTRSRKVRPEYAQML
+EAARRGAFGAILAYSTSRLTRRPREAEDLIDLVERHGVQIKTVVSGDWNLETADGRAVVR
+TLAAWDAAEAERTAERVARACEQRAAEGRTHGAVPYGWTRDADGTEHLHPERAQVIRDAA
+AHVLEGGSLRSFTLDLNARGVGSPRGGKWTAPQLKQLLLRERNAGRLVRRDPNNPRHRPV
+VGKGIWPQILDEETHDRLVAHLTDPTRRKSRGSELKHMMSGILICGVCGARCRLMPGGKS
+PDGTPRPPSYGCRECFGVKRRVAQVDEWVSYMARVRLAEKDAPALLAGDDEGARKAQRER
+DEARAKLDRAADAYAEGLIDSHQLTRISANLHKKREDAEARLARARPLGGLSFDRGASPV
+QVWRRAPVAVRRTLVEMMMTVTLLPGGRGSRFDPEQHLRIVMNDLKTSVSDILVTSGTVP
+DRPTGSEDSDPPRRE
+>ACLBLIBL_02198
+MQVEEDDRRVVAVVEDPVREPVVCEAARRVLAGESLNSIARALNERGAPTAATDREEASR
+LWTASKVRQMLQRPGYAGLRVYRGEGVGKAAWEPLIEREQWDELQALFESSRAAQGPQDH
+RAAYLLTGIARCGVCGSKLVRRATRSGKVVRKDGTVAPKRRYDTYACAAGIDRAGAGFHV
+SMSMVHLDDYVSRLVVERLSRPDVLECLAGTEGTQSDERVALRAEIAGYREHLERARAYA
+AEHLRMDLLIDQEARLQPKIDTAERRLRELAAVDPEVRRLAEAADVRATWDALDLEGQRH
+VVRVRMTPSVLPRTRPGRRGLDPERVDVTWLSDCLESP
+>ACLBLIBL_02372
+MVELVSLRKTNEVAAYVRASMDRKGDRWTVETQLRKIRALAEAKDWEVVEVYDDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNDRRRAEGIPASSWKAFGWTREGELIEAEADA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSAFSVDAVRYLLANPLYAGYIKHYASG
+ELYPVQGDAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEDDGPDREALLT
+ERNALVERVKELSPLLLDVRQPVLEITEAIRGGKARIDQIDAEILDRSVSVAAKLLGDVD
+ESLGTMERREVVESKWKALDMDRRRMLVDELVTVTIEPIAPGHVKFDPDLIRIEPRRD
+>MHAAABBN_00303
+MVELVALRKTNEVAAYVRASMDRKGDRWTVDTQLRKIRALAEAKDWNVVEVYEDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNERRRAEGIPASTWKAFGWTREGELIEEEAAA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSEFSVDAVRYLLANSLYAGFIRHYKTG
+ELYPVQGEAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEAAGPDREELLT
+ERNALVERVKELSPLLRDIHQPVLEITAAINDVKARIDEIDAELLDRSVSVAAKLLAEVD
+EPVGTAERREVVESKWKALDMDRRRMLVDELVTVTIEPIMPGHVKFDPDLVRIEPRRD
+>MHAAABBN_02232
+MRAAIYLRISLDRHGDGLAVERQREDCKRIIAQRGWEHVATYEDPSVSASSRTVTRPGYE
+RMVRDWQAGRFDAVVCWDLDRLTRQPRQLEDWIDAAEQRGLHLVTANGEADLGTDAGRMF
+ARIKAAVSRQEVDRKSARQVRAAQQRAELGKGWGPRRPFGFAEDKVTHDPAEAAVVRRMY
+DDFNAGVGQREICRRLAAEGVRTSTGREWTQPALRQFLRNPRNAGLRAYRGEIIGPAEWA
+PLVSESVYRAALDRMDAPTKRVGGSGAKHLLIGVARCGVCDSPVGTNYTATHKRQYACRA
+GHVARSAEAVDAYVSEVAVGVLSTRGAAAFTRHDDAGQVELSAEADRIRARQEALAVEFA
+DGTLTAAQLRAANARMAERLEQVTAAMVAAEGNAALRPLLEAESVAAGWERLDIPRRRAV
+IDTLMNVRILRTSQGSRFDPASVEITPRTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001512.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9a9c9b01367d34bfc15e392a632a2b7fd27278f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001512.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02220
+MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV
+GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI
+RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA
+>MOLHKGIG_00733
+MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>NAFOICDF_02096
+MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA
+GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV
+RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS
+LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA
+>MHAAABBN_00464
+MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>LFPAFLNI_00697
+MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV
+GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001525.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad8d6914a73119477f63aafabdacdb4f9e6b2311
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001525.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02239
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL
+>MOLHKGIG_00719
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>NAFOICDF_02111
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL
+>MHAAABBN_00450
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>LFPAFLNI_00683
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001526.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..462ca2d14519ba5ba4c01ea4382017393ecf9653
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001526.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02240
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR
+>MOLHKGIG_00718
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
+>NAFOICDF_02112
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD
+>MHAAABBN_00449
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS
+>LFPAFLNI_00682
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001530.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db754045782275cc53b4615a94ea14d81ccd31bd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001530.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_02244
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR
+TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV
+VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI
+VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL
+EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK
+PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP
+DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF
+AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP
+DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS
+>MOLHKGIG_00714
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA
+AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAL
+>NAFOICDF_02116
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA
+LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA
+GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL
+TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL
+LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR
+EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI
+GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV
+DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR
+LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA
+QEAASA
+>MHAAABBN_00445
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
+>LFPAFLNI_00678
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001531.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..543802ad5d2d5b3f4f6415ff937ed9a8f7f7fddc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001531.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_02245
+MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG
+FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA
+DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL
+VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR
+VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA
+RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH
+GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA
+>MOLHKGIG_00710
+MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE
+SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF
+EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR
+AGRDAVRAILADLAGPASG
+>NAFOICDF_02118
+MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR
+PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV
+RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH
+DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG
+VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD
+VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD
+AVRAILADLRAAGAA
+>MHAAABBN_00444
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
+>LFPAFLNI_00677
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001532.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c37fc33693b85ce3ba0b60e3d244ed1a24d6e9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001532.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02246
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>MOLHKGIG_00709
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARAR
+>NAFOICDF_02119
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>MHAAABBN_00443
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
+>LFPAFLNI_00676
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001533.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..494bf2a8bcbf26cf684e779c18a0526e28e3b427
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001533.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02249
+MTEKTAAAAAPTSDAAPRVPFTKGHGTGNDFVLLADPDGNVHLEAAQVAVLADRHRGIGG
+DGVIRAVPSRHVEEGRALLAAHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLSEKGLVD
+LAPGESITIGTRAGVKTVSRLAHGYAIDMGPWSYLDPELAEEAASDAMVLAAGLADPRPA
+LSVSMGNPHTVVPLASFEDLEGLDLTRAPEVDPAPSHGSNVEFVAAHEPLVREGVGRARM
+RVHERGVGETQSCGTGACAVAVAMRAWSGEGGSDSWLVEVPGGVLGVDFVAHPDGTEHVV
+LAGPAELVFDGELTV
+>MOLHKGIG_00708
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLNPELAEEAASDSMVLAHGLTDPR
+PALSVSMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGTDSWLVEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTA
+>NAFOICDF_02121
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQHVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLPDPR
+PALSVSLGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWAGDQGTDSWLIEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTV
+>MHAAABBN_00442
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAERVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR
+PALSVSMGNPHTVVPLASFADLEGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTA
+>LFPAFLNI_00675
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR
+PALSISMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAAAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGTEH
+VVLSGPAELVFDGELTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001535.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb27101a433d2558ec19ecb98ab365ae6ddc5cb4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001535.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_02251
+MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNRLYGNLGNLRAVKDARP
+GMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEV
+FPSTLPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAV
+EVTLLGQNVNTYGVEFGDRGAFAKLLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETP
+NVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHAAITTDIIVGFPGETEE
+DFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEE
+MATLVGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTE
+AHPFFAVADPAPEDYSLRRSRAGDAWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS
+>MOLHKGIG_00706
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>NAFOICDF_02123
+MTLTDPTTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQP
+DLVVFNTCAVRENADNRLYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDV
+VFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPSTLPTKRESTHSGWVSISVGCNNTC
+TFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAKLLR
+ACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRS
+AKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPG
+TPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKATERGRL
+SGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGDAWD
+RAQAESCGAPAPGAAGGSGATSLGMPTLRPRF
+>MHAAABBN_00440
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>LFPAFLNI_00673
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001542.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f283a89badd90b3a9579654cb0baccb7178b669
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001542.fa
@@ -0,0 +1,89 @@
+>ACLBLIBL_02259
+MVLPRPTRRRPARGAQGVFDAERADDPAGSRDADRDASDDFDPWVDEEDAPEDADAEPTP
+PAGVRRPTAADRALEQVREHARAQREAAAAAEEPAEDADVDLEVEEPGRAAGPAAPSSPA
+AAVPSSTPEPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL
+TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI
+PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML
+VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK
+AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD
+ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS
+SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ
+YREDVVPEKTEKVIDEDIGEDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL
+MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDAPPSGGSGEGGAPAAAPAAPASAGP
+RDLVQEDLDARPAAQSWDDEDDDEGSEDAWQLTGR
+>MOLHKGIG_00695
+MPAVSAVRGSLVGMATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLR
+ALHTLWMGLATPVGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVG
+RVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLV
+GGVPSAADAFEDMLGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSI
+PQRIAGGYDWLTGQDPEGASEQRAARRAERRRAREERREAEDLAAPLSVDAETGRTHPDH
+DQSYLDGPAAGAHAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEV
+GSHAAPEAETTQVLPRPAPRRAARGEQGVFDSEQAAADARDAGRDASDDFDPWVDEDDAP
+EDADAEPQPPAGVRRPTAADRALEQVREHARAQREAAAPAAAAPEEDAGEDTPFALDDAP
+RQGSGAAAPSSSSAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKE
+RSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYA
+VASSDVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGY
+VVANLAKMPHMLVAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVP
+HLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRV
+LRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIK
+ANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHA
+VVEHVKSQMQVQYRADVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLR
+VGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDAS
+AGTGDGDASASAAPRDLVQEDLDSRPAAVDWNDEDDDEGSEDAWQLTGR
+>NAFOICDF_02130
+MATRTSPARSSSSSAKSRSGSSRPAKGSSGKGASAASPDLDRQPAFARAVRTGWMALATP
+VGAAVRKAGPDVRIARDDRRDGTGLLLVLVALLVAAVEWWGLRETAVGGVVHDVVGGTVG
+WFAFLLPVVLGVVAVRCFRHPLDHRANGRIVIGLLLATVAGSGIAHLVGGLPSAAESFAD
+VLHAGGIVGYLATVPLASLLTAVPVWALMVALAVFSLLVITATPLGSIGSRLRGAYAWLT
+GQDAEDAEARREQRRAERADRREAGEHRGEQTTADLFGDDRPGGRTHPDHDQSYLDAHGS
+SAAPAPARRPGLLARLFGRGHEEPAPAGRVSAPRAYESAVVEEAPAASRAASGSHAADEA
+PAAAVEPARPARRRNAAPRRAAATEVFDAEAPRGRRSAPPADDDFDPWVDEDSADDLDRA
+DDADTGALEVVPPAGVKRPTAADRALEQVREHARSQREATVEEAEKAEEHDDEAWDEHET
+LVLPTAAASAPAPAPAAVVPSVSRPEPVPEVTPEPARPSRPPQDGGHPYELPQSALLPAG
+PQPKERTESNDRVVQALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEK
+NIAYAVASSEVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRNDHPMIMGVGKD
+VEGGYVVANLAKMPHMLVAGATGAGKSSFVNSMIVSILMRSTPDEVRMVMVDPKRVELTA
+YEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGFKHVDDFNRAVRAGEVKLPP
+DSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVV
+TGLIKANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNE
+SEIHAVVEHVKAQMQVQYREDVVPEKSEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSML
+QRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATINGDTPPSRPAA
+PASAAAPAPAPAAATEAAPDRWASADLVGDDLDSRPAATSWDGEDDDEGSEDAWQLTGR
+>MHAAABBN_00432
+MATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADLPAAPLRALHTLWMGLATPV
+GAGFRKLGPDVRIDREERRDGTGLLLLLLAALIAAVEWWGLRGTAIGRVVHGVVGGTVGW
+FALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAAEAFEDM
+LGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRLAGGYDWLTG
+QDPEGASERRAARRDERRRAREVRREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGAH
+AAGASRPGLLARLFGGRRAREDQAADAAPEHTAGTAYDSPVIHEAEAGSHAAPEAETTQV
+LPRPAPRRAARGEQDVFDAERAAANARDADQDASDDFDPWVDEDDAPEDADAEPQPPAGV
+RRPTAADRALEQVREHARAQREAAAPAAASLEEDAGEDTPFALDDAPGQGSGTAASSSAV
+PASTPAPVPPVTAEPARGTQSPLGGDVSYTLPQSALLPAGPQPKERSEANDRVVAALTTT
+FTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPIPGK
+RAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAG
+ATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAE
+ALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVDELA
+DLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATSSVT
+DSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYRA
+DVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMES
+RGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDASASAGPRDLVQEDLDS
+RPAAVDWNDEDDDEGSEDAWQLTGR
+>LFPAFLNI_00665
+MATRTSPTRSSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLRALHTLWMGLATP
+VGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVGRVVHGVVGGTVG
+WFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAADAFED
+MLSAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRIAGGYDWLT
+GQDPEGASEQRAARRAERRRAREERREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGA
+HAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEAGSHAAPEAETTQ
+VLPRPAPRRAARGEQGVFDAEQAAADARDAGRDASDDFDPWVDEDDAPEDADAEPQPPAG
+VRRPTAADRALEQVREHARAQRESAAPAAARQEGDAGEDTPFALDDAPGQGSGAAAPSSS
+SAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL
+TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI
+PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML
+VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK
+AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD
+ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS
+SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ
+YREDVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL
+MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSAASGDGDASASAAPRDLVQED
+LDSCPAAVDWNDEDDDEGSEDAWQLTGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001545.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d75e828df71fcc94cd151c761a3104b09e519d4c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001545.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02264
+MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ
+LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA
+AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG
+>MOLHKGIG_00691
+MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV
+ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP
+GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>NAFOICDF_02132
+MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI
+GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF
+ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG
+>MHAAABBN_00428
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>LFPAFLNI_00661
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001546.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..810034f2e769b266413887b7ddc89a9bd33362fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001546.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02265
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG
+>MOLHKGIG_00690
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>NAFOICDF_02133
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD
+>MHAAABBN_00427
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>LFPAFLNI_00660
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001556.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12215eabd51fe5435010253c65a88efba87e0c79
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001556.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02283
+MADPARAGRLAQRIKVLVAEALRRSVKDDRVEAVTVTEVRVTNDLQHATVYYTVLGDEAT
+AAAAHEGIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGATYAGEADPYRTSEPGSEADDAPRA
+>MOLHKGIG_00680
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>NAFOICDF_02144
+MADPARAGRLAQRIKVLVAEALRRAVKDERVEPVTVTEVRVTNDLQHATVYYTVLGDEAV
+VAAAQEAIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGAQYAGDADPYRTSGDDDEQD
+>MHAAABBN_00417
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>LFPAFLNI_00650
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRSAEPDADADDAPRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001557.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..909134b6a505802abca2b4f6dc375fca2be87fb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001557.fa
@@ -0,0 +1,81 @@
+>ACLBLIBL_02284
+MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS
+KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG
+EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR
+PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP
+GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ
+PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA
+RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP
+VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG
+KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI
+IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE
+VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC
+GIGLGSFNDIKEGDVIETFEMREKPRA
+>MOLHKGIG_00679
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>NAFOICDF_02145
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK
+PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA
+SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS
+KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP
+AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG
+GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA
+DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE
+AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG
+AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH
+AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL
+EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG
+RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA
+QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI
+HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA
+LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL
+KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV
+>MHAAABBN_00416
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>LFPAFLNI_00649
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001558.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d18b4496cb32001fe6880a1c75d9a491e0d1871
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001558.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02285
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRVSGHVTVWATELDE
+DGTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGLIQQGVN
+RHMIQVNLGTLEAVLPPPEQVPGEDYSHGRRLRAYVVSATRGNKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVEHAEDPAQMIANALSPAKTVSVEVLDADQHSARAVVPEHQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGSDASAPAR
+>MOLHKGIG_00677
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
+>NAFOICDF_02147
+MSALRMLVAERDIPLDRLVPAIEQALLIAYHRTPGAIKGSRVELDRSTGHVTVWAPEVED
+DGTCVGEFDDTPNGFGRIAASTARQVIFQRLRDADDAKVLGEFKDREGELVSGVIQQGSH
+RHMVQVDLGSLEAVLPPPEQVPGEDYRHGRRIRAVIVSATRGPKGPSVTLSRSHPNLVRR
+LFALEVPEIADGTVEITALAREAGHRTKMAVKATRPGVNPKGAAIGEMGSRVRAVMTELG
+GEKIDIVEHADDPAEMIKHALSPAQALSVEILDADQHSARAVVPQHQLSLAIGKEGQNAR
+LAARLTGWRIDIVGDAAQQPGADAAQQPGADAASEMAPATEAGAEA
+>MHAAABBN_00414
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
+>LFPAFLNI_00647
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001559.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20ac00cb4e76d8742ee60e67ff82575fc951582f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001559.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02286
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+AAAAGEQTAEHTEA
+>MOLHKGIG_00676
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>NAFOICDF_02148
+METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG
+LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA
+RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA
+EQTEA
+>MHAAABBN_00413
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>LFPAFLNI_00646
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001562.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49400830b17e4280b130774f245fe143e2f20de4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001562.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_02289
+MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE
+ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH
+VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG
+PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT
+PALRTYERVGFERRGTFATVLY
+>MOLHKGIG_00673
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>NAFOICDF_02151
+MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG
+VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT
+LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP
+FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP
+SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY
+>MHAAABBN_00410
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>LFPAFLNI_00643
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP
+RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001563.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..970e05b54bfbb0c5fca65ad77f0c9ada9e672d7a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001563.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02290
+MPVSLGMPSAPPPVLAPRRATRQIRVGSVGVGSQHQVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAAAEHGTSIRIGVNAGSLDPRLLKKHGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEEVTEG
+LKDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE
+EANRIAAEMGVGEESGDQAAAGAPVVSVH
+>MOLHKGIG_00672
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIIARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
+>NAFOICDF_02152
+MPVSLGMPSAPPPVLAPRRRTRQIQVGRVGVGSEHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDADALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAATEHGTSLRIGVNAGSLDPRLLQKHGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LKDVTVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE
+EARRIAAEMGHEDGEGEAAPAGAPSVTVH
+>MHAAABBN_00409
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
+>LFPAFLNI_00642
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001570.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..257f6f95caf713f750b0e7420578fb291ae3397e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001570.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_02303
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGSEGETLEVGAPLVTFTVEGAGGDGGDTESGGRVPTLVGYGAAPDTGKPGRRARRGGSA
+GSATSAAPAGEPERGRAPSTSEEAPAGAARPQPEAAEPERADEAPEAQPASGTSGERPRC
+TPPVRLYARREGVDLTAVSGSGVGGVITRADVEAFLAGGGAPAAEPTASAAAPAEAGTSG
+GVRTLGGRPRTESVPVKGVRKATASAMVASAFTAPHVTEFLQVDVTETMELLAELKASRE
+YRDVKLTPMTLAAKACLVAMERTPDVNARWDQASGTILQQNFVNLGFAAATPRGLMVPNV
+KDAQAMSLTELADAIRELTGRAREGRLSPAELSGGTFTLTNVGVFGVDAGTPIINPGEGA
+IIAIGQVRRTPWEHRGEIVLRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTM
+V
+>MOLHKGIG_00660
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
+>NAFOICDF_02159
+MTRTVFRLPDLGEGLTESDLVTWRVSAGDDVVLNQVLAEVETAKAVVEVSSPYAGTVAEL
+HAQEGQTVDVGSPLVTFDLPGDDAAPSDGPAADGRVPTLVGYGAAPESGAPARRRRRPAS
+SAGESTPETGTSAEPAPAPAESAPAERPRSTPPVRLLARRLGVDLESVTGSGDHGVITRA
+DVDAAARAASDSAGSEAPAEADAAPGVRTLGGRPRVVVEQVRGVRKATAQAMVSSAFTAP
+HVTEFLTVDVTESMELLDELRRDRAFRDVKVTPMTLALRACVLAMERTPEVNARWNGQDG
+TIERRHFVNLGMAAATPRGLLVPHVKDAQALDLRGLAVEVAALTERARAGTLTPAELTGG
+TFTLTNVGVFGVDSGTPIIHPGEAAILCLGAVRTQPWEHRGQIALRQVVTLSLSFDHRLV
+DGEQGSRFLADVGAMLRRPGMTLALV
+>MHAAABBN_00397
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAESDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLAMV
+>LFPAFLNI_00630
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPVGEPARGQAPSTSEAAPAGAGRPQPEAAEPARADAAPEAVRGAASGERPRCT
+PPVRLYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAATPPQSDAESGSTGGV
+RTLGGRPRTEAVPVKGVRRATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFR
+DVKLTPMTLAAKACLVAMERTPDVNARWDEAAGTIVRQNFVNLGFAAATPRGLMVPNVKD
+AQAMSLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAII
+AIGQVRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001572.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3f84436abed344a99c6d212bb22def5121c3e74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001572.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02305
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>MOLHKGIG_00658
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA
+>NAFOICDF_02161
+MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR
+RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE
+LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS
+EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV
+LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL
+TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ
+RDLQLHLDGLDAGEEQA
+>MHAAABBN_00395
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>LFPAFLNI_00628
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001573.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efc711603d3450ee363ddc6cf4fb623d1e240b99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001573.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02306
+MTTRRPQDAEPPFELVEQDEIGYETSHVDAFLARAREAREGGAPLTADEVRQARFATVNG
+GYATDEVDDELDRLEGELAAAEREAFVSERGDEDWSADLEERVAELVARADRAPAERFRR
+PSREDATSYDVDAVDALVDRLRVTLAGAEGAAAPDARGGLTADDVRRASFGEAEGDRGYE
+EGQVDAYLDAAVDVLLRRA
+>MOLHKGIG_00657
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
+>NAFOICDF_02163
+MTPTSPEARADFEHVGPDEIGYEPAHVDAFLERARRAEAGEGDLTAEDVRQARFATVNGG
+YAADQVDDELDRLEEVLMGREREDAVGDGAWDRELAERSQELLGRADRAPAERFRRPSAD
+DAQSYDVDDVDALVDRLRATLTDGSDELTADDVRRAGFASAQGGDGYDEAQVDAYLDAAV
+DVLLRRG
+>MHAAABBN_00394
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
+>LFPAFLNI_00627
+MTPRTTPDTEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEGSTDPDAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001574.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e2274f1cf9cd19fc6f0c25cd8d7d319290ae897
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001574.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02308
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSYTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRVVMPELTEERRKEYVKLVKSK
+AEEHKVSVRNARRKAKDALDKAVKDGEVGEDEGARGEKDLDAMTKKHVDLIEEMAKNKEQ
+ELLEV
+>MOLHKGIG_00655
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>NAFOICDF_02165
+MIQETLTSAQEQMERTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDVSALRNIEKALSDSEVGANPSNDGKVIRVVMPELTAERRKEYVKLVKNK
+AEEHKVSVRNARRKAKEAIDKLVKDKEIGEDEGARGEKDLDALTKKHTDLIEEMAKKKEA
+ELLEV
+>MHAAABBN_00392
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>LFPAFLNI_00625
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001575.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..948402e93919fea89a315ef1edd1e52b4b28425b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001575.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02309
+METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD
+RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG
+VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>MOLHKGIG_00654
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>NAFOICDF_02166
+MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS
+IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ
+VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY
+TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL
+GEEIGTSVTP
+>MHAAABBN_00391
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>LFPAFLNI_00624
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001581.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dd64d45df1d44925c9c4cb69cd79572ede99c39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001581.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02318
+MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK
+GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG
+LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK
+VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF
+AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL
+AGRLRRR
+>MOLHKGIG_00645
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>NAFOICDF_02177
+MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK
+AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ
+IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK
+EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ
+RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR
+LRGRKG
+>MHAAABBN_00382
+MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK
+GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG
+LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF
+AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
+>LFPAFLNI_00615
+MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK
+GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG
+LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK
+VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF
+AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL
+AGRLRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001583.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7b9b9abd5654efd4d206f91bd614c3de47acc9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001583.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02321
+MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA
+FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA
+HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV
+SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW
+DLHVLQHRGALRGLRASR
+>MOLHKGIG_00641
+MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>NAFOICDF_02184
+MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT
+VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET
+EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA
+ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR
+LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT
+CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS
+SRWDLHVLQHRGALRGLSGPR
+>MHAAABBN_00378
+MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>LFPAFLNI_00611
+MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001588.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd9e3a98ed335f697d9c7be6a8483bcf91d34276
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001588.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02353
+MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHADP
+ADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALP
+AQFWVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADD
+AAASEVRADVAPEAGTGEAAGAWREDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPA
+LRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERFLAGRDGRYSTKPIKGTA
+ARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATV
+HQLVSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLL
+GADGAVSLSIVIRTAVLAAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGT
+ARTTTAPPRSR
+>MOLHKGIG_00580
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGSRRWAVVSASPERFLSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQLVSTVTGTARAGIEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA
+>NAFOICDF_02247
+MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALP
+DGGEARWSMVGDGVDVLGEEEGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGE
+GLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQFWVRPSRYAVADHVAGALSCC
+VVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAPEAPGVWREDGAAYAEQIAR
+CRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVV
+SASPERFLSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRND
+LSRVCEPGTVQVPALMAVESYATVHQLVSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKR
+RTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPDAPARWSVGAGGAI
+VADSDAHAEHEEVLLKARGLRRALTRAAGTA
+>MHAAABBN_00313
+MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA
+>LFPAFLNI_00581
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGE
+GLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQFWVRPSRYAVADHAAGVLHCC
+VVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVEVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001589.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3ada7d56dbf388c79ec6f9bc8ed118ad21d32f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001589.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_02354
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTADLDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDAFLA
+DPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVLAHL
+HGSLFEHRCAECGAPADVDPGAPADAEAAGSEADLEAMLREAPPTCPACGTGRIRPGVVW
+FGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNPVETELS
+GAVTHALRGSAGAVLPALVAGV
+>MOLHKGIG_00579
+MADPHPVLAASAPVLADPHPVLAASAPDLDPDALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDARTGLWERFSAEELATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPGLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECWAPADVDPGAPADEATAGSE
+ADLEAMLREAPPACTVCGDGLIRPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIV
+QPAASLPFVALGAGAAVVEVNPVETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>NAFOICDF_02248
+MSPTQPSDPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLAT
+AEAFAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGA
+DVLSHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRR
+GRVRPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVE
+VNPDRTALSDAMTHVLRGPAGTVLPALLG
+>MHAAABBN_00311
+MADPHPVLAASAPVLAASAPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>LFPAFLNI_00580
+MADPHPVLAASAPVLADPHPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001591.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fcc313ab7618e1b9a03e852d04810d41cc72db1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001591.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02359
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG
+>MOLHKGIG_00574
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG
+>NAFOICDF_02250
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG
+>MHAAABBN_00306
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG
+>LFPAFLNI_00575
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001592.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..689862a57e6eaf5a84c606fdcc48ddb15ba617eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001592.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02360
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR
+>MOLHKGIG_00573
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA
+>NAFOICDF_02251
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR
+>MHAAABBN_00305
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA
+>LFPAFLNI_00574
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001600.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f225043f5b13c6262143ff4b7b4915e362618c78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001600.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_02382
+MVASASLYGGTQNLFKHTLAKVGIETTFVQDPDDVAAWTAAVRPNTKAFFGETLGNPRGD
+VLDVAAVADAAHAAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIV
+DAGTFDFAQHAERFPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSA
+ISPFNAFLVNLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRY
+LPKGAGAFVSFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQR
+AAGVTPGLVRLSLGVEDLEDILADLERGFAAAASAGERE
+>MOLHKGIG_00561
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVAGWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDVEDILADLERGFAAAARRGDDDAGERA
+>NAFOICDF_02266
+MSTQPTPRRGFSTTQIHAGTDAPHAFGATALPIYQTTSYDFPSAQVAADRFALADLGPIY
+TRIGNPTQSAVEEKIAALEGGVGALLLASGQSATTFAILNVAGAGDHVVASASLYGGTQN
+LFKHTLARVGVEVTFVQDPDDLDAWRAAARPETKAFFAEALGNPRGDVLDVAGVAAAAHD
+AGVPLIVDNTLTTPYLLRPFEHGADVVVHSATKYLGGHAAAMAGVIVDSGRFDFARDPER
+FPGFNEPDESYHGLVYARDLGVGSPLGANLAFVLKARVQLLRDYGSAISPFNAFLVNLGL
+ETLSLRMDRAVASALAVARHLEGHPQVESVSHPGLESSPWHARAQELLPRGAGAFVSFEI
+AGGAAAGAAFVDGLELHHHVANIGDVRSLVVHPASTTHAQLAEDEQRAAGVTPGLVRLSL
+GLEDVEDILADLDKGFAAAAAALDAADAAEQD
+>MHAAABBN_00286
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLADDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
+>LFPAFLNI_00564
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTKAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVERVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001613.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3956706fd208951432e34352b10b84538a50ac3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001613.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02402
+MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR
+AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ
+>MOLHKGIG_00545
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>NAFOICDF_02285
+MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR
+RPDRSLVRRGDLGLWARPGEDQWRRAAGRR
+>MHAAABBN_00270
+MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>LFPAFLNI_00548
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001618.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e7106c84a5e73048c68ec4f44a8c5c3f1e77beb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001618.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02410
+MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI
+AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS
+LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL
+>MOLHKGIG_00539
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>NAFOICDF_02292
+MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI
+GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV
+RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI
+RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF
+GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL
+>MHAAABBN_00263
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>LFPAFLNI_00542
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001622.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95430f2b2929d678cf9851784955ca82d25d2b31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001622.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_02415
+MSQDRRAPIRNPFLEPGASVPGAPPRRADADPEDRLAEFRLGPAFGGRPAQPRRPQGFGG
+RTAPGEGTTTTPRPDGTAAAEPADTAAEPVDTAAEPAANPKTARPAESAEAADAPAPAPA
+PLPTVRVLAVCTGNICRSAYVQHTLQAQLNALLGDRGRAEVTSAGTEPNQALTVPEPLRE
+LSPSRRVRAALTEHRPQQLTAASLWGQDLVITAADDHLEEVLREDPGAVRRTFTVRGIGT
+LLGEHGEEIAAAVPPGAGLAALVDAMADLRVRLIGRGEEPDADLPDPFRGPAEGYAQMVE
+TARPIVELLAWEIARALDGDLVEDDEPTRV
+>MOLHKGIG_00534
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADRVPGPVPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAEVTSAGTEPNQ
+ALTVPGPLLDRAPSRRVRAALTQHRPQQLTGRSLAGQDLVLTATDDHLDEVLREDPAAVR
+RTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAALRSRLIAHGERPDADLPDPFRG
+PAEGYAAMAQTAQPIVELLAWEIARALDGDLVEEEPTGA
+>NAFOICDF_02297
+MSWFERPALRSPFAAAPGMDAPADDGAGGPLRILTVCTGNICRSAWAHHVLQARLDAALG
+ADVVEVSSAGTGPNQALAVPEELLTLAPDAGVRAALAAHRPRRLTARVLAGQDLVLTATE
+AHRDAVVREAPAALRRSATLLDAGALLADPDAVAPGGGGRALVAALEAARREGRGLDAGR
+RGLFPAGRRAADLADPFRGPAEGYTEMTRALEPALAAVEAAVVRAVEPAR
+>MHAAABBN_00258
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADPATPRQRATPTERTVAPAPVRAAEPASPASPAGRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA
+>LFPAFLNI_00537
+MSRDHRPPIRNPFLPPTPEEPEVPTRDGGHPAGDGGDAGAPAAATAREDRLAEFRLGPAF
+LPHPADPAAPRQHATPAERAVAPATAAAAEPASPAAPADRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001624.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71f1af8e762d7a80662f0fb94c7c5595a32ea2db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001624.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_02420
+MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL
+VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG
+VLPRP
+>MOLHKGIG_00532
+MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV
+ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA
+>NAFOICDF_02302
+MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD
+GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP
+>MHAAABBN_00253
+MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV
+ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA
+>LFPAFLNI_00532
+MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI
+ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001628.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..925e3491bbc7c9daaeb895a9c7e199293a0cbc11
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001628.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02424
+MSAGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGAGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGVGPEDLVVVHDELDIPFDALRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRSFSKPEQDALPLHVDRAADAVEKLVT
+DGLEAAQQAFH
+>MOLHKGIG_00527
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALAAFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDALPLHVDRAADAVEKLVT
+DGLEPAQQAFH
+>NAFOICDF_02307
+MTGTTLIVGLGNPGPEYERTRHNVGHMVAGELASRMGVGFTRHKAGAVVATGRLGIGGPR
+VVLAMSTGYMNTSGRPVSALTNFYDVAPEDLVVVHDELDIPFETLRLKRGGGEGGHNGLK
+SITASLGTKDYHRVRVGIGRPPGRMDVADFVLKPFTKQEQELLPLHVDRAADAVEKLVTD
+GLEAAQQAFNS
+>MHAAABBN_00248
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT
+DGLAPAQQAFH
+>LFPAFLNI_00527
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGIGSEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT
+DGLEAAQQAFH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001629.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2a51318da4cdbb1d0655e4ff5b252046b12fcd7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001629.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02425
+MSDKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPIHLLLPAQETTLAVRNPNALLT
+VVNEAGEEHLVLPKDIQRHALKDTVEHLDLIEVRRGEKVVVDVTVHVEGEVAKGNDYVLD
+HVTVPLEAEATHLPESVTISVEGREAGEHVYATDVQVPAGTTLQLEDEIVIATVSEVVEQ
+DLGDESVQEEQAAEGEAAEGESAEGESEGSED
+>MOLHKGIG_00526
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPVHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGTEYV
+LDYATVPVEADATDLPEVVTISIEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVNEVV
+EQDLGDESVQEEQAAESAED
+>NAFOICDF_02308
+MSDQIKLKVTRRTDFGKGASRQARRAGQIPAVVYGHGAEPIHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHPIRQTVDHLDLIEVRRGEKVVVEVPVHVEGELSTAVDAE
+YVLDYPTVPVEAEATDLPENVLISVEGREPGQHVYATDVQVPAGVTLQLEDEIVIATVSE
+VVEQDLGDESVQEEQAAESAEGAEGEGESEGSEESAEGESEGSED
+>MHAAABBN_00247
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGNDYV
+LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVSEVV
+EQDLGDESVQEEQAAESAEGESEGSED
+>LFPAFLNI_00526
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL
+LTVVSEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVIVEVTVQVEGEVARGNEYV
+LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQLPAGATLQLEDDIAIATVNEVL
+EQDLGDESVQEEQAAESAEGESEGSED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001630.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acfbcb6fffcb93592bd586c5a2fdf5eb6e83fbb9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001630.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02427
+MKITETAIPGLLVIDLDVHGDNRGWFKENWQREKIRALAAEHPRLATLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQSQYTFLNLADPTAAIAWPIPLEEAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHDRTTWDLEDPDSWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCAEAGVPLAHVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGRNFVATMASLAERGIDP
+AVVDDQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYTAGKEGVAPRPTNSALDLGPLAVVGYTAPDQRGRLRDHLSELTGDAR
+>MOLHKGIG_00522
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLAALAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGRYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPSAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNAAAVAELARRCTKAGVPLAHVSTDYVFDGALPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC
+>NAFOICDF_02310
+MKITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAQVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSAATTAEYMAGKEGAAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLSEAAGGTR
+>MHAAABBN_00244
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAGHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVVRAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAG
+HVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRTYLRR
+>LFPAFLNI_00522
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIALEDAELSDKDRAHPMLDD
+VVPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMADPASWPREHFRGLRAV
+VNASAMTAVDTAETTEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGALPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001631.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e768e0e815a0fd8b02306da0b65d546101d48411
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001631.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_02432
+MSTRARSSSTPTAPSVSVVIPVYNGAPTLPLQLEALHTQVGAPAFEVVVVDNRSTDDLDG
+AVRPFMESGPPLRVVRADGHQGSSYARNRGIAAARAPYVMFCDADDVVSRHWVATGAAAF
+ATAPIWTGSVTHLPAAVFEQGLEAVRDLLGDGPRPQDGPGREVPGPFPVLMGGDFGASRE
+LLVAVGGFDQSFPHAGDDNDLAFRVLRAGHRLVEMPQVRVASRGKTSLQTAHRIAFRSAR
+AHALLADRYGLWERSRATTWASEPVRCLGAAVKMAAHPTRADWRGLACRTAMASGTLAGA
+VEYHLLRRRPAPQVGLGLDPDDTALPGEEPQGAGGPGHPELVSVIIPAYNAEAYIAEQIE
+SLAVQVDAPEFEVIVADNGSTDRTASTAREAAERWGLTLTVVDARGPASASHARNVGAMA
+AAGGVLLFCDADDFVGPEWVRELAAAVRSREDALAVGTLLHRRFNDAAVLAAYGIPPEAG
+EPRTDAAGYPVVHGGFAGHLPTVAGNDFGVRRSLYLAVGGMDSSFPGGSEETDFSWRAQR
+RGAVVVHAPRAIVHYRLRSTPQTVFRQQRIQQVGRMLLWMRHRGDGMSGPSWRVSVTEVA
+RHLPAYLLVRERAARLRHARIAGGHLGALQGMVRYRLLKRIPPRRLVDGSSVPRA
+>NAFOICDF_02316
+MNQAVSVVIPCHNAAGSMQRQVDALLPQLEETDELLLVENRSADGTRRIAEEAALRDARV
+RVLNAPDKAGANHARNIGAARAHNPIILFCDADDVVHSGWVRSLRQVLGTDGIAGGSATP
+VDEEGRRLGPDLGLHETFGGPAYPLGATMGVRREVLETIGGFDESYAGGHDETDLAWRAA
+RAGWPTHFVPEARIDYVQRPDARSALQQRRLYARTSIQVWVQNPDLVDQSAVSLRGALNG
+VRLGLPLGIKMIRGTATARDAARWGWALGVLEGHLRYRVLGRPPARVAPPIPPAPHPAEP
+NRPCA
+>MHAAABBN_00206
+MTVESVDVSVIIPMHNGGELIHEQLDALAAQRTDLNWEVIVGDNRSTDGSPDAVRARADS
+FPVPLAVVDAFRVQGASHARNAAAAAARGEVLAMCDADDRVAPDWVEQAFRGVREIAPMV
+AGANRLLSHPQRPDAPLLNPRILHGRGAQTCNAAVRRDVFLASGGFDESLPPYGVEDSDL
+SARVLAAGHTIAPHPGLVLYFRETTGLKAKLRKIHSSGQAEAVLWSRGHEAQGTPLAESQ
+FVVALAALPADAVRTARARELRSLPKWTLREAAVRTGRWRGYRRWVKTGKAGEPRLPFLD
+GRGGAA
+>MHAAABBN_00237
+MFADADDVVSRWWVRNGARAFESSDLWSGGAPFMTDEQMREGVEGARRAFDDSDEWHAPV
+PGDLRNAFPVLMGGDFGVTREVFERVGGFDHSLGAVYEDNDFAVRAHLKGIRVDEAAAVR
+IAFRGKWDMRFRTRLVRRSAKAHSLVTTRYELGRQSHFPNPWVEFVRTGASAALMTLGCK
+TPDWEGVRLRAQTAAGAAAGRVEYRWMRRGPQPQIGLGYRRADSSPFSQADAAGAGENSE
+EVLAASVVIPARNAEGWIGEQLDSLAAQCDAPLFEVVVADNGSYDRTAQIALSHPTPFQV
+RVVDASGVPSASHARNVGARLARGHVLLFCDADDFVGDRWAGELYRAVTSGPQLVARGVL
+EHSRFNDVDVLAAYRIDPAQDLHDTEDSPRIERVSDGFAGYLATVPGNNFAIRRDDYLKL
+GGMDPAYPGGSEETDFVWRAQEAGFTVVQAAGAVVYYRLRTTPAAIFRQQRNQQRGRMYL
+WTRYRGRGMSGPSVKASVFAISRHMPMWPFLRRDRGRALAWAYTVGAHVGALEGMARYRR
+PALLRSRRPGSDGGTAA
+>LFPAFLNI_00516
+MSRPVSVIIPCHNAAAWVDRQISAVLAQLRADDELVLVDNRSTDTTYERLEAAAAGDRRV
+RTVSAPERPGANHARNVGIAAARNPLLLFCDADDLVTGGWVEAFRAALQNAGITGGAATP
+VDADGCRIGSDLGLHEIFGGPAYPLGACMAIRKDVVNAVGGFDESFAGGHDETDLAWRAE
+RAGWPTAFVPDARIDYLQRPDAAATVRQRRAYARTSIQLWARHPETVNPHGVSVKGAVRG
+VLRGLPNAVRVLRGRASADQAAQWGWSLGLLEGHLRYRILGKPPAAHTPRPDASA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001633.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd805d68506e2806cbaa40c706bf36aa467309f3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001633.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02438
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGDTLVYCHTPARW
+VYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVVKERIEEAYGLT
+DVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRAHAERFSEDQIA
+RQVRTQLGQLQNHARNKGAM
+>MOLHKGIG_00513
+MTDMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVVKERIEDVYGLD
+GVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRRHVEKFSEREFA
+LRIRALVEGLPGA
+>NAFOICDF_02321
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV
+>MHAAABBN_00233
+MSEQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFEDAHIVTS
+PLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKKRIDDVYGLD
+GVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQAHAERFSEAQFG
+RRIRALVAESPAGPAHRGRQ
+>LFPAFLNI_00512
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKERIEEVYGLI
+DVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRSHARRFSEFEFG
+QQVQAQLGWIGISR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001638.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65eb5df187b1ca8a8f6027b49e5356763d0cad91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001638.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02444
+MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP
+ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV
+PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA
+RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH
+AVADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQHE
+AWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERYG
+MTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA
+>MOLHKGIG_00506
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLLL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPRD
+ATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAAPAPSDTAGDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA
+>NAFOICDF_02328
+MTRAVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAVQAPDAGLRLLL
+PAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVVPADVAGAL
+LPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGASVHVVQHG
+LLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAASADPTATGS
+TGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQHARWEGAGI
+AVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRYGITRWMPG
+ADPTPTPALVAPTADPAAAIARDLWKEHA
+>MHAAABBN_00226
+MTDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRGSTGDDVPRLLL
+PPGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAAGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRVPEPTPPLASPTTDP
+AAAIAEHVWKESA
+>LFPAFLNI_00505
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLYL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARIGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001642.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82bde4186b9b9b69b4e5bcff5c831669a235d4d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001642.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02448
+MAERVEPVRGEDGDDGSVAAPERRRSRLPGWASVLLNVVVAIAVVAVVQALWVKVYSVPS
+GSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWAQPLPPEGPVENAVRTFGDIT
+GIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLHNDLPFAPGRLDCESDV
+MSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGCARFVTREDVVGEVFVT
+IWPPSNWGGH
+>MOLHKGIG_00501
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH
+>NAFOICDF_02332
+MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV
+SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG
+EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY
+EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC
+AHFVRDEDVVGRVFSTVWPPSNWSGH
+>MHAAABBN_00222
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH
+>LFPAFLNI_00500
+MAERVEPAHGDDVDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPS
+GSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLT
+GIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEV
+MSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDCARFVTREDIVGEVFVT
+VWPPTHWGGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001643.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c45a991c6fb20fbad6f8b76535d355b4af04bdfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001643.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02449
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>MOLHKGIG_00500
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>NAFOICDF_02333
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>MHAAABBN_00221
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>LFPAFLNI_00499
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001649.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd6d1d74e73c225c190a06e511135cc00d803c53
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001649.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02457
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEFPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAAEGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLVPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>MOLHKGIG_00490
+MAHASETPLAYRAPAQQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDIASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVA
+ALARAVSENTARVYGSF
+>NAFOICDF_02341
+MATTTSAQSASTQSASTEPGIPSAYRPPATPADLGDGPARDTREEKSGRKRRLEYPPAPE
+PLPVPVVDNHTHLDFRDGLVRVDVHQAMDAAEAVGVVGAVQVACDVESARFTVEAIEAES
+RLLGAVALHPNDAARLTARGEFEEAFAVIAELAEHPRVRAVGETGLDFFRTTDEAGHAAQ
+EESFRRHIRLARELGKALQIHDRDAHDDVVRVLLEEEADGGLPPHVVFHCFSGGPDLART
+CAERGWHASFAGPVTFKANDDLRDALRLLPRELVMVETDAPFLTPHPHRGRPNAPYLIPV
+TLRGMAEARGEEVAELAAAVAENTARVYGEF
+>MHAAABBN_00211
+MAHASETPLAYRAPAPQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCTEHGWHMSFAGPV
+TFKANDELREALRTAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>LFPAFLNI_00489
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001653.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a7f2ebb733a4b2ec9efafff113ee467f1b4d9cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001653.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02463
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR
+>MOLHKGIG_00484
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR
+>NAFOICDF_02347
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR
+>MHAAABBN_00202
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR
+>LFPAFLNI_00484
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001661.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4291c71db09c88435e4e0380fd0a8af956c508f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001661.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_02471
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR
+>MOLHKGIG_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
+>NAFOICDF_02356
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG
+>MHAAABBN_00193
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP
+>LFPAFLNI_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001662.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13108f0ce3ca43fe69ca93996dcd3c706c49119f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001662.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02473
+MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL
+TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH
+RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI
+SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP
+DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE
+ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV
+TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR
+>MOLHKGIG_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>NAFOICDF_02357
+MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI
+AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR
+NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA
+AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD
+PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL
+RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV
+DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA
+>MHAAABBN_00192
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE
+RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>LFPAFLNI_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001665.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbede970412d03453f18ac30e3982cc12fb340b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001665.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02476
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV
+>MOLHKGIG_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>NAFOICDF_02360
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA
+>MHAAABBN_00189
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>LFPAFLNI_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001666.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ce85b2b89b2c36c6c2db534d75e791664d64a53
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001666.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02477
+MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE
+KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL
+RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE
+>MOLHKGIG_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>NAFOICDF_02361
+MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA
+AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA
+TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA
+EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG
+INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL
+RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV
+IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE
+>MHAAABBN_00188
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>LFPAFLNI_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001673.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d7b60e551413ef4747945aa32af231a6ef5cdd2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001673.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02485
+MSHHAHAVHAQDPTLANRYGTDQDRPSRRRLWVGLGVLGLLGAVLLAVWLGLNLSVGNIE
+YKDVGYTIEDDGNATVTFQVLVPEGVQAECDVLVMDSHAAPVGFRTVRLVSVPQDQRDTP
+SDAQQVYTVDVRTVVRGDSGVVEACRKL
+>MOLHKGIG_00462
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV
+>NAFOICDF_02369
+MSSTPAPAASAPETTLATRYGVGQRRDRRRLWTVLGAVALVLAVATAVAVALGNSVGRVE
+AEDVGYRIDDAAHAAVTFQVTLPRGVEAAACDLKVMDARYAPVGFHTVRVSAGPDHPAGE
+TVTYTADVRTVGRGVTGVVEGCRPA
+>MHAAABBN_00180
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV
+>LFPAFLNI_00462
+MSHHAPAVRAQDPTLANRYGTNHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGIVETCRKV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001674.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8c7875eb6f788890f1ae837e3e302563ad2699e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001674.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02486
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG
+>MOLHKGIG_00461
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>NAFOICDF_02370
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA
+>MHAAABBN_00179
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>LFPAFLNI_00461
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001675.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebdc9ae00a6b953f44479ed3532af53becc711df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001675.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02487
+MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG
+VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP
+RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE
+SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA
+>MOLHKGIG_00460
+MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA
+>NAFOICDF_02371
+MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG
+STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP
+VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE
+RLTHDDLLVQAVGRTVSTAAAAAAAAG
+>MHAAABBN_00178
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA
+>LFPAFLNI_00460
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001676.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9042e65a3dcf69ff082daa20dd7a9f6cd6d69ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001676.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02488
+MTAGEVAQEQESVQTAADAAPVAGPRWVRPADAEPAWEGLPVSYEDVEAARETLRGVSEV
+SPLQLSRSLSRAVGTDVHLKCENLQRAGSFKIRGAYVRMAGLSEAERVRGVVAASAGNHA
+QGVALAAAKLGISARIYMPRGVALPKLQATKDHGAEVVLHGSTVDESLAEAQRWAAETGA
+VFIPPFDDPAIIAGQGTVGLEILDTLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTV
+RVIGVQAATAAAFPGSLEEGRVQVLESVSTIADGIAVGKPGNLPLQITAELVDAVVTVTD
+DEIAAALVHLLERAKLVVEPAGAVGVAALLAGRTADLGFELGSTVAVLSGGNIDPMLLLK
+SVQSGLSAAGRYMTVRIPLRDRPGELATISRIIADSDANVVRVDHTRVGPELSMGGVHIT
+IDMETRGPEHSAAVLEALREAGYSPVPIH
+>MOLHKGIG_00459
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPDLSMGGVHITIDMETR
+GTEHSAQVLEALRAAGYSPAPLP
+>NAFOICDF_02372
+MTAGGAAPAPWLRPADAQEPTGDRLPVRLEDVEAARGVLEDVAEHTPVMLSRALTDQLGT
+PVHLKCENLQRAGSFKVRGAYVRMARLSAEERAAGVVAASAGNHAQGVALAAAKLGIHAR
+IVMPRGVALPKLQATQDHGAEVQLYGSTVDEALAEAQRYAAATGAVFIPPFDDPAIVAGQ
+GTVGLEIMDDLPRVDTVLVGIGGGGLIAGLAIAVKERARREGRTVRVVGVQAATAAAYPV
+SLREGRVQVLESVSTIADGIAVGRPGALPFDIVSGLVDAVVTVTDDEIAGAMVHLVERSK
+LVVEPAGAVGVAALLSGRARDLGFDLGTTAVVLSGGNIDPMLMLKSIQSGLSAAGRYMTV
+RIPLRDRPGELATISRVIAETEANVVRVDHTRVGPELSMGSVHITLDMETKGWDHCEAVL
+TALRESGYSPLRLT
+>MHAAABBN_00177
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPAELPVTLEEIERARATLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP
+>LFPAFLNI_00459
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001680.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..332b45f6cc6f425ec8a629fd41737b205699e4d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001680.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02505
+MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG
+GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT
+TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV
+TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR
+HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG
+>MOLHKGIG_00451
+MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG
+GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT
+TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV
+TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR
+HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>NAFOICDF_02377
+MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG
+GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN
+TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG
+IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV
+LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV
+TPTLQIKDGEGVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVRH
+GEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRIV
+SGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK
+>MHAAABBN_00172
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>LFPAFLNI_00454
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001681.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc3f4c27b463de0a6dd91e2877bd3b6ceac05c0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001681.fa
@@ -0,0 +1,51 @@
+>ACLBLIBL_02506
+MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP
+TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>MOLHKGIG_00450
+MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>NAFOICDF_02378
+MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV
+ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA
+YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV
+AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR
+PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV
+KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS
+ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA
+RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA
+AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG
+IALSLRG
+>MHAAABBN_00171
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
+>LFPAFLNI_00453
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001683.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d83de0c3e9c427ca66fe881e1d16106d7582cca5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001683.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02510
+MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA
+PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL
+AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV
+RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG
+>MOLHKGIG_00447
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>NAFOICDF_02381
+MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR
+ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT
+PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH
+LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP
+ERALRGAIACVRAGDWDALRR
+>MHAAABBN_00168
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>LFPAFLNI_00450
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD
+PERALRATVARVRAGDWAALRPSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001684.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f28c0063da465b9de6ae22ef1d6a3ada2b215e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001684.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02511
+MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER
+GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE
+AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA
+>MOLHKGIG_00446
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>NAFOICDF_02382
+MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL
+ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ
+HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD
+RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG
+HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD
+AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA
+EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA
+>MHAAABBN_00167
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
+>LFPAFLNI_00449
+MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA
+EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH
+LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA
+GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH
+GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA
+AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE
+AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001685.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4086d1ce45d5809b6e96183126589fd18c8d5774
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001685.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02512
+MLEWIEETVLHAAAQWWMLPLTLALCLLDGIVPVFPSESVIVALAAIVRDGQPFSLWALW
+AVGFAGAFLGDILAYAIGRAVGVDRFRWMRTPRVRASVAVARHHLNGHGALLLFTGRFIP
+GGRVAINLTAGAIRYPLHRFVVLDLLSTAAWSAYSIMIARLTTGWLDNALLQIAVSVTGA
+ALVGVLLDRALKAVLRRRLGTGVKGLRQAEDEALR
+>MOLHKGIG_00445
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNFTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR
+>NAFOICDF_02383
+MVQALEQAILAGASHPWALPLAALLCLLDGLVPVFPSESVLVALASIVEDGRPFPLAALW
+AAGFVGAFLGDVAAYGAGRGVGVTRFRWMRHGRVRRTIVMARRNLDSHGALLLFTARFIP
+GGRVAVNLAAGAMHYSPWRFVGLDLVSTALWSVYSIAIARLTVGWLDSTVLRMAVAVLGA
+ALVGLLLDRAVKALLRRRLARDGHRLGADEQAALR
+>MHAAABBN_00166
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR
+>LFPAFLNI_00448
+MLAWLEEAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGSGVKGLTLAEQEALR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001686.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b305cd2cfc94f2592dead8f3fa61fd6a7f39d23a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001686.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02513
+MTAQQQAEPFDAVEVIRAKRDRQTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEISRWTDAMIASGERMDFSGLTAPDGRVLPTADKHSTGGVGDKITLPLAPLVASYGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLTNEQMMRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTVALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAMLAGAGV
+TDVDPAQNLANGKAMDVWHRMIEAQGGDPRADLPTAAHTEDVVAEADGVLAELDAMAVGL
+AAWRLGAGRERQGQPVQAGAGVELHVRPGERVARGQKVMTLHTDTPERFARAKAALEGGW
+AVAEKGEAEAAALRDRSVILDRIG
+>MOLHKGIG_00444
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERAKAALAGGW
+AVGELDDAAARTLRERSVILDRIG
+>NAFOICDF_02384
+MTTTSMPAQPAAPEAFDAIEVIRLKRDGHRLDPERIDWVVDAYTRGVVAPEQMSALAMAI
+LLNGMDREEIARWTAAMIASGERMDFSGLSAPDGRRLATADKHSTGGVGDKITLPLAPLV
+ASYGVAVPQLSGRGLGHTGGTLDKLESIPGWRADLTNDQMMRQLGEVGAVVCAAGAGLAP
+ADKKLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR
+TMVDLGRDAGVDTSALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM
+LAGAGVTDVDPAENLANGKAMDVWHRMIQAQGGDSHAELPAARHQETVTADADGVLTELD
+AMAVGLAAWRLGAGRERQGEPVQAGAGVELHARPGDAVRAGQPLMTLHTDTPERFDRARA
+ALAGGWAVTAADEAEAAALRSRSVILDRIG
+>MHAAABBN_00165
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+TAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERARAALAGGW
+SVGELDDDAARALRERSVILDRIG
+>LFPAFLNI_00447
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVAQGQKVLTLHTDTPERFERARAALAGGW
+AVGELDDVDARTLRERSVILDRIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001688.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5da3e993b2a689e322784840b726481a325a52da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001688.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02515
+MSTAAQTNPVQPTPAGTGRAPSAEAPREGGTVVVRSWTTPIVFTVFTVLALVVFGLNAPD
+AAATFRVSTEADAFRIPDLVADGAGGGWIVTAILVVLTVLAWMRAARGRAVGAVLGISFA
+LVFVAGFLIWVVGSAANTSVFLTGLIAGSFALAVPLIFGSMAGILSERAGVVNIAIEGQL
+LAGAFTAALVGSMTGSPWAGLAAAVVAGVLVSVILAVFSIKYLVNQVIVGVVLNVLVAGL
+TGFLFSTVLSENSSGLNSPPRFETLRIPGLADIPVIGPILFEQTLLGYGMYLIVAVIYIG
+LFHTRWGLRVRAVGEHPKAADTLGINVLRTRYVNVLLGGAVAGMGGAFFTLVQSSSFSRE
+MTAGMGFIALAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVT
+IFAVAGLVGRSRAPAASGVPYVKE
+>MOLHKGIG_00442
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLVAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TDGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>NAFOICDF_02386
+MSTAAPARESATPSERAGAASSGVVVRHWSTPVLLSVFTLVSLVVFALGASDSTAVFRIS
+EASDAVRLPDLLADPAVTGWALTAVMAAITAAAWVLTLRGRRLPGWAAGLFALAFTAAFL
+VWVVGAATNNEVFLTGLIAGSFTLAVPLIFGSMAGILSERSGVVNIAIEGQLLAGAFMAA
+VVGSLTGSPWAGLGAAIVAGVLVSWLLAVFSIRYLVNQVIVGVVLNVLVAGLTNFLFSTV
+LTADSDLNAPPRFPDLRIPLLADIPVIGPILFDQTILGYLMYAIVALLWFGLFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYVNVLLGGAVAGMGGAFFTLVSASSFSKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQFVFAILGTPVPSPFMAMLPYLVTVFAVAGLVG
+RSRGPAAAGEPYVKE
+>MHAAABBN_00163
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPETTATFRLSH
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTVVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
+>LFPAFLNI_00445
+MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSN
+ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI
+WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV
+VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL
+TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR
+VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA
+LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG
+RSRGPAASGVPYVKE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001689.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91cedc5b8aa6e04cb81870c8b4f74b1d2f803f8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001689.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02516
+MSQNPPQTPASEPVQPPGGAPVPAAGVTGADAPPAPERGSQESVLREILSGNAMVTALAI
+VLSLAISAVLIIVTSPDVIDAAGYFFARPMDTLSAAWTVVSDAYLALFRGSIVNYRADSF
+ADMIRPLTETLTVATPLIIASLGVAIAFRTGLFNIGGQGQFLIGAAFATVGGVYLDLPLG
+VHLLLVIVMGALGGLLWGAVVGLLKAYTGAHEVILTIMLNYVALHLVSYLLNTPFLRRAG
+TNNPISEQFPDSAAFPALLGDGFRLHWGFVMALVLTFLAWWMLERSTLGFRLRAVGANPA
+AARTAGISVKGGYVAAMAIAGALAGLGGVAHISGTEKVLTSGIAGQFGFDAITVALLGRS
+HPVGVLFAGLLFGALRAGGVTMQTQTGVPIDIVLVVQSFIVLLIAAPPLVRAIFRLPAPG
+SVRARANADVVTQPALAGAAVPGAAAEAVPAETGSATTSKGEGR
+>MOLHKGIG_00441
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPATTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYVAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+ALTGAGGHAAAPSTGVQEAAAAAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>NAFOICDF_02387
+MSTAVASRPAGARTQEDGSALRRLASSNGAVTVLAVLLSLVISAVLIVVTDEDVQDAAGY
+LFARPQDALTAAWKAVSGAYAALFRGAVFNYEADTFTDMVRPLTETLTVATPLIIISLGV
+AVAFRAGLFNIGGQGQFIFGAMVATWTAVHLPLPFGLHLLVVLLAGVVGGVLWGAVVGVL
+KAWTGAHEVILTIMLNYVAVNVLAYLLNTPVLRRAGTTNPVSEFLPESGMFPKLLGDGYR
+LHWGFVLALLVTAFTWWLMSRSTLGFRLRAVGANPAAARTAGMSVKGTYVAAMAISGGLA
+GLAGMTHVSGTENALNTSVAGSYGFDAITVALLGRSNPVGVLFAGLLFGALRAGGVTMQT
+ETGVPIDIVLVVQSMIVLFIAAPPLVRGLFRLPAPGAARARRTADVVTQPAVAGAAVPGA
+AGLASVPSAQTQDAAATAVAADPADPVAGTGPHREKGQDL
+>MHAAABBN_00162
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTVLAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPPGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVHLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLVAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQAAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>LFPAFLNI_00444
+MSTAAPQRPAPESDPRARPAPADSALRRVLSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQEAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001692.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f312ca6e83ede85721b8cf01b6a7cf3e9c53a1c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001692.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02519
+MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG
+YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT
+AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG
+VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE
+VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA
+WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH
+>MOLHKGIG_00438
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>NAFOICDF_02390
+MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA
+EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH
+TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE
+GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI
+AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD
+EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF
+AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR
+>MHAAABBN_00159
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>LFPAFLNI_00441
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001695.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f9569e6880916a4f79754dec748f7e638f78962
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001695.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02522
+MSTTAETTIAAPRTGRIDPKYTRDKGGRGNFEMLAWLFMRVSGVILVLLIAVHLTSNLLM
+GDGIQGIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTERGTARFWLTMI
+LYIATAVIITLGTLVIFTFDPCMVDASGALLEGSPAFCG
+>MOLHKGIG_00435
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
+>NAFOICDF_02393
+MSTTAETPLAAPRTGRLDSKYVRGESGKGNFEMLAWLFMRVSGVFLVVLVFAHIFANLMV
+GDGISGLDFGFVAGKWANPLWQLWDLALLWLAMLHGANGVRTIINDYAERDGVRFWLSMI
+LYVATAVIIVLGSLVIFTFDPCMVDASGALLEGSPAICR
+>MHAAABBN_00156
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
+>LFPAFLNI_00438
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001696.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a50b161d8beff3c5168a5e75d4108090951e833
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001696.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02523
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP
+YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>MOLHKGIG_00434
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>NAFOICDF_02394
+MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP
+YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>MHAAABBN_00155
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>LFPAFLNI_00437
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001699.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..758f658642acbcd56cffba9d2ed068cfec57fc38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001699.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_02527
+MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY
+PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM
+RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV
+FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA
+A
+>MOLHKGIG_00430
+MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA
+LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY
+ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL
+WLVKAFNPQVAAYTRQGRRA
+>NAFOICDF_02397
+MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA
+KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA
+GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI
+ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA
+>MHAAABBN_00151
+MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY
+VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL
+VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL
+VKAFNPQVAAYTRQGRRA
+>LFPAFLNI_00433
+MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV
+PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG
+ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI
+GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001700.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5e79ba3325cb184d53ca5a6994e8a522c1e3fff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001700.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02528
+MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD
+QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL
+VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED
+VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA
+QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI
+ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG
+VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI
+EALRYE
+>MOLHKGIG_00429
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>NAFOICDF_02398
+MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD
+ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI
+VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP
+EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP
+EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA
+LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG
+LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK
+DPIEALRHE
+>MHAAABBN_00150
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE
+SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>LFPAFLNI_00432
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001707.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..617e6587eb5ec2a72b8741cda53f9652b9d9c9d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001707.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_02537
+MDALDLPALAGARALELPGSELTHPFGPEADVYKVRGRVFMLVLEARGAMLVNLKAVPED
+GAALREAYPAQVTPGYHMSKRHWISLGPPPADPHDDDAPARLDAALVRDLVTESYLLVLE
+RSVPRRDWPVDPATFGRG
+>MOLHKGIG_02019
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>NAFOICDF_00761
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVVKVQGKLFVVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLVVAKLPRTRRPVD
+PDTFGRA
+>MHAAABBN_01728
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>LFPAFLNI_01956
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVMKVQGKLFAVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLIVAKLPRTRRPVD
+PETFGRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001708.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a053d8b19f80bb5fdd5851be07ae7b17e1822e6f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001708.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02538
+MTAKVLDGKATAAALKEELRERVSALTERGHTPGLGTVLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEEILAVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRRHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTQNLDELLGQADVVIAAAGSAHMVRPEQVKDGVIVLDVGVSCV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLSNVVEAAERAADAEDWAGER
+AEA
+>MOLHKGIG_00421
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVTPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>NAFOICDF_02407
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTLGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIRSIQKELPGDATEEQILDVVRELNEDPECTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>MHAAABBN_00142
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDIQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVGLAGKHVLVIGRGVTIGRPAGL
+VFTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>LFPAFLNI_00424
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAAEDDGRAGER
+AGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001709.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40782fedf20b7c03e6b90e4845e9ad6c90a9a045
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001709.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02539
+MTQTPDINTQPLSEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTALMDHGDTL
+MGLSLAHGGHLTHGMKINFSGKNYKIAAYEVEPDTYRIDMDKVREKALEAQPKVIVAGWS
+AYPRQLDFAAFRSIADEVGAKLWVDMAHFAGLVAAGLHPNPVPHADVVTSTVHKTLAGPR
+SGFILSTEEFKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLQGAQIL
+AERLTAPDMTELGISVLTGGTDVHLVLVDLRESQLDGKQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVAEIVAAALKPSPDVQALRARVVKLTEDFPLY
+DGLEGW
+>MOLHKGIG_00420
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>NAFOICDF_02408
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEQW
+>MHAAABBN_00141
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>LFPAFLNI_00423
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001713.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c231b5717c08faada5c27d6c1b0e418ad2e3d24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001713.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02545
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR
+>MOLHKGIG_00414
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR
+>NAFOICDF_02413
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR
+>MHAAABBN_00134
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
+>LFPAFLNI_00417
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001720.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a063bfed135c200c47c7d3e13ab005e94135a5ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001720.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_02553
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFRDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQEDGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKMFPHSMGEWTPDSKTAVATMGADDFR
+SNEKSVTMPADDTLTIEFTGEDGKTTVLKEGLKVLAGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLEAAGLNPNNGLAAIEG
+GLDKLDAETAEGVKKAIAAAYEEGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGIYQAVIEDCKKHGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFILESAGTVAVKNAAGETLISHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIAKVEEYLKEHDTEGLDLRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPQRKVGELDNRGSHFY
+LALYWARELAKQTEDAELVAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
+>MOLHKGIG_00403
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPVAEELEAQEETILGELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
+>NAFOICDF_02422
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFNDLLPEEQRV
+NDALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQADGYALPEYVDDPQTDKEKDA
+RKRYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKKFPHSMGAWTADSKTAVATMGQDDFR
+SNEKSVTMPKDDVLSIEFTGQDGTTKILKEGLKVLEGEVVDGTFMSAKALDAFLAEQVTR
+AKEEGVLFSAHLKATMMKVSDPVIFGHVVKAYFADLFAQYGEQLAAAGLDPNNGLAAIEA
+GLDKLDAETAEGVRKAIADAYQNGPDVAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGH
+MWDKDGAERDTLAVIPDSSYAGIYQVVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFVMEADGTVEVKDSAGEVLFSHEVEAEDIWRACQTKDVPVQDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEQYLQGHDTEGLDLRIMSPVEATKFTVERMRRGEDTITVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLINGGGLFETGAGGSAPKHVQQLVGENHLRWD
+SLGEFLALAVSFEHEAAHNGNHRAQVLADTLDAATGILLIEGKSPERKAGQLDNRGSHFY
+LALYWAQELAKQTADAELAAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYAPSMDK
+VSEVMRPSATLNGIIATLGA
+>MHAAABBN_00126
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQAHGYALPEYPDEPKTDAEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHEVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEGLDLRILSPVEATKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQLLEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELEAQEETILAELNGVQGSPVDLGGYYAPEMEK
+VTSVMRPSATLNAIVDKLSV
+>LFPAFLNI_00409
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTDEDGETTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRNSGR
+MWNKHDQTQDTLAVIPDSSYAGVFQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELGAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001721.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdfe715b109d350c82db5f32fe3507771b069a10
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001721.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02556
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG
+>MOLHKGIG_00401
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG
+>NAFOICDF_02425
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG
+>MHAAABBN_00125
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG
+>LFPAFLNI_00407
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001722.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd4635c772b2ec426729a30c7bba316cf50eec4a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001722.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02557
+MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG
+TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF
+TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP
+ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI
+TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV
+TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT
+LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR
+GRALEVSAD
+>MOLHKGIG_00400
+MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>NAFOICDF_02427
+MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE
+WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL
+WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG
+TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY
+VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ
+SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP
+LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG
+LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED
+>MHAAABBN_00124
+MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>LFPAFLNI_00406
+MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001723.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd7ae5a3556e7ac684b28717319b398ff3cd456a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001723.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02558
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPRD
+HADRHAWDVALADAVAAHEPDWVLCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVSGCTVHVVDAGVDTGPILAQAAVPVLDTDTESELHERIKVQERALLLRV
+LGELSRR
+>MOLHKGIG_00399
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
+>NAFOICDF_02429
+MRILALVSGSGTNLQAVLDAVASGALPLEVAAVGSDVPGVQGLARAEAAGIPTFTVAPAD
+HPDRAAWNVALAEAVAAYEPDWVVCSGFMRILGAPLLEAFPGRIVNTHPALLPSFPGAHG
+VRDALAYGVKVTGCTVHLVDAGVDTGPILAQAAVPVLDTDTEEVLHERIKVQERVLLLRV
+LGELAAGRSPRQA
+>MHAAABBN_00123
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
+>LFPAFLNI_00405
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001724.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c3f92d01df43e6cc7f888ccb9914e7c9d7d86c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001724.fa
@@ -0,0 +1,19 @@
+>ACLBLIBL_02559
+MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA
+ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP
+>MOLHKGIG_00398
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>NAFOICDF_02430
+MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA
+LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT
+VRAQQTCADDFTATVERRTGVAQLGG
+>MHAAABBN_00122
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV
+RAQQACADEFTRQVEERTGVPQLRP
+>LFPAFLNI_00404
+MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL
+VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV
+RAQQACADEFTRQVEERTGVPQLRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001726.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa2255b312d6411879b7858245465c16aba688c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001726.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02561
+MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF
+PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP
+SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL
+WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI
+GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV
+VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP
+VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG
+>MOLHKGIG_00396
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>NAFOICDF_02432
+MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE
+VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR
+RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR
+LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG
+RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG
+>MHAAABBN_00120
+MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>LFPAFLNI_00402
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001729.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dc6decaa5fea6f116b73343c6604912470f2489
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001729.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_02565
+MSAVSDAAPVSPRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMAFTGY
+GSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGGTRTT
+VRTDRMGVVDAVLDVEMEPGWRTATLHVGDDEHVTMDLYICHPDARIGLVSDIDDTVVVT
+SLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQTLTRFL
+GRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQHDPEIY
+ADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQLEDLG
+ILPVGFVDVQPEGWKEDILGDDEVLSAAEHGAAALGDEADAPDTAAEPRVPAGEAAVGDG
+AADEAEAAEAGGSR
+>MOLHKGIG_00391
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDDRSTDEEAAR
+>NAFOICDF_02436
+MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA
+FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD
+LVTTVRADRMGVVDVVLDVELEPGWRTAVLRVGDEEEVTTDLYIASPDAKVGLVSDIDDT
+VVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQTL
+TRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQHD
+PEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQL
+EDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQD
+>MHAAABBN_00115
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAPGQRDGRPADEEAAR
+>LFPAFLNI_00397
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDGRSADEEAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001731.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a1a9e862b0a7c8ed9e4f2495286a130a371f784
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001731.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02568
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD
+>MOLHKGIG_00388
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>NAFOICDF_02439
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD
+>MHAAABBN_00112
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>LFPAFLNI_00394
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001732.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51f4fdb5609fecbec39db0b0fdb225efcab3656f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001732.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02570
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQSQVVDAGDMAVNPFNIGEAIEAIQQDA
+MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFAAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ
+RIGDRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLITLMADRRASRAAAGEEQGR
+>MOLHKGIG_00385
+MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR
+>NAFOICDF_01755
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATETSPFAQAQVVDTGDMAVNPFHIGEALESIQQDA
+MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAAYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGLTSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAEGGVDA
+>MHAAABBN_00109
+MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR
+>LFPAFLNI_00391
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDQAELTGVAASHVAYDLISLMADRRATRAAAGEEPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001734.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5080d71612b960076bf5ea95efa7f682993fe331
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001734.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02572
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLVGQ
+DVWQRVFTARSPRVAQVGGATAGLYCIVYGVAGALIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGATAEDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTLGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDAAARERL
+>MOLHKGIG_00383
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASLFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIAATDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGAVAEDAATE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>MHAAABBN_00098
+MTDTTVPLIILALYIVFVVGVGIYARRKATSDSSRDYLTGSGDVGVWVNGFAIFAAFATG
+GTMLGNIGLSYVGGWGYITAYNAGVALGYVITTFFLAKTLKNMNVATVPEFIRKRFHGRT
+LNILVPIILMATLVAYVVAQMKVGGLLGEQLFGFPYEWSVIVVGLVYIFYTFYGGMRAVT
+LTDFVQGLLMISVVVICGGIAFGQHGGPANLYEMAVAIRPKWEGTEQFPLISYIGAFIIW
+ATVNAVLPHTVMRIFAAKNERQGRASLAIGLGLYVLTAIATTIFVVAAVIIVQGEEELAS
+ADSTFLIFLAEQTPSWVAGLAFAGIFAAVMSSVSAMLLALGGAFAYDLVAELRPSMSDRS
+KRRLTSISVLGFGILTLVLSLNPPELLTLLYTAAMGMLASGLFFPTLLGIWWKRMNSSGA
+LAGLIVGVGSYLFLLWGTGMPSLSQVTVSIPLSLLACIVVSLMTKPPTDAEMERITIAHE
+REFLIQGQDDLIETAERH
+>MHAAABBN_00107
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSALKERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPIFRGEATASEDGATAEDEIPE
+TAAELASNRGWVLLLGAVVLGLAIVVPNVVAALTIAYDILVGGLFVAIVGGLVWQRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>LFPAFLNI_00389
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTVGLFALMLPLSLANAGGWGAMQERLGAEFFSWDGIGVQSIVTYSVVYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIIYGVAGAVIGMAARTVTADIATQDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATASEDGATAGDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTPPTDP
+AVLEAWRVRSRHGVDAVAGASLTRNPGACDPPMPARWSGQTMRRRAILPQAPPGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001737.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f68623effa0534171b183ca7d7ab512f4fd6dab3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001737.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02575
+MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>MOLHKGIG_00380
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
+>NAFOICDF_02447
+MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>MHAAABBN_00104
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>LFPAFLNI_00386
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001741.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e26289842e489aa8e565502f87e5b92b737e5ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001741.fa
@@ -0,0 +1,79 @@
+>ACLBLIBL_02592
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED
+>MOLHKGIG_00370
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>NAFOICDF_02451
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG
+>MHAAABBN_00086
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>LFPAFLNI_00377
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001745.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2064e86961737cdb060a2fb46d7e3e7190e570a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001745.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02598
+MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG
+ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV
+ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+SALLRCIDHVVEQLG
+>MOLHKGIG_00363
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV
+AALLRCIDHVVERLG
+>NAFOICDF_02457
+MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE
+ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD
+NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV
+ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+TALLACIDHVVARLG
+>MHAAABBN_00079
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
+>LFPAFLNI_00370
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001747.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77f6406b5eef94995aa6e393cc3cece30d94ab92
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001747.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02600
+MPRRTAAPAPDPADPRRAHGSPGRRRDAGDTDDEEQVPHMPTGRIKFYDSAKGFGFAQTD
+EGEEVHVPSSALPAGVTELRGGARVEFGVAEGRRGKQALSLRVLDAAPSSVRNHRPRPAE
+MAVLMEDLIRWLDETSNGLRRGQYPQSGQAKKMAQVLRRVADDLEA
+>MOLHKGIG_00361
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQASNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
+>NAFOICDF_02459
+MPTGRIKFYDSAKGFGFAQTDDGEEVHVPAAALPAGVSDLRSGTRVELGVAEGRRGKQAL
+TVEVLDDAPSVVRNHRPSPEKMAVLMEDLIKVLDQTSNGLRRGRYPQRAQAQKIAAVLRR
+VADDLEA
+>MHAAABBN_00077
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
+>LFPAFLNI_00368
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001748.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88c86a363726b02733c838c4d0dfc8a7cf457723
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001748.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_02601
+MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL
+>MOLHKGIG_00360
+MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW
+PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>NAFOICDF_02460
+MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP
+ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS
+>MHAAABBN_00076
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>LFPAFLNI_00367
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001749.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf622344088b2c10f503e0da725656f47a2f7702
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001749.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_02603
+MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDE
+PDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSSGDGTMAVALPLEGVRSSVER
+VTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPD
+RKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDPLGGPG
+AAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ
+HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEVSHTGPLGLVA
+PSGAGASVVDAARRSRLLRAGERFRRASAERRPRAGTPAQAPAEGAASPGEEEPGPAAPD
+RP
+>MOLHKGIG_00358
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAGPPTGPLALAAP
+SGAGASAADAARSSRLLRAAERFRRASAERRRRASAPAQAPQADPPSPGEDDPAAERDAR
+P
+>NAFOICDF_02462
+MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELL
+RQLDDDLSHNRDEVSIYLTTMSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADG
+PALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRSGEGSLAIALPLHGVRTSVER
+VVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG
+RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITRE
+EDVAAAMGRIESEAGRMHRLVEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPD
+RKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYTPEGTPIEIAVGTRDAFGGDS
+GVDGTRHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQHG
+GSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTGGSTAAGS
+AGALETGQRRRLAWAGERFRRASAARRQAQAGTSPAQAARDGA
+>MHAAABBN_00074
+MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
+>LFPAFLNI_00365
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001753.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75cc70f8f347603fff90378e675febf1a2233da8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001753.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02608
+MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE
+AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN
+>MOLHKGIG_00353
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>NAFOICDF_02467
+MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY
+QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER
+>MHAAABBN_00069
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>LFPAFLNI_00360
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001759.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a75c6a27e8213b2bd5c510d8690b86bec78f8d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001759.fa
@@ -0,0 +1,75 @@
+>ACLBLIBL_02625
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV
+VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA
+AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG
+SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF
+FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP
+EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV
+VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL
+AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT
+RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE
+EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL
+STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG
+VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR
+ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG
+RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP
+>MOLHKGIG_00344
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>NAFOICDF_02477
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV
+VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA
+AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP
+LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY
+RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER
+VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE
+ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV
+GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR
+WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL
+AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG
+QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA
+PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA
+LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP
+PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA
+>MHAAABBN_00060
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>LFPAFLNI_00351
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA
+AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL
+EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT
+VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG
+YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV
+RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV
+LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW
+ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP
+DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT
+TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP
+DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR
+RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW
+EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001762.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80428720ceabf529a2d1ddc146f335226c06f2d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001762.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02628
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+>MOLHKGIG_00341
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>NAFOICDF_02480
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+>MHAAABBN_00057
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>LFPAFLNI_00348
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001764.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8d87b4bbc36c05388ae60475d7d5ac63cb445d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001764.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_02673
+MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE
+HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT
+DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA
+RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL
+HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL
+RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV
+GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR
+AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF
+>MOLHKGIG_00339
+MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD
+RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL
+RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL
+ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL
+DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW
+DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA
+AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA
+LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF
+>NAFOICDF_02485
+MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA
+VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE
+RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ
+SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT
+AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH
+RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW
+EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT
+VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL
+DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF
+>MHAAABBN_00055
+MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG
+RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
+>LFPAFLNI_00346
+MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG
+HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001765.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e53e81428263441b8fd68a4412a0957191e807bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001765.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02674
+MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI
+NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL
+HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED
+>MOLHKGIG_00338
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
+>NAFOICDF_02486
+MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS
+AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE
+QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS
+>MHAAABBN_00054
+MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL
+NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD
+>LFPAFLNI_00345
+MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL
+NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL
+NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001766.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f706528442892fd6769e89c0ee1eec22501d7d95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001766.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_02676
+MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG
+GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR
+RRSEG
+>MOLHKGIG_00337
+MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD
+>NAFOICDF_02488
+MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL
+EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF
+LEKHAQERKQG
+>MHAAABBN_00053
+MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD
+>LFPAFLNI_00344
+MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE
+GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001772.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..597679a58776dc44e78bc055e8203b32f3e57425
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001772.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00008
+MKHRSLTLTAALAVTALGLTACGDSGDAGAGGDEKYTVGINQLVSHPALDGAREGFKEAF
+SDAGLEVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTAAAVKDKPVVFM
+AVTDPKGAELVASEEAPGGNVTGVSDRNPVQEQLQLLKDVNPDAKTVGIVYNSGEANSAV
+QVEQAKEAGQELGLEIKEATVTNSSEVQQGVQSLSDVDGIYVPTDNAVVSALETVVGFGE
+ENDIPVISADIDSVDRGALGTYGIDYKAHGKQAGEMAVKILKDGANPGEIAVGFADPANL
+QLVLNPAAAEAYGVEIPAELSDEADRLVEG
+>MOLHKGIG_00327
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
+>MHAAABBN_00043
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
+>LFPAFLNI_00334
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFEDAGLDVTFEEQNAQGEQATVTSIASTFANDADVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPKGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGKEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001780.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77b3420a6bf3d7cf693e7ee6bb6b889de0bd58e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001780.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00127
+MFPITDDQEALVDAVRDFAQQRVAPHALEWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERKDAILIFEELSKADPAFAAYISIHNMVAWMIDSYGNDEQRAQWIPELMSMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDDYVLNGVKQFISGAGSSDYYVVMCRTADTGAKGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVANRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMAVKLETAHTLLMRAA
+DALDRNDPDTVRLCAMAKLVATESGYEAADAALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIGG
+>MOLHKGIG_00243
+MDVLAEAGELGLGGIYVGEEHGGTGLARTDAILIFEELAKADPAFAAYISIHNMVAWMID
+SFGSDEQRARWIPDLVGMEHLASYCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISG
+AGSSGYYVVMCRTADTGARGISAVVVHKDTPGLSFGPSEKKMGWHTQPTRQVIFEDVRVP
+VADRLGEEGDGFRIAMKGLNGGRLNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQA
+LVFELADMSVKLETAHTMLMRAADALDRNDPDTVRLCAMAKLVATESGYEAADTALQLHG
+GYGYLHEYGVEKLVRDLRVHRILEGSNEIMRMIVGRGLIG
+>MHAAABBN_02255
+MFPITDDQKALVDAVRDFAEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEYLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVADRLGEEGDGFRIAMKGLNGGR
+LNISACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELAEMAVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
+>LFPAFLNI_00243
+MFPITDDQKALVDAVRDFTEQRVAPHALDWDAEKHFPVDVLAEAGELGLGGIYVGEEHGG
+TGLERTDAILIFEELAKADPAFAAYISIHNMVAWMIDSFGSDEQRARWIPDLAGMEHLAS
+YCLTEPGAGSDAAALKTRAVRDGDHYVLNGVKQFISGAGASDCYVVMCRTADTGARGISA
+VVVHKDTPGLSFGPNEKKMGWHTQPTRQVIFEDVRVPVAGRLGEEGDGFRIAMKGLNGGR
+LNIGACSIGGGLAALDKATRYLKERSAFGEPLTTKQALVFELADMSVKLETAHTMLMRAA
+DALDRNDPDTVRLCAMAKLVATEHGYEAADTALQLHGGYGYLHEYGVEKLVRDLRVHRIL
+EGSNEIMRMIVGRGLIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001781.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abc61c48acdf511f2ce32f28a29ced2d082cdeee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001781.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00142
+MEPLNLSSPGLSPAVWRVTTVSRVEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIK
+QLEAALGVTLLERTTRRVDLTDAGRLLLDRSRQLLTDLASLEHDVREVGRGAAGILRVGF
+VGSATYRLMPAIVRAARDAMPGVRLQITGEKITPALEDALLENRLDVAVLRPPVRAAELT
+LTPVEAGRLLLAVPAGHRLAAEDGPVALADLVDEEFVSYPRDSALTAIVQEAARRVGFRP
+RLVQRAGETSTVMAFVAAGLGVAVVPDDVRRPGAVSGVAFRPLSDMPDVELAVAAKADAR
+SPLVPAFVELACRTAAALAEAGEDPTPDPDRPAQET
+>ACLBLIBL_00807
+MDVHQAKAFLAVAEELHFGRAAGRLQIAQPALSRTVKQLERSLGTDLFVRSTRRVELTAA
+GLALLEPARTLVQASQTAREAVQSALAGETGTVRLGFAGASTHGVVGQLARSVRRRRPGL
+TLEIHSSQFSHLGLERVLEGSLDVAIGRWDFIPHELASRVIAHEEAIVALPADHPHAQET
+GPIDVGLLRDEPWVTLPSGLGSALANRLTTLATSAGFAPRVVQQAPDSFTQMVLVAAGLG
+CAVTLDSVRDNSATPGVVYRPVAGDNPPLEVRMLWRSLDASPALRAVLDLAPAAEPAGVA
+PARTDAAD
+>MOLHKGIG_02037
+MVGITLRHMEYLVAVIDEGSMTAAAARLHVTQATVSMALAECERRLGVPLLVRQPAKGVA
+ATLAGHRMAVQARRILGLVHEMEASVPAMPGELAGDLEVGCVPSLSPQAVPVLAEHFSRR
+HPRVTLHYREGAATDLQREVLQGRLEMAVMFSRQQAPGLRSIEVARAQLKVMLPEGHRLA
+AAHEVAFADVAQEPAILIDLPPSTERSLEFMRAAGVEPTLRWSSNNLATVASLVGAGLGW
+SLRYTLPGEQPAARGLVEIPVADPTPPNAVCAVVPDGDRVDQRVRHALEVLRRVLSEEEG
+RPDVDCA
+>NAFOICDF_00104
+MEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIKQLEAELGVRLLDRTTRRVDLTEA
+GRLMLERTRSLLADLASLEHDDDIASAVKPELLLDVQQGADGNSTVYDFVLDPVSEKTHP
+TAIRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001784.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b47b308f681bf90ec0a3cc8bdce6777b03e5b87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001784.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00189
+MKSSLLTATGLPRAAAVLAAAGLLLTGCAADPTLDENWPEIRQKVVDAQSLRLQMDGEAA
+PDAEGSGQDSEITAAAADLSGATDDSHLKGTMDMDMGADSVDMEILRLGEEVFLKMAADG
+DGVPAEMAMFEQLVGDRWMLMPADEADSMAGISLKEIMDDLEADMPAAEAFDGKDLKAEK
+VELDGQEYLKYALPEEFHDFARTMYVHPDDETLHRLEGTGGEDAEADTTATFSEWNAVQA
+PERPAEDQIVDMAALQGLTG
+>MOLHKGIG_00200
+MKTPARLAVGMLAASGLLLTGCASDPTLDESWPEIRQKVVDAESLRLRVEGTAADKEEEK
+DDASASAAPSASLGTDASQSLNVDLAGATDDSHLKGTMNMDMGAATMDIEVLRRDADVFF
+KLKADGDDLPQEMGMFSTLVGDRWIKTSADQAAQMDISLQEIMSDLEEDMPAADAFDGKD
+LKAEEVELEGRTYLKYALPEEHHEFGRTMLIDPESTTLYRLEDVNSEDEDVDANATFTEW
+NAVEAPEAPAKEDVFDLAELQELAG
+>NAFOICDF_00125
+MTPRLSRASLTALLGAGALALSACGGDPAPAASSSAEAASSSAAGPTVSTSPNGSDAAAS
+SSSESAASESSASDVPAGQAPEAEVVWKDIQQGLDEAESVHILAEIDGGSGSEVQRVDLA
+GDVAGTTVQGSVTGDSADFTGTMDFIHVGGQTYLKMDGSGGGDASRMAEALDGRWLVDTQ
+GMIPVDEMNPQVFLDEMKQEFSTVTDAELAAMEGEVVQVDGEEMYRYSDDSSWTMTVDKD
+NHVREFRDTKSSGEGTVTMDRWNQVTPAAAPPAAEQVTMDELSQEIASSGAGSSAGATAS
+ATVDG
+>NAFOICDF_00145
+MKSPKIAAAALLATGGLLLSACATQPTLEESWPEVRQKVVDAQSLHLKMDGTAKEDASGS
+ASASSSSDIQSGTIDLAGATDDSHLKGTVAAKMGDGEVNMDILRLGQDVYMRINKAEGGQ
+APEGMDAFQQIVGDRWMLMPADQASGMGELSLGTVMDDLEEDMPAADAFNGKDVKAEEVD
+LDGRKVLKYALPEEHKDFGRTMYVDKETKELYRLEDVNSVESEADATATFTEWNAVQAPE
+RPAEDEVFDMQKLSEGLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001789.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..260520b8c216e4dd10110dd313b016b629205d52
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001789.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_00230
+MPAPPPPAASPPHADGRATSDGNAFSRAMRPVNTVMERFIPSSLMFSILLTAIVAVLALI
+LTPTAPVDVLMGWGNGLSGLLAFMTQMALILLLGHILANTGPVRALLTALARVPRSAVQA
+YSFVFVVAALASLVTWGLGLVVGGLLAREVAAQGRERGLRLHFPLLVAAGFSGFVVWHMG
+YSASGPLTAATPGSFLEDSLGGRTVPISDTVFTWWNLTAAAVAIVAVTLVLYLIAPRGDD
+RIHELDVDARERAVVTEPELETPADRLDASRIPTLLVGLALAAFLVVHFVQGGTLTLDIV
+NWSFLALIFLLVRSAQELIQLTAHAASNVGEILLQFPLYAGILGMMTASGLIQIFSDALV
+AVANPTTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLSAGAELGVDPAITIMAVSYGDQ
+WTNMIQPFWALPLLAIAGLRMRDILGYTTVVLLVTGVVFAGTMLLVSL
+>MOLHKGIG_00153
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVPAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
+>MHAAABBN_02167
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLGGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVSAPEIETPADRLDASRVPTLLVGAMLVIYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTSTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
+>LFPAFLNI_00161
+MSATSTRPPTPRPPGRAAREGTFFSRAMRPLNTTMERFIPSSLVFTIVLTFAVAALCLLL
+TPAGPADVVVGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAY
+IFVFVVAAAASLITWGLGLVVGALLAKEVAAQARECGLVLHFPMLVAAGFSGFVVWHMGY
+SGSGPLTVATPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDR
+IVELEIDARDQDAVSAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVN
+WSFLALILLLVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVA
+ISNPVTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQW
+TNMIQPFWAIPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001790.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5273e83bb4e478b702c577bdc8c6409ec7e87afa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001790.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00239
+MSRRRRVRPLSTAAALAVVAGLCAPGALAQDPVPAPDAPEVRSAVEDLSRPASPAEERSW
+DAARAELAEDTAGDAFYRPPATIPARPGTLIRSEPSAFYLDPVKLIRVPARATRILYSSV
+DAQGRPMAVSGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGEQYEGVGIS
+SLLGRGHTVVVTDYEGLGTPGAHTYMVRESQAHAVLDSVRAAAQVDGAEVTASSPVALAG
+YSQGGGASAAAAELAPSYAPELDLKGAYAGAPPADLVQVADRIDGGSYSAFLLYAMSGQL
+AAYDVDPAVYLNEHGRQVLTDAVETCVTDSGEHGSLDSSALTHTGQSFPQLVRTDPQLAG
+ILAEQKLGAEGRRPEVPVMIAHSLTDDVIPYRTGRELGLRWCAEGARVRFDPILTPTHMG
+GYVAALPRMHSFLDAALADRWTPNSCGWF
+>MOLHKGIG_00145
+MAPVRRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVEDLSQPATTAEDA
+RWNAARDALAAASADDPFYLPPTTLPSTPGALIRTEPTAFYLDPVRLVQVPAHATRIMYA
+SQDAQGRPIAVTGTVLTPTAPWTGAGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVG
+ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVAGSGVTATAPVAL
+AGYSQGGGAAAAAAELAPDYAPELDLKGAYAGAPPADLVQVAGRIDGGLYAAFLLYAMAG
+QLAAYDVDPATHLNETGLTALDGAAETCLAGSLAYAHLDSATLTHTGQDFPELVRSDAEL
+AGILAEQRIGAQGRRPDVPVMIAHSVTDDVIPYRAGRDLGRRWCAEGARVRFDPLLTPTH
+VGGHVASLPRMGAFLDATLADRWTADSCGWF
+>MHAAABBN_02159
+MAPARRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDA
+RWNAARDALAAASVDDPFYLPPAVVPATPGALIRSEPAAFYLDPVRLVQVPAHATRIMYA
+SQDAQGRPVAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGAQYEGVG
+ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVSGSGVTSTAPVAL
+AGYSQGGGAAAAAAELASDYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAG
+QLAAYDVDPATHLNETGLTALAGAAETCVAGSLAYAHLDSATLTHTGQDFPELVRSDAEL
+AGILAEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTH
+VGGHVASLPRMGAFLDATLADRWTADSCGWF
+>LFPAFLNI_00153
+MAPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDARWNA
+ARDALAAASADDPFYLPPATVPATPGALIRTEPTAFYLDPVRLVQVPAHATRIMYASQDA
+QGRPIAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVGITSL
+LSRGHAVVVTDYEGLGTPGAHTYMVREAQAHAVLDAVRAAAQVSGSGVAATAPVALAGYS
+QGGGASAAAAELASEYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAGQLAA
+YDVDPATHLNETGLTALAGAAETCMVGGLAYAHLDSATLTHTGQDFPELVRSDAELAGIL
+AEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTHVGGH
+VASLPRMGAFLDATLADRWTADSCGWF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001794.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..016c68b5c8d52b0202ab129d558bb4425931200a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001794.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00309
+MTVCLGNICRSPAAEAVLHRKLAEAGLADEVTVTSAGTADYHVGDRPHELTRAVGGELGY
+AFESVGVHLAAGHLDEADLVLVMDESNLADVRALAATDEQRAKVRMMGEFASDADTAGVL
+EVPDPYGHPRAQFEDMYRQLEDAADGVVAAIRDGRL
+>MOLHKGIG_00083
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLHDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDEADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADSAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
+>MHAAABBN_02096
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDDADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADRAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
+>LFPAFLNI_00077
+MGVQLSAELVDDADLILVMDEANLADTRRLATTDEQRDRIHLMGEFASDADSAGVREVPD
+PYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001797.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6b2d3b169f9847fcece2ef27b6383d663335c8e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001797.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00352
+MSTSLHPPQAVIGEPEVLEDVRADVVSHPAWLRLKAAATALQGLQAKDGSVPDPADHPAA
+GGHVETITAAVAELAPLFPHDAAYLAALPRDFARWRDGGFGVPDFLDSLVAFQPQEHRVD
+GIRHLVVFPMYTQNGSSSRHVEALLVEAIWPEFIAQLEAGDYGNRLFLSLRLLDFTPGYE
+TNSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVAAAAEITRLDLPEDAAELVADQD
+LAEQTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDLTAFRETVRIEREL
+SARAAAGEELTAVQAQTLRHAKLVQYAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHR
+RHVVQWRDVKLTIDWDRLAEAVVELGDAIDRLYWESIDRPKTVHWLKAYELVASVVAPHP
+ASVWAQGLPREVLAGPPKEMTDLVLDDEFPLSMFFEALGKKLRGVIESTAGIRAADA
+>MOLHKGIG_00051
+MSTTLQPARTDGVASEAPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEVTQLELPAELAELLSSQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTGLEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMRGVIESTAGIRGTDA
+>MHAAABBN_02064
+MSTTLQPAQADVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+KHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAALEAGDYGNRLFLSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
+>LFPAFLNI_00046
+MSTTLQPARTDVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLTALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLANAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001799.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..340367af964506fa76b927b6c513286753b73fd5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001799.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00400
+MTSSLTTRRTFLGASVGALALAGLTACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEGTSVHWHGL
+ALRNDADGVQGLTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMDHGSMSQDSSSGMP
+MKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDTAYR
+VGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGHAYG
+IIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYDWGI
+NGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVIIKP
+RQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>MOLHKGIG_00628
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADTVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTTTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>NAFOICDF_02201
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>LFPAFLNI_00603
+MTSSLTTRRTFLGASVGALALAGLAACADPVISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRHTIVFDFEADNPGQWLTHCHNAYHAVAGMMGVFSYIH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001800.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31f34fb612aed1646faa3609ec489f4020147a49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001800.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00401
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPNTDLPEPLGLAEST
+DRGQSWTVLSRGGQSDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGAGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>MOLHKGIG_00629
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPK
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>NAFOICDF_02200
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPEYG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>LFPAFLNI_00602
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001804.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4bbdde5f94bf5ab38db023acca10d735009cc6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001804.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_00459
+MESTQPFVLSLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQHHVGK
+FPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEERLVV
+EWSADPVNWAKRGPLAARFPVLEIADPSTEAFPGFDHVLLSYGDLQSMVTETRYAGWRTA
+LEAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPAQPER
+YTFSLLRVFGSNTPQVQIDAAEKHYKEALMTRRFGLNRN
+>MOLHKGIG_02273
+MPHSDPVPEPFVLTLGSVLDAAGLDPHEVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HLGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGGLQSMVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSNTPQAQIDAAEKHYKEALMTRRFGLNRN
+>NAFOICDF_00408
+MPLLASLEERLVVEWSADPVNWVKRGHLAARFPVLEIADSTTEAFPGFDHVLLSYGDLQS
+MVTETRYAGWRTALQAVHGIYLIADDAASQCYVGKADGERGVLGRWEAYARDGHGGNVAI
+RDALELDPAQPERYTFSLLRVFGSNTPQAQIDAAEKHYKDALMTRRFGLNRN
+>MHAAABBN_01965
+MESTQPVPEPFVLTLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HVGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERHRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGDLQSLVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWAAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSSTPQAQIDAAEKHYKEALMTRRFGLNRN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001806.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6c4ad5e8cd2683dddb9d41471e2b319978b11ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001806.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00463
+MTRLLPGDSLTLDLAPEDPADLLARLRAAGVAMNESAERLITDARVCAVVPERVTVVERT
+LAELGLPDGGTLPELRRAVEAAGLRECPPTVAPLLRLVTLDQANAPDSLLRHGRAPDDSA
+HVFSPSLSDEPGVHRGLYLRVVDHVPWLRGFVCDDLHVFGPEDRWILAL
+>MOLHKGIG_02259
+MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR
+>NAFOICDF_00700
+MADLIDRAGIELTLAGDPHELLTQLQAAGVRFNDSARTLLFRPALARDLQTSRPVRVVER
+SLTDLGLPNGGTLPQLRRAALAAGLAPCPPAVAPLLRLRTLDQVNAPDSVLRHGRAPEGS
+VHVLSPSLGEDPRVHRGFYLRVVDEAPWLRGFMCDDLHVMGADDRWVLSAPTSAP
+>LFPAFLNI_02190
+MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001807.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d7ecd9b4b3fea144442c9877476acbce2c73018
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001807.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00516
+MTITAAETQSLTAEATAVLAAMPGVSYAQFLAEAPEVPGIVAVVADQAARARLGVEAEET
+GLLAVTVAPYGLRARDVRAAFQSGRTAVSPLRQALAALLEDELGLDVERTSPGAAGAGFT
+LTPESEDALTAWMRAHLTLRAWATQDASVLADVADQVNADLAPALALDGVAAPSAHLRER
+LAAMTAAARRSATI
+>MOLHKGIG_02221
+MTITAIDTSSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVADESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGGSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>MHAAABBN_01937
+MTITAVDTPSLTAEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGVGFA
+LTPESEETLTAWMREHLTLRAWVAQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
+>LFPAFLNI_02160
+MTITAVDTPSLTTEAAAVLAATPGMRYAEFLTAAPAVPGIVAVVAEESARAALGLTPAAG
+DVLAVDVADESLQCREVRAAFQSGRTGVSPLRQAFAALLAGELGLDVERTSPGAAGAGFA
+LTPESEETLTAWMREHLTLRAWVSQDASALEGVAREVAADLAPALQPGALEAPVAQRVAA
+MRASARRSATL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001808.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af946fc31d932a8f95e21cf4d9674d3c992e78e7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001808.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00530
+MEHIDETALPAPQDRVATASREVDAPAGVVFELIADPARQPEWDGNDNLAGAEPGQRVTA
+AGDVFVMTLRKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGIRDEPRCRVT
+HTYDWTELTDPGRIRRALRTGPEQLRASIDRLAELARTQPQA
+>MOLHKGIG_02214
+MEHIDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRVQKALRTGEGQLRASIDRLAELAERQG
+>MHAAABBN_01927
+MEHIDETALPAPEDRVVSATHHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLAELAERQD
+>LFPAFLNI_02153
+MEHFDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLADLAERQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001809.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6f51753fd5718c085a52adab2a253f10a6e3c9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001809.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00531
+MASVSFRSATRQYPNAPRPAVNRLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSSG
+SIHIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRAQIAQ
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKDGTLQQVDTPRSLYEKPVNVFVAGFIGSPA
+MNIFRMPVAADGVHWGESVIPVDRATLADAGQSVDLGVRPENLEITDRGGLAVEVDTVEE
+LGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>ACLBLIBL_02650
+MARLVLNQITREFGDFVATDRVSLEVDDGDFLVLLGPSGCGKTTLLRMIAGLLEPSSGSI
+EVDGDDITALPARKRDLAMVFQSYALYPHLTVEKNLAFPLRVRKLPKAEIAARVRAAAEA
+VEIDHLLSRKPKELSGGQRQRVALARALVREPKAFLMDEPLSNLDAKLRTATRRELAALH
+RRLGATFVYVTHDQVEAMTMATKIALLNGGRIEQYGTPEQLYDTPSSVFAAGFLGSPAMN
+LLDATLTTTDGRITAFAPGVEAVLWEGATPERDVVLGVRPEHLSVFAGGAPEAVPTAGAA
+LRGTVELVENLGREQLVHCRVGDERVTVSCAREEAWQAGELVVIAAPLTRLHLFDRRSGR
+RLEWRPAAQSEAPLRAAMAPSAGRPQENASRFRAARGGATAPASRSADVRSTEEAAQSEA
+SLRTATR
+>MOLHKGIG_02213
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTAVDLGVRPENLVVSDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>MHAAABBN_01926
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTTVDLGVRPENLVISDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHADTGERLNR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001815.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c28745acc01005a79ffe9cd8a9d1d6145ca54cd3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001815.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_00561
+MSESTGFSAAEKAAMAERAEELRAQRGGKKKADALQDLMEKIEAMPEQDRALAVAVHQIV
+TEVAPELEPRTWYGMPAYARGKDVLVFLQVSSKFDVRYTTLGFNESAALDDGPMWPTAYA
+LTALNDDVRARIADLVRRAVG
+>MOLHKGIG_02188
+MSESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLATIEEMPEPDRALAVAVHRIV
+TEVAPELDPRT
+>MHAAABBN_01902
+MSESTGFSAAEQAAIAERAQELRAQRGGRKKADALQDLLVKIEEMPEQDRAMAVGVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG
+>LFPAFLNI_02133
+MTESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLAKIEEMPEQDRAMAVAVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001816.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d80330e74a961adf0950cfc8e2cfe25e0a4594aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001816.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00562
+MPSSAAPPSDAASSRPDRRGSSGSVGTASRTLLLVVVMALFIWLATSVRLPDIDTLRDRL
+ASFGFWSWLVFVLAYAGVALTPVPVTLMALTGGVLFGAVQGSVLSVAGALLGSIGAYWIA
+RALGRDVILRGLGRHADTVEEHLEDAGFLALLTLRVAPGLPYWPVNYGAGALGVPSGMFV
+GSTAVGVIPGQVSLVALGAFAVHPGVLNGVILGAGWLAVGVLTVWAARHWRRAANHDDGE
+GGED
+>MOLHKGIG_02187
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAETVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLTVGGLTLWAVRHWRRAARSAEEP
+ENPQSGHDTPSPRRRRGVS
+>MHAAABBN_01901
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRGLGRHAETVERRLEDTGFLALLALRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
+>LFPAFLNI_02132
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAATVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001822.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddb5cfafb06f02cba3fb039a1130cc7509a552dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001822.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00637
+MSEHTPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVLD
+LAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGLLPQV
+QAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHASS
+VHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYEVIRG
+KGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVIQ
+PELDAAEMRALHSSADALRREARSLGF
+>MOLHKGIG_02135
+MSEHTPAHTPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVL
+DLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGLLPQ
+VQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHAS
+SVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYEVIQ
+GKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVI
+QPELDAAEMRALHASADALRREARSLGF
+>MHAAABBN_01843
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
+>LFPAFLNI_02073
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001824.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa18c18f2a5a3fb962d9e9bf07bf157eb6367155
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001824.fa
@@ -0,0 +1,19 @@
+>ACLBLIBL_00670
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASESAQSSESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSTFETTDCEGAHIAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPELTLDEAIA
+ASAGA
+>MOLHKGIG_02108
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGAESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA
+DA
+>MHAAABBN_01815
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGVESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA
+DA
+>LFPAFLNI_02048
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASASAQGSESSSASASSLSAAPA
+DYAAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTCTAQAQR
+LSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001826.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4abf05d95572e00393887f2e624fa4230a0b760b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001826.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00679
+MSGGRPAGALTVSVVIPVLDDAAHLRECLRHLARQTRPADEVIVVDNGSADESSAVARKA
+GARVVAEPLRGISAAAAAGYDAAVGDVILRCDADTRPPPDWVARAAGRFEAEPDLAALTG
+PGTFYDQPRLLARLRSRAYGAAYRFGAGAAVAGTALWGSNLGLRAEAWRAVRGRVHRRRP
+DVHDDLDLSFHLGLADVGSVVHDRRLHVGAAGRIFTSLPARVRQLRMAVTTLRLNWALLS
+PGMRWVRRARRSR
+>MOLHKGIG_02100
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>MHAAABBN_01807
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAVLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADSGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
+>LFPAFLNI_02040
+MTPARPTVSVVVPVLDDAEHLRVCLALLAAQSRPALEVVVVDNGCVDDSAMLARAAGARV
+VHEPRRGVPAAAAAGLDAAVGELLVRCDADTRMPADWLERIVARFDADPGLDALTGPGTF
+HDQPGLRGRVRAALYTGAYRWGAGAAVAATPVWGSNCALRAEAWQAVRTRVHRERGDVHD
+DLDLSFQLALAGRRIRFDPDLRVEVAGRIFHSLRQRVRQGRMAVTTLQVNWARLSPGRRW
+LRRAARSRPRPHWGRGPDGQSRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001828.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38a5a1b4c02f8c4bcc651429bbd3f504ba2b9529
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001828.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00687
+MTDADLDDMCRLLGDAEAMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+>MOLHKGIG_02091
+MTDADLDDMFRLLGDAEVMRYYPRAKSRNEVRRWINWSKDNYATHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPEHQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPRGAPIVVYSSHGHEA
+>NAFOICDF_00603
+MTDADLDDMCRLLGDAEVMRYYPRAKSRNEVQRWINWSKDNYAEHGFGLWVIEHRATGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRYGFETLCATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+>MHAAABBN_01799
+MTDADLDDMCRLRGDAEVMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKRTRDPSRAPIVVYSSHGQEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001830.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4659cf5bb201a04f619ac5a0413b2b93b8f8fad0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001830.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00690
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGIVAAVGPSVTSLKPGDRVVACLISYCGACARCLSGQTTLCLNQEALVRGPEEKPRLT
+LEDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPHAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVG
+AVLGITGTGVDHAFEAIGLPVTQQLTQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVLMGSSNIQRDIPLYADLYVQGRMELDHMVSQEISLDEINAGYERLLNGEVIRSV
+ITSF
+>ACLBLIBL_00775
+MKTTAAVATAAETPLTITEVEIDDLRADELRIRMVASGVCHTDAIVRDQWYPTPLPAVLG
+HEGAGVVEEVGDGVHGFSAGDRVLLSFSSCGHCRACHEGQPAYCADMFALNFGGRRLEDG
+STSYTLDGEQVSSHFFGQSSFAALANVPARCAVKVDDDAPLELLAPLGCGIQTGAGAVLN
+VLRPEPGASLVVFGAGAVGLSAVMAAKVARCGTIIAVDMHPDRLRLAEELGATHTLQAGE
+PVAERIRELTDGGTEYAVDTTGVAAIFGDNVDALAPRGVLGVVGAAALGTEASFDIGTNL
+PKGITIRTIVEGESIPQVFVPRLMALHAAGEFPFDRLVKSYPFAQINQAFEDSKSGETLK
+PVVVFDQA
+>MHAAABBN_00094
+MTRSTSTRIQGAVLQTLSATAPYAQSRPLEVQDLQLAPPQGREVLVRIEAASVCHSDLSV
+VQGLRPRPVPMLLGHESAGIVESTGPEVASVAVGDRVIMTFLPRCGECPACRTEGRLPCS
+EGTAANERGDLLSGGRRLSTEDGPVAHHLGVSGFATHAVVDARSVVRVEHDVPADIAAVL
+GCAVLTGGGAVMNAVSVPKGSTVVVVGLGGVGMAAAIVARALGHEVIGVDGISTKRDLAV
+ELGAQQVYAPQEALDAEVRGDLVVDATGNPRGFETAVELTGPGGATVTVGLPPADAMSSV
+SPMALVAQARTIVGSYLGSAVPQRDIPRFVELWRAGRLPIERLISSHISLEDINQAMDRL
+DSGAEMRQVILFDQEQPSQGQE
+>MHAAABBN_01796
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGVVAAVGPSVTSLKPGDRVVACLIAYCGACARCLAGQTTLCLNQEAVVRGPEEKPRLT
+LQDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPQAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVE
+AVLGITGTGVDHAFEAIGLPVTQQLAQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVAMGSSNIQRDIPLYADLYVQGRMDLDHMVSQEISLDEINTGYERLLNGEVIRSV
+ITSF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001836.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e30a074a553cd38cae316dc5aa59bb49c831a215
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001836.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00766
+MSTHDHDHDPADPRRATTSAPASLEPEIEAMHAARGNEEDRDWALLLVGVLVVDGVSTAA
+ARRHLRRAAEAVAQSGEGPDELFGTPVEFAAQMRADAAEAGEPIVDSTPDASWRDVPVVG
+FTVAAAISVLFFVVWLVRDGLTTEYSWGLLAGPVLMSLLGVGAMTLWERLLPRVSRLVAV
+LAAGAAFVVVVGGLAGWLVTGGGTETLFTGSTFWLLALAPVHAALAWLANRVLPEARPVA
+TSSADPLDDDAWARELAGTLRLRMQLSDARIREIVREAQAHAADAGRPLAEEFGAPAGYA
+SRFAKDGVAGKRRMAWFFTALAGLVVLTNVAGAVEDGGIDAWSVAQILVLVLVVGVSWRE
+YRAAVRRRDAVAPGAGGR
+>MOLHKGIG_02054
+MLVLLILATRLPGVVAGERLSVWDVAYLLLAVVVLVSEWRDYRAAVRRARR
+>MHAAABBN_01760
+MTIRPHSDPVTPDATWRDVPVLGFTVAAGIAVLFCLVWLLRDGLTTDYTWGLLLSPVLMS
+VPGAAVMVLWERLLARVPRLAATLVAVAALLALGLVLAWWLVEVNAQTHLFTGSTFWLLA
+VAPVCAGLAWLAHRLLPPARRPVGEPPAALDDDAWARRLAGVLRLRKDLPDARVAEIVRD
+ARARGAAAGRPLAEELGSPESYAAGFQKDRVAAPRRRAWAVTALVLLILATRLPGVVAGE
+RLSAWDVAYLLVAVVVLVWTWLDYRAAVRRARR
+>LFPAFLNI_01988
+MLLILATRLPGVVAGERPSAWDVAYLLLAVVVLVSEWCGYRAAVRRARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001837.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1a698ba30d2561b19ada98e01f6765b0cf5dfdb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001837.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00772
+MEHTLVRPPKAAPGDRIAVVSPSFAAPGFAPEVHEQAMRRLRELTGLEPVEYPTTRELGA
+SPEDRARDLNAAFADPRIRAVFATVGGEDQITVIGHLDAAAVRADPKPFLGYSDNTNLHQ
+WLWAHGVASFHGGSTQVHLGPGPGVDAVHAASLRAALLTGERLEITEPGESEDVGVDWQD
+PRALAEFGQREPVAADDDGLGGPGASPWRWAGPQRSVTGRTWGGNLEVLQWVLAAGRGPV
+DVAALRGGVLLLETSEELPSATDVRRMLRVLGERGILGEVAAVLAARPPVSDFDVRPDAQ
+ERARLRRAQADVMVETVHRYNPDAVVCVGVPFGHTRPQWILPHGGEMTVDGVEKRVWAEF
+G
+>MOLHKGIG_02044
+MRRLAEVTGLVPVEYPTTRQLGASPESRARDLNAAFADPQIRAVIATVGGEDQITVIGHL
+DADAVRADPKPFLGYSDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAAL
+LTGGRLEITEPGESEDHGVDWLDPRALTEFGTREPVPGPHDDGARGVGAGASPWRWAGPR
+RAVTGRTWGGCLEVLPWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGES
+GVLGAVDAVLAARPPTRSFEVPRGAEERARRRAEQADVVLEEVGRYNPDAVVCVGVPFGH
+TRPQWVLPHGGVMTVDGAERRVWAEYC
+>MHAAABBN_01750
+MASRYAPGMTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEY
+PTTRQLGASAEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVRADPKPFLGY
+SDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASMRAAMLTGGRLEITEPGESE
+DHGVDWLDPRALTEFGERDPVPCPHDDGARGVGEGASPWRWAGPRRAVTGRTWGGCLEVL
+PWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPP
+TSSFEAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTV
+DGVERRVWAEFG
+>LFPAFLNI_01978
+MTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEYPTTRQLGA
+SPEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVSADPKPFLGYSDNTNLHQ
+WLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAALLTGGRLEITEPGESEDHGVDWLD
+PRALTEFGTREPVPGLHDDGARGVGGAPGAGASPWRWAGPQRAVTGRTWGGCLEVLPWVM
+AAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPPTSSF
+EAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTVDGVE
+RRVWAEFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001844.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f3afd247a4117b17da89f86cc0538def7c874a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001844.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00848
+MLRSFTPGRPSLTVSDAAAAAGTTRATARRVLHTLVHEGYAVQEGRDFRLTPRVLELGHG
+YWTGTSLAEILSPVLTRASQELEQSCSAAVLDGPFLLYIARVHTERIIRVNLDVGTRMPA
+FLTSMGRVLLADLPPATVRRVLEAAPRTPRTPRTVTDVEALLEEIAQVRRQDHAVVTAEL
+DDHLSSVAVPVRGPDGAVVAAINTALPHRTPGAAEPSADEQTRAAVAQALPVLRAAARDA
+EDALVALRR
+>NAFOICDF_00785
+MSLPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARRSLLT
+LVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGVLHGA
+HLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPATAQT
+LTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALSTRRGRLG
+EALSPAAAEAAAAEALPVLREAADDAEAALELLGR
+>MHAAABBN_01703
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
+>LFPAFLNI_01931
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001845.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f966d598c9fb127347a7139adb0fca1535df9f76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001845.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00849
+MTLADAYVFDAVRTPFGKIGGKLAGTRPDDLAAHVIRTIVDRAPGLEGLRRESAQDVADE
+LKGRPIEAGTDRARPDRIDEVVFGNANGAGEENRNVGRMASLLAGLPVSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVMLVGGVESMSRAPWVLPKTSRPFPLHNLEAVNTTLGWRLI
+NDAMPKDWTISLGESTERLRERFGITRERQDEFAARSHQLTAKAWEEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRKEDGTVTAGNASPMNDGASAALLGSEKGAEILGLQ
+PIARIAGRATAANEPDFFGYAPVEAVNLALKRAGIGWKDVAAVELNEAFAAQSLACLDAW
+GVDPEIVNAWGGAIAVGHPLGASGTRVLGTLARRLQDTGDRWGVAALCIGVGQGIAVVLE
+NVDAR
+>NAFOICDF_00786
+MCVDRTSLARPRGRAYGEAMSLTDAYVFDAVRTPFGKIGGKLAGVRPDDMAAHVVRALVD
+RAPGLEGLRAESAQAVADAAAGHPIEAGTDAAAPQKIDDVVFGNANGAGEENRNVGRMAT
+LLAGLPLSIPGTTVNRLCGSSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTSR
+PFPMHNLEAANTTLGWRLINDAMPSQWTVSLGEATEQLRERFDVSRERQDEFAARSHQLT
+AKAWDEGRYDDLVTVVPGTDLERDETVRPDSTPETLAGLRTVFRKENGTVTAGNASPMND
+GASAAFLGSEKGAEVLGLPPIARIAGRATAANEPNFFGYAPVEAANVALRRAGITWKDVA
+AVELNEAFAAQSLVCVDAWGVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLQATGER
+WGVAALCIGVGQGIAVVLENVDAR
+>MHAAABBN_01702
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
+>LFPAFLNI_01930
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001854.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccfa0b874152f264ef45c8cd9c13f7a91cb91bcc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001854.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00901
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALISKAERFIELAQERRAALITA
+AVTGQIEIPTED
+>NAFOICDF_00840
+MCSRYLGYLVLSSFFLEQVNASTYGTKMPRANWDFIKTIEVWAPDFDTQRCIADYLDRET
+ATIDALIAKQVELMNRLRERRQAVIDRAFVSTSEIVILRRHLVLNDSGAWGEDPTGADDV
+AVLRSTEQTVDGYWAISDPALRTLSQTERQNTRLREGDLIVTKTSGSFKHVGKTTLVDNE
+VAEGGYGFGNFMQRLRLKSTMIPKFLWWFMRTDQARSWINLVATTSTGLMNLNGSTLGRM
+EVPLPSLVEQREIADHLDRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>MHAAABBN_01647
+MARIVEVMTRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>LFPAFLNI_01878
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALIAKAERFIELAQERRAALITA
+AVTGQIETTSELHRRW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001855.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa4d4a530ee36646125e2b7a807c5246722502ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001855.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_00902
+MAIHNESELETYICEYLQSHGWLYSANDEGYDRKNAIFPEDVHAWLVENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFTGAHESESVDLVLFVNGLPVATIELKTDSTQSIGHAKKQ
+YRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTKM
+LAAVREEGVGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDD
+QLQEAVRQIERTSGTVVAVDRKNLGGEPTSKSALVKQTLLQGNRIIVVTLQTFPAVLELL
+KGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVL
+KNFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQK
+VRIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGE
+ITDDDFGLEKVTERSMNPPVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLG
+TKLDAAGVYDWAEVDAFAEVWVVWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRV
+NELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDV
+QLVSIRQNKTSSGDIGLTGGTALKGTTAVGGGQVHEKQRGPLEDVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTD
+IVGRGGDPSKMIVAAIGEYLYLTVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASA
+TPSRVRKGN
+>NAFOICDF_00841
+MAIHNESELETYICEYLERHGWLYSANDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYEHMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RERNSKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPENISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAHLLDGQAKAMVVTDSRAAAVRYKRQMDQYIHDMGYTDVGTLVAFSGEI
+TDDDFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSENDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYDWDEVDAFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNHDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQAREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASAT
+PSRVRKGN
+>MHAAABBN_01646
+MAIHNESELETYICEYLEQHDWLYSPNDAGYDRKNAIFPEDVHAWLAENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+SSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLA
+AVREEGAGASYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQL
+QEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLKG
+DSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLDDGGEADTESILAAEVAATG
+RPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKN
+FTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVK
+IIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGEIT
+DDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLSG
+VLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLEAVTDPNLIHDLGTK
+LDAAGVYDWDEVDAFAEVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNE
+LVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQL
+VSIRQKKTSSGDIGLTGGAALKGTTAVGGGQVREEQRGPLEEVIEKINEIFAGEGVDASP
+SQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIV
+GRGGDPSKMIVAAIGEYLYWKVRSEGTGPVDVAHGRSAVFADETAPSQGTSVDERARATP
+SRVRKGS
+>LFPAFLNI_01876
+MAIHNESELETYICEYLEQHGWLYSPNDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQREQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPYG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQKGEFRPEGDRAAVGKQTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVDTLVAFSGEI
+TDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYNGDEVDVFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGEIGLTGGAALKGTTAVGGGQVREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFVKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRSEGAGPVDVAHGRSAVFVDETAPSQGTSVDERASAT
+PSRVRKGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001861.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c20cdb35b0828bd822756a7852b30f04f39a0e89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001861.fa
@@ -0,0 +1,88 @@
+>ACLBLIBL_00929
+MTPTFSAQDHDDLDRVLTATGGIPDPADLQHLADDAVAQVRRWLADARGHEADFAAQQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAQQAPGFLPPALRAVFGVGGRAAPL
+VPRVAVPVARRVLRRMVSHLIVDARDRQLGEAIAALRDERTRLNVNLLGEAILGKGEADR
+RLEGIAGLIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLYELARDNGTFINL
+DMEEYHDLDLTLNVFTGLLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMELMQASLMGWPVATVASKQEADTNYKRVLNYALTPEHLRHVRIGVA
+GHNLFDVALAHRLMDRRGLGPEQVEFEMLLGMATGQAAAVKADVGSLLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADEALFAREEERFRASLAHLDAEVPRPSRGQDR
+SRGEDGVRPAAVDGFANTPDTDPSLPGNRAWARGILEAIPGSALGAERARAHRVGTAEAA
+RAAIADTQAPGAAWGALTGAQRAEALDAVGRALHAGRGRLLEVAAAETGKTLDQGDPEIS
+EAVDFAHYYARLARGLDEVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+AAPQSERTGAVAWELIVQGLRDSGLFDDGGPLAAHDPADLVRLVTMADEDEEEVGTALVT
+DPAVERLILTGGWDTAKLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVHSAFGH
+AGQKCSASSLVVLVGSVATSERFHRQLLDAASSLHVAHPADPRAQMGPVIEEPGEKLRRG
+LTELGEGERWALRPRELDATGRLWSPGIRSGVRPGADAHLTEYFGPVLSVMTAATLNEAI
+DIVNAVDFGLTSGLHSLDPDEIAHWLERVHAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWVDAPSSTSESPAADRAGEGTAAGTPAAAERSWLDAARALDERAW
+AATFGSGTDVSALAAERNVLRHLPVPVLVRRASGPAEHLLRVVSAGLRAGAPMTVSIAPT
+PAAQAPGTDDLSAEALRGQVDELVRTAGAGRAEGAAPVSVVVEDAAAFHDRARQLAQIPP
+AAEGGGDARIRLVADWAQDREGARAAGAALHAALGDTPDVAVYAGPVVSAGEVELLPFLH
+EQALSVTAHRFGTPDHLTDAIL
+>MOLHKGIG_01931
+MTAMFSAQDHDDLDRVLSATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATAHPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDGGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPVDPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGAEADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEKLVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALILPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>MHAAABBN_01627
+MTATFSAQDHDDLDRVLGVTGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRRMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASVTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSEADGAGASWLETARALDTQAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALVPPAAEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>LFPAFLNI_01850
+MTATFSAQDHDDLDRVLGATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTLQHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADAGLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGSLTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSVADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALIPPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001865.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..343defd4c1b7bf5d5f873b61e6bfd6af072a434b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001865.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00966
+MFYNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFA
+GTVVMDANDIGRNALGRDTAASAAVLEAAFADNPLGQGRERTPLAVVVRMD
+>MOLHKGIG_01892
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARPAGDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>MHAAABBN_01588
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPARPADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP
+AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPAEAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>LFPAFLNI_01812
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARHADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001866.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..311117d200cc2bd019609eaeeb40e75b64a03edf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001866.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00980
+MTPQPAAAPAEHVAVVHALRAFSEGAEHAVDEAGRGIGLHRTDLKALAHLMRCADEDRPV
+TATDLGAHLHLTRAATTAVVDRLVASGHARRRRDDVDRRRVLVEHTDSARRDGAAAFLPM
+SLRISGALTPFTAEELRAALRVIEAATAALQAPPDAPAAPVPG
+>MOLHKGIG_01879
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>MHAAABBN_01575
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>LFPAFLNI_01799
+MTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRALAYLMARAAAGEPV
+TASDLGAHLHLTRASATALVDRLAAAGHVRRRRDEGDRRRVLVEHTDTARRDGQRAFQPM
+SQRLSAALEGFSVAELRAAVRVLEAATAALTDPTPEDP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001867.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49aac1ec009549c66b7840d0296d4315a0418910
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001867.fa
@@ -0,0 +1,57 @@
+>ACLBLIBL_00981
+MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAG
+RPSAWLRFGLAAALFVVWFAVMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAF
+RDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVTDVAGPIPAEDGEAVQFLAFV
+DSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI
+DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQ
+GILSILVIGAATDYCLLLVARHREELLVREEVTASLLAAVRGSFGAITASASTVALALLI
+LLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGRAAFWPTVPSPENARRRATRR
+AERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL
+QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAE
+ASVTTDEAPAPAGPPPGVTGGGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADP
+GESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNTTSQRDLVVVIPLILAMLLVI
+LSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAF
+IVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPARAE
+>MOLHKGIG_01878
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALAVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLIVRSLLIPALVRDIGPKVWWPAKVD
+>MHAAABBN_01574
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALTVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAE
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPAKVD
+>LFPAFLNI_01798
+MPTAPDLSAFRTPAAPGRPSRGLRLGLAAALAVVWFAVLGLGGPVFGAIGDVSSNDQATF
+LPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVVDVA
+GPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRAEVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVW
+VATTVGLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVWDIGPKVWWPAKAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001873.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83d86e86d9cf4a222fd43be57ddfd6f02aa2ee17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001873.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01199
+MSTSRRRLTQGLAAGAACLALPAGLSAPAAAAPSARSSRTPDSAALQAALEALVQWPVAG
+AVCAAASPAGLVELAAGRRSTASPAPARPQSVARVASVTKAMTATVAFQEIERGTLRLDS
+TIGEVLPGLWPGRESVTLGQLLNHTSGMPDAVWVLMDHVSLWDLPLEHVRDVVARSYPPR
+ELVELAKQDGWWFEPGTDWGYSNTGYVVAQLMVEAAAGRPLSSLIRDRVFRPAGMHRTRL
+EEGALVRGAEMEDAAVRPGQTMRLQTIDQSVFAGAAAVNATAGDVVRFYQALMRGRLVGQ
+ASVDAMVTPVGAARAAAYGYGIFQVPDPVRAGEVLYGHDGGGFGSASLAVSSRDGSRAMA
+FAFVGRPYWAAGANEVWPRQTAVLRAAMSLSGTAGRPGGSAGRAAAGAAHAAVGGTRLG
+>MOLHKGIG_01679
+MRPTRRQFAQGMAAGLAGLVLPPAVASSAVAAPQGPNPRSGRGRDERAIQAALDAVVQWP
+AVGAVCSVVGPARRFDTASGTRGLHANAPARANSVARIASVTKGMVATVALQEVERGTLS
+LDSTIGGVLPGLWPDVEDRVTLSMLLNHTSGMPDAIWVIMRGQSLFELDFDELADVVSRS
+YGQRELVELAKQADWWFEPGTDYGYSNTGYVVVEMMVEAVTGRRMPELIRDRVFRPAGMH
+RTRLEHGTLVRGAEMQDAAVRPHEAKALETIDQSIFASAAAVNTTAADVTRFYQALMRGE
+LVSQQTVDLMVTPVGPATQAGYGYGLFLVADPAPEHAGEVLVGHDGAGFGSVSLALCSRD
+GERAFAFTYIGRPYWQEGWDEVFAKELALMRTAFVVNAADAPASRDRLVRGGAAASRRAV
+ADMAARGARLV
+>NAFOICDF_01217
+MTRDTPSADRPPLSADALRPIAAALDRWLATQTEVRRVPGVQAAVRLGDELILSTAHGVA
+DESTGERLTTRHLFRVASHSKTFTAVAVLRQVELGTLRLDDTVGALLPGYADTPLAGVTL
+RELLSHTAGAVRDGADADHWILDRPFPDAAALQALVRDHGTAYAPQEHFKYSNIGYGMLG
+AVLEHVTGRPYAEHVRASVLDPLGLTDTHADLTDDVAARAATGHTRAGGRARARVTVEQT
+TTGALAAATGFVSRAEELSAFYASLALGARGVLSDRSLRLMHRAEATFRRGGGTGTYGLG
+LLGQEVGGRRLLGHSGGFPGQITRTLFDPATGLAVSVLTTAVDGPAEALAVGVVQLIDLL
+TAPAADWQALPGGVTAADLDRLAGRYVSLWGATDVLRGGTAERPRLVLLDPAAPAPADAA
+EELRALDATTLRVEDADGFGACGEPIPFDLDAAGRVTRMRVTGVSAWPEEAYRARRGDAW
+RHADGVDGAEAEPDAHEEAAPVLVQAAAFADLDPATAYRLWALRQAVFVVEQDCPYQDMD
+GRDMEPATVHLWVCDEEDAPIGTVRLLDDGDHARIGRVVVDRAHRGRGVAAALMEAALEQ
+VGERACVLDAQAHLEHWYGRFGFAADGPEFLEDGIPHVPMRRPEAGRRTP
+>NAFOICDF_02117
+MDFIVRPCTPEDEPSWLRCRVLAFLDTQNHDDVHAAHPVPDPDVADPADSLQWVAVVRDG
+PDAGTVAGILDASVGAADGDDAGLATIDTLAVHPDHRRRGLAGRLFEAVLERLPERVGHV
+DVWTREDEAANAWYRAHGFARDHVYLQVHLESWVDGDDVAALIRTPPALSAPVKGLFHAS
+LEDEAWIRERFHRVVRVSRYVRPVGMTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001875.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a00307281428b7fc1bb8ca3669ed081f3665068d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001875.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_01225
+MTGHEHPRPEPLSAAVDEQMLEDFLNQHLLGSRSGVKAFRAAEQTWAGTPQEDALRRLGD
+AVQDDQERLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKAAMWHVLEALAPHEPVLDAGEMAALYERAQDQQRAVQRIAEDTLLERFLR
+>MOLHKGIG_01669
+MTGHDHPRPESISAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWDVLEQLAPHLPAVDAAEMQALRQRTADQQREVQRITSATLEGRFLAG
+>MHAAABBN_01374
+MTGHEHPRPESTSAAVDEQMLEDFPNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMQALRQRAADQQREVQRITSATLEGRFLAG
+>LFPAFLNI_01599
+MTGHEHPRPESTSAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMHALRQRTGDQQREVQRITSATLEGRFLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001877.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba453b9ac2bba72918c437d9201649c187291beb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001877.fa
@@ -0,0 +1,19 @@
+>ACLBLIBL_01324
+MAVEEQRLALPVDGELPEGFAVQGLRIASGVLPRREEAAVTVRVLD
+>NAFOICDF_00436
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRRYEPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLEAHAAEVRRRRDLEDRALALAAAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEEATTERANAAFATLFQALAEAGSAPAGPPWT
+ALRPVPSAADVVETVLAVPLSGPAPAGLRVDGHEVVTGTLPRRVERYVDVRADAGEVDLL
+DDAPGGALPHPGLLGLMDAFDVEDAGTAPEIRQILADPEAGHVELAVTVREEAGAGQG
+>MHAAABBN_01950
+MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRCYAPGQIRTAAQIRVLRA
+AGLTVDDVRSVLADPASLPARLETHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPA
+RPGPVAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFVTLFQALAEAGSAPAGPLWT
+ALRPVPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLL
+DDAPGGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
+>LFPAFLNI_02180
+MSPLMTVGEFALATGLSAKAHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPARPGP
+VAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFATLFQALAEAGSAPAGPLWTALRP
+VPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLLDDAP
+GGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001884.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..078b03c2b28c9aaa2a84cc6810da376b62974778
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001884.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01635
+MNRPPEHDWDDLPGDEADPDDDLDVFGFVHEDADDDPDEARRLGAPAAAAGGRRRGLLRR
+RGTGSHPAAPGRSRRGSRLRGGIALGAAALAFLAVVVLVVQGFLGGADHDGIEGEELTFS
+VEPGEDLASVARRLDSAGVVASARAFERAAEDSASGVVRAGDFVMRERMPAADALAVLQG
+TADGAVHYVLVERGRRLTEVLDALAESTGLPREELAAATQDPARYGVPAEAQTLEGWLDP
+GEYRLPVEASAEEVVDALVRPVLADLAELGVDDPDEQRRVLTVASLLEAEALPRDYRTVA
+GVIENRLAPDNTETRGLLQIDAAVTYGLGVRSLSFSAGQRQDASNPYNTYVHPGLPPGPI
+GMPSDAAVAAALDPADTDAYYWVTTDIATGHTEFSRTYEEHQEHVRTLQRYCASNPGVC
+>MOLHKGIG_01253
+MTGDHQHARREDHWDDLLDDEADVHDDLDVFGFAHEEADEADVGAPSQPVGAAGPRRPRT
+FLRRRGTGSHPASRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLSGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVGSARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGATDGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAQDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAGQVLDALVRPTLAELEALDVRDPAEQQRVLTIASILEAEALPQDYQ
+QVAGAIENRLAPDNTETHGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
+>NAFOICDF_01532
+MSAPPPPPWREDETDDDLDVFGLVDHGEDEPEPEPERVERQPAPPRPVGRARRPRVRTGG
+SHRLRAIGRNLAVERPRGAVVLAVAALAVVLVAALLVVLFSRPADRQAVSGDRVTFTVEP
+GEDLASVAARLDERGIVASDRAVLDAAEDSGQTSIGAGEYVLREQMPAADALAVLQGRAE
+GASHYVVVGRGRWLSEVLDGLAQSTGLPRADFEAAAEDPTRYGVPEQAPSLEGWLDPGEY
+YPPVGADAEQVLAELVKPRLAHLRAQGVTDPAEQQRIVTIASILEAEALPKDYPRVAGVI
+DNRLNDPDAETRGLLQVDSTVNYGLGRRNLQFSAAQRADESNTYNTYQHTGLPPGPIGMP
+SDAAIEGAVHPEPSEDLYWVTTDIATGHTEFSRTYEEHSVHQEEFRRYCAQNPGVC
+>MHAAABBN_00972
+MTGDHQHARREDHWDDLLGDEADVHDDLDVFGFAHGEADEADLGVPSQPVDAAGPCRPRT
+FLRRRGSGSHPAPRVDRGAGRRRTALVLGTVLVAFAVVVGLIVRGFLGGPDHTAVEGDEV
+TFSVEPGEDLGSVAARLDRAGIVASARAFERAARDTGSGLVRSGDFVLRERMPAAEALAV
+LQGAADGAVHYVLVERGRRLTEVLDAVAEATGLPREELEAAAHDPTRYGVPGEAGTLEGW
+LDAGEYRLPVDATAEQVLDSLIRPTLAELDALDVRDPAEQQRLLTIASILEAEALPQDYR
+QVAGAIENRLAPDNTETRGLLQIDATVTYGLGVRSLSFTSGQRQDASNPYNTYVHPGLPP
+GPIGMPSDAAVEAALDPAETDAYYWVTTDIGTGHTEFSRTYEEHQQHVRTLQRYCASNPG
+VC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001886.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f90f15eae6ce1b81cebfe8afb3fc984d2ba24895
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001886.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_01734
+MNALSLNPRGGAEHLARHAGLVAALRERPVVVETEAAGDRAALRAANELGLRRVGRELRF
+LVR
+>MOLHKGIG_01155
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>MHAAABBN_00874
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>LFPAFLNI_01105
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001891.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d778e612466a4376794ef8ffddf6b27a107f2cc6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001891.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_01991
+MSTAETTRTGERRGRTGPRLPHRWRRPALAGLLIVLSLILAPEQVAQGTAHPVAAALMLA
+AAVVAGAGIVRSAVAALRVKTIGIDLLVATAAIGATLLGNFWEAAAVTFLFALGHALEDA
+TLAKTRSALGDLVATAPETAVVLEADGTQRTVAAHEVPAGATVLVKAGARVPVDGVVLTG
+TGAVDEASITGESLPAEKSDGDDVYAGTVATAGLLHVQARGVGADTTLARIIHRVEEAQE
+ARARTQQFMDRFSRWYTPAIMVLALVTGLITRDVPLALTLLVIGCPGALVISIPVAIVAG
+IGRGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVALEDGREDEVLGWAA
+RLEAASDHPLAAPIVAAGRDRGLLSGAMATDVDVVLGRGLTGTVEGRTVAVGNVALLRES
+GADADRTARVEAVAAELAAAGRTPMAVAVDDVPVGVLAVADTVRPEAAGMIRELHRIGVR
+EVVMLTGDQPGVAHAVARQVGVDRVRAGLLPEDKLDAITAMQAEGRVVAMVGDGVNDAPA
+LASADIGVAMGAAGSGVAIETADIALMGDRLELLPQALGLAQRTVGVMRQNIAVSLVTVA
+ALLAGVFAGGVTMSIGMLVHEASVLLVIANAMRLLRPAAGSGRGGSRAAQSRSTTSNSSS
+SAPVATGAGRPSDSAA
+>MOLHKGIG_00946
+MSTPAVTRPGRPRARFALSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAMYAGTVATAGLLQVQARGVGADTTLARIIHRVEAAQEAR
+ARTQQFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPIVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDHPGVAQAVARQVGVDDVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>MHAAABBN_00665
+MSTLAVTRPGRTRARFTLSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAVYAGTVATAGLLQVEARGVGADTTLARIIHRVEAAQEAR
+ARTQRFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPVVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDQPGVAQAVARQVGVDHVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>MHAAABBN_01109
+MVTLAVAAVLLVAGLVVEWTIHSEPVALALFWGAILIGGVYPLRSAIRAVRHKRLTITVL
+LVVAAIGAIALGVIEEAAMLVVIFSLGEAMEAYATDKARGSISALMELAPPTANRLNDDG
+ATKTVAVEELHPGDVVLVRPGERLPTDGAVIDGASWVDASPVTGESVPVEATAGTEVFGG
+SLNGNGVLRIEVTKEYYDTVLARVIEQVEEAQANRSGAERFADKFGAVYTPAMFALAIAV
+ALVLPLLGFEWREAIYRALVVLVVSCSCALIISVPVSVVTAIARGARDGILIKGGIYLER
+LADIKAVAFDKTGTLTRGRPTLAQVTPLDGISEDEALTLAAAVETGSEHPIATAIVAGAR
+DRGLTIPAVQDARALPGAGMEATLDGRTLHIGRPTDEDRTDGTAGPALAHAEAEGCTAVV
+LRDDTRPLAVVAVADQLRPDAESTLTELRDLGVERVLMLTGDNATVARSTAQALGLDDYR
+AELLPEDKSAAIRELREKHGVIAMVGDGVNDAPALANADLAIAMGAASTDVALETADVAL
+MADELDRLPAAIRLSRRARNNIKINIALSLTVVAILIVAALAGWMSLTTGLLLNEGSAAL
+IILNGLRMLRPGRGETRRAQVDFGTRQGSDLNSGRPCAPGSTTDGHSVAAGSSYDQREHG
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001893.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e65f551fa36402c32012e955d1a5cf2692bc6d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001893.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_02190
+MSTHQHDHGHPRPEASEQTGREHGAPAPQVDPDEDPRAFWEGRYGGERVWSGKVNATTAA
+LVAGLGVTPGRALDLGCGEGGDVLHLAEAGWDVTGIDLSEAAVARARDAARERGVTQRTR
+FLAADLSDPAADWGAHEAGAAGYDLVTASFLQSPVALDRRRILRRAADSLAPGGHLVLVS
+HGAPPPWAPPQLAERGDFPSPAAELAALGVPADGDARWEVLTAELRERDTTGPDGRSTRL
+KDTVVVVRRR
+>ACLBLIBL_02581
+MHSTTDQHAASGRYGDEHAELYDLMYGSLPDWKQLPALCRRVRPAARTVLEFGIGNGRLA
+LPLAEEGFEVTGLEASGVLAGQLAARARDLPVDVVVGDFRERLTQDRFDLCLLMTNTLFM
+TEGVADQRRVLRRAAEALAPDGMLIVETYDPQVYLEKPAVSNFSMPLGDDALLTDTVIVD
+RLNCSVHIHHTVVRRGEVTVLRERSSWLTPRELDLVCEEVGLKRTLRFADLAGSPITDST
+RNVVSCYERR
+>ACLBLIBL_02669
+MTGATRHDSPSQNPQEFWEGRYRYAERVWSGRPNPSLVNAVQHLAPGKALDLGCGEGADA
+IWLATQGWLVTGVDISATAIARARREAQRQQASAATRFVTADLARWEPDDGPYDLMTASF
+LHSPVPLPRIAILQRAATTVRAGGHLVVLSHAALPPWVDAADHPAHSFPSPARQFVELNL
+NEHDWLVLSIQTHTRHATAPSGEAAELTDGVLLLQRR
+>NAFOICDF_02089
+MSDQHSPGHEHRHGGAAPQIDPGMDPREFWENRYGGEQVWSGKVNATTAALVAGLDLPDG
+PGRALDLGCGEGGDVVHLAEAGWHATGVDISEAAVARGREAAAARGVAERTRFLAADLTD
+TSADWGARDDGAAGYDLVTGSFFQSPVALDRARILRHAASLVAPGGHVVLVSHAAPPSWA
+PPEVAARGDFPTPAGDLEALGIMTEGDEDWEVLVAEVRGRESTGPNGEAGHLDDGVVVVR
+RQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001905.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ab495fc38ad520936d6e28448364fa575c4aef6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001905.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_02337
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>ACLBLIBL_02342
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>ACLBLIBL_02640
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
+>ACLBLIBL_02651
+MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK
+RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK
+ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI
+LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT
+EAMGMLNHHFAAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001910.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec75fdd95cb249039ae37b1a0b539bd08b38105b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001910.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_02394
+MDAIRGTAILLMLLLHATMIPAVVGGMEPVPWLVAITDATAPFRMPVLMFLSGMLLDRAL
+AKPAKRYLSGKFRVLLWSYVVWAVVYFMVMGRPGELFRPWTWVQTLYLWFLAFLLAYYVL
+ALVLRRIPAIVVAVAALVPHVVLVGAERGFLARFFLYMTVFFAGAAFTRFLAARPGILEP
+RRRDGHLLVGLPLLVVGVVAIRSGGALPHPAGAVVGAVAAVAVAMGLVLVVQALVPRPRG
+PLVRVGQQSLVYYCVHYPVMVLVVRLGERLSWDVVVVSLVSLVAAVVVCAVIAEGRDRVP
+VLDALFRAPAPPRRRRPVTH
+>MOLHKGIG_00369
+MSTTPTPPVSHGSAPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGKPGSLLSVE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFELPTAGRVRARPRTRATVPGAADAVPAQTAEPASTTAPLPVVEP
+ASPPQPAAGPTPAAEPAAGAPARVRAPRPRPRHAD
+>MHAAABBN_00085
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
+>LFPAFLNI_00376
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001916.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c739916df9b49a0dcbf9339b58ec7c3981824308
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001916.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02566
+MAAVRALRTLLAEGYATPEAPVAVTGAGWPDYDARVLPGLAAAQELAGVDVDYLRHVDRV
+SDAGIDAASLADLGTLFTYVLRGERFSEGHIGAALANGKVGRMLDRLAELVPQVR
+>MOLHKGIG_00390
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>MHAAABBN_00114
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>LFPAFLNI_00396
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001918.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43f16febb7ad2e5d8b4d1a993caa8e2b7cd4b38b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001918.fa
@@ -0,0 +1,36 @@
+>MOLHKGIG_00041
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITEWLPE
+SINHVFFTNAGAEANDHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSENDEQEAERALAHLRDVIELEGPSTVAAVVLEAVPGTAGIF
+MPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEECMVANAKRIGEEII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>MHAAABBN_02054
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRNLTPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGEEVI
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVKDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLALADEEVAAG
+>MHAAABBN_02171
+MTAPAEAGLLDRDAAHLWHPYGAAGARQLYAVRGARGVHLDLEGPGGERHRAIDAMASWW
+SVVHGHGHPALVEALTRQAAAFPHVMFGGLTHAPAVDLAERLVAHTPAALEHVFLADSGS
+VSVEVALKLALQYQATRGRPSRRRFLTVRGGYHGDTAAPMGVCDPVDGMHAAFTSLVARH
+LFLPRPPAARWVPEGFAAAPTAPDAAPAGHWEADDAALAAWEDEARAFTAAHADEIAGVI
+LEPVLQGAGGMRVYDPRCLTVLRELCDEHGLLLIADEIATGFGRTGRWLACEGAGVAPDV
+LCLGKALTGGTMTGAAMLCTAEVAETVSRRERGMPGALLHGPTFMGNPLMCAVASASLDL
+LTDPRDGWAAQVPRVEAGLRAGLAAAADLPAVTDVRVLGAVGVVELDRTVDVEPVTRAAV
+ARGAWVRPFRRLVYVMPPYVSTDDDVATICAAVTGAVEEVCA
+>LFPAFLNI_00036
+MSEHQQHVGRRDPRISDEAIERGRRAHELDRAHVFHSWSAQRDLNPMTILDAEGSWVWDG
+EGRPMVDFSGQLVFTNVGHRHPKIVAAIREQAETLATVAPQHVNDARSEAARLITERLPE
+SINHVFFTNAGAEANEHAVRMARLHTGRHKVLSAYLSYHGATRLTANLTGSLRRVGSDSA
+SDGVVHFQPAYTYRSAFGSESDEQEAERALAHLRDVIELEGPSTVAAVILEAVPGTAGIF
+LPPPGYMAGVKELCREHGILLIIDEVMVGFGRVGEWFGHQLTGVTPDIVTFAKGVNSGYV
+PLGGVAMSDDVYESFATTPYPGGLTYSGHPLACAAAVAAITAMEEEGMVAHAKRIGDQII
+GPRLAEIAAAHPSVGDVRGAGAFWAVELVRDRQTRERLAPLGQVAPVMGRMMAEAKDRGL
+LLFMAENRFHLCPPLNISDEDLRFGLDVLDQVLTLADEEVAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001919.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b589b3700047a22438e9bd5cc52dd4967352842c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001919.fa
@@ -0,0 +1,40 @@
+>MOLHKGIG_00048
+MDTSAPRTSPSTPPASAAHITPEGGSLRRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALAAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSATFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>NAFOICDF_00296
+MNPTDSPRTAGPAGSTAAAASPEPHTGLKRTLAARHLMMIAMGGAIGTGLFVASGNSIAT
+AGPGGALLAYVVIGFMVFLLMQSLGEMATYLPVSGAFEEYATRFVSPSFGFAIGWNYWYN
+WAITVAAELVAAALVMRYWFPDVPSWAWSALFLALLFGLNALSTRAYGESEFWFSLIKVV
+TVVVFLVLGVLMIVGVLGDAAVGTDNWTTGEAPFVGGAPGILAIFLVAGFSFQGTELVGV
+AAGEAEDPERTVPKAIRTVFWRILLFYVGAITVIGFLIPYTSPNLLGSDIEDIAISPFTL
+VFENAGVLAAAAVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPM
+NALVVTTAVGALCFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRKAYVAQGND
+ITDLPYRAALFPLGPIVALLLCTVVILGQNYEAFLNGVDLVAVASAYIGLPLFLALWIGH
+KLVTGSKGVRPEEADLTRGRA
+>MHAAABBN_02061
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>LFPAFLNI_00043
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRQAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001920.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebc8d48099de96c2581e428ffdf845211a774c52
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001920.fa
@@ -0,0 +1,29 @@
+>MOLHKGIG_00073
+MRHPAPLPAALLHGPFTAAQARAAGIDRNRLRRSDVERLARGLYRRREATPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDGVHVSRPRD
+RGRLALPGVISHRTALPPADVERVRIGGLAWHVTAPPRLWVDLAALLDDDELVILGDHLV
+RRAKLSGGPGAAERARAALAQAAEASPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALT
+AAGLPEPALQLEARDPEFSLHHPATADLGYRQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGYRNITVSSSDARRGFTRVIVEVRRHLGDAGDLSRKESEWGVNGTSERPLT
+>NAFOICDF_00261
+MERWPPHTDIMSRPPRDLPAVLRRGPFTTASALALGVPASRLRRSDVRRLRRGVLVWTGA
+TDGGSTVDPALPPRPAAASGADTPWVLASRLTPSEQETLAGVLAAAPDATASHLTAARLT
+GLWLPTRLAADRTLHVTRPPGTANSAPAGVRMHRRRPTSEGAQLVRGSGPPLDGPIPVTG
+PARTWRDLASLLDLAELVVLGDRLVCSSGPERADPLCSRAALVQAAARPGQRHAVLARDA
+AALVRDGAHSPPETRLRLALLDAGLPEPELQLEVWDPAFSRSRPATADLGWRRHGVVLQY
+EGAGHDDPVQVRGDTLRDAAFQRRGVVVIRAAAADLAEGFRGTTALAEAALRRRGWTPGR
+E
+>MHAAABBN_02086
+MRRPTPLPASLLDGPFTAAQARAAGIDHNRLRRSDVERLARGLYRRREAAPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDEVHVSRPRD
+RGRLALPGVTSHRTALPPADVERVRIGGLAWYVTAPPRLWVDLAALLDDDELVILGDHLV
+RRAELSGGPDAAERTRAALTQAAETSPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALT
+AAGLPEPALQLEVWDPEFSLHHPATADLGYPQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGYRNITVSSSDARRGFTRVIVEVRRHLGDAGGLSRKESEWGGDPASERHHA
+>LFPAFLNI_00067
+MRHPAPLPAALLHGPFTAAQARAAGIDLNRLRRSDVERLARGLYRRREVTPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDDVHVSRPRD
+RGQLSLPGVTSHRTALPPADVERVRIGGLAWYVTAPPRLWVDLSALLDDDELVILGDHLV
+RRAQLSGGPDAAERTRAALAQAAEASPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALR
+AAGLPEPALQLEVWDPEFSLHHPATADLGYRQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGCRNITVSSSDARRGFTRVIVEVRRHLGDAGDLSRKESEWGVNGTSERPLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001923.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef19adfe27efb493b28b9ddb3f29c5c3d4aa2c09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001923.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_00227
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>NAFOICDF_00111
+MTTTYMHTDAEDTIHSTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKAGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAAF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>MHAAABBN_02240
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>LFPAFLNI_00228
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFAEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001926.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfe77eaf8d81552139a65a12119da9dd36f28a16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001926.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_00387
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRASHPPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
+>NAFOICDF_02441
+MAPWLPTRSRRPFPQVTEGGEAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSAASASPSATLTEMVTETA
+GPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAAV
+YLWHADALGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFPD
+KASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLPQ
+ITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPARP
+>MHAAABBN_00111
+MAPWPPTRSRRPFPQVTEGGGAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPEASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYAGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPAEQSAQVYATSAYDGSTENFAQVSLETDNVLSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPARP
+>LFPAFLNI_00393
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRAFHHPAEDVEDQGAALDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTAAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVPTSQIAMPEEQSAQVYATSAYDGSTENFADVSLETDNVFSDGNETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001927.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65136de166ed6680eb3a2933ff06c9f42bc2de76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001927.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_00395
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSGVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>NAFOICDF_02433
+MDTAANPALTTDLRSPRRVAGKDVRPVGLGCMNLVHGYSGFLSEREAVDLVVGVLADGTD
+HLDTATLYGGGLSEEYVGKALTRVGADVRDRVLLASKCGLSRDADRPIDGRPETLRAQVD
+ASLRRLGQDRIDLYYLHRLDPRVPVEESVGALAEAVAAGKIGAIGLSEVSGATLDRAATE
+HPVAAVQNEYSLATRNPEWGLLEACRRHGAALVAFSPVCRGLLTDAPPVVADLPDGDMRH
+AMPRFQGPAWEANLRLREEFASEAARLGVPAASLAVAWVLAQGADVVAIPGTTDPAHWRE
+DRGAEEVSLTLEDLARLDALVNHATVQGRRYSDAQQASVDTEDAPQQG
+>MHAAABBN_00119
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>LFPAFLNI_00401
+MDATPHPRPAEPGPLPDPAAPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001929.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3779b53b3f7636ff66d980e2662a920bc5cda3b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001929.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_00476
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>NAFOICDF_02355
+MTAEQTTQPTSDAPCTRPLQEEAPVVSVVMGSDSDWPVMGQAVEALRELGVPVEVGVVSA
+HRMPHEMVDFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLRSLDGLDSL
+LSIVQMPAGVPVATVSVDGARNAGLLAARILAAGTDDGAAHLRAALQDVAAGLNAQARAK
+GARLHERAADGA
+>MHAAABBN_00194
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
+>LFPAFLNI_00476
+MTATPQTPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEM
+VEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSLLSIVQMP
+AGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAKGARLRER
+MAADR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001935.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9de63c4bbb5284820ee99c8e349191e2e498d1d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001935.fa
@@ -0,0 +1,25 @@
+>MOLHKGIG_00787
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>NAFOICDF_02037
+MTSSGPATPPADWSALLRQAAATLRAAGVDSPRADAELLLSHLLGGDRGTLLARVLAGAA
+PGPGQAEAFGALVERRAVREPLQHITGAAAFHGLTLEVGPGVFVPRPETELLVEEGIRAL
+AVLDGPARVVDLCTGSGAIAAAVAAWAEERHRDVAVTAVEREDAALAWARRNLEPRGVDL
+RQGDALVACADLDGTVDVVLSNPPYVPDAELPVQAEALADPPTALYGGDAAGLRIPRGII
+ARAAGLLRPGGRLVMEHHEAQGEALAAEARLGGRFEDVRVLPDHTGRERFLAAVRTGALV
+APPSDGRMEP
+>MHAAABBN_00518
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>LFPAFLNI_00754
+MSAPAWSALLRDAAARLTAVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALVGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPAAG
+AVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDTPGLRIPRAIAHRAADLL
+APGGLFAMEHHETQGPALLSALGADRRFTGERVHQDLTGRDRFLTARRSGEAAAGAEVEE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001939.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04034e8dde2d443f078b2133589310756c6d5a3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001939.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_01064
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEVGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>NAFOICDF_01712
+MFTGIITHLGTVLSLEERPETDTAVLTVDAGGALDGLPAGGSLAVDGVCLTALDDDAASA
+APGVFRADLMGQTLRMTSLGGRRPGDRVNLERCLRPTDHLDGHVVQGHVDGTGTVLAVSP
+HGDWTTLRIGLPARLARYVAAQGAIALQGVSLTVTGVSPADAREHWFEVGLIPATLEATT
+LGRLAAGDTVNLETDVLARYAERLAAIPAPTTEEPHA
+>MHAAABBN_00783
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGRALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>LFPAFLNI_01011
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDEPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001945.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78cdfb4912af995ce4ecfa4f55e22685f9e46943
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001945.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_01290
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>NAFOICDF_00710
+MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVSALTRALQGV
+ATGLLDDHLKHCVLDAAKLSDEAAVEKIQEATDAINRLVRS
+>MHAAABBN_01009
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>LFPAFLNI_01248
+MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001947.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3358b792552988ac1728411f23aca223127cf389
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001947.fa
@@ -0,0 +1,32 @@
+>MOLHKGIG_01357
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>NAFOICDF_01431
+MIGLLIGGVLGLILSGLGTPLFIRYLVKRGYGQQVRDDGPQTHKSKRGTPTMGGFVIISA
+LVLGYLLTHGILALLGSELAGPTASGWIVLLLTVGMAFVGWIDDYTKIAKQRSLGLTPKG
+KIILQGLIGTAFAVLALLFPNADGVTPASTAVSFVRDIPWLELAFAGPVVGVVLFVIWSN
+IITTATTNAVNLTDGLDGLAAGATAMVTGAYVLVSLFQASQSCGLTEGAEACYVVRDPMD
+LGLLAAVLTGALLGFLWWNTSPAKIFMGDTGSLGLGGALAGLAILSRTEILVVILAGLMV
+AITLSVIIQVGWFKISGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLISLVCVIIGLALF
+YGEWLLQHGALQAVAR
+>MHAAABBN_01077
+MIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+LVLAYLITHGLLAVLGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPASGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>LFPAFLNI_01312
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001949.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0825f41401003cea731331012bce35f0b600d1e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001949.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_01405
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>NAFOICDF_01402
+MTEHTQHDDAARPALVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHVLDSG
+VDLADPDAIAGAARAMDLRQSTDPDVESVVVGGTDVTDAIREDRVTDVVSTVAVVIPVRE
+ELQRRQRAAIAGAGRIVAEGRDITTVVAPDAHARVLLTASAEARMARRSGQLQRAGAGER
+DAATLERQVSGRDARDSAVSTFDRPAEGVALVDSTELDFEQTVAAVLAAVQDQAGVDAVP
+GR
+>MHAAABBN_01135
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
+>LFPAFLNI_01355
+MTEHTRDDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEGV
+DLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVREE
+LHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGVD
+AGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVKG
+GRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001951.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e584acecd095c3e3e461767b0d7cc8ec76361a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001951.fa
@@ -0,0 +1,37 @@
+>MOLHKGIG_01410
+MVQQRVVRAPGRSDPGGSVPPTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVA
+HTLTTALRAQTHEHANQLHTALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAA
+QARERGVALTWSAELTAPAPLRPLDLLTVLGNLVDNDLDAAAAPDLSAVDRWVDVEVVSD
+ATGLVVQVADGGPGPSDADRRRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVAT
+DSGTVFTVEVPREPTPQEET
+>NAFOICDF_01396
+MRHPWSIARRVAASLVLLLSVIAVFSGWAGWRQARDATFVVEERHVLGVARLAAREEVVV
+DALGSPAGAAALQARIPSVVDDAGVSWLTLLDARGTRVASWRPEQVGTAYPAPVDRALAG
+ESWTEVSATGPAGISVRALVPVRDAEGAVVGVLTMGVRVSELEVAASAQLPRLAVTFALT
+LAAGLGAALLVARYLHRVTLGRGPEDLAESFLLSAAAMDSLEASLVVLAPDGSIRQHNAA
+AVHALGLPARTEDGTVPAAARLPEELARALEEHADADFPARVGDRLFVVRQRVLGAARPR
+RGGAVDDAAREGISPAPAGTRVLMLHDRTDLQRLTDDLALSRTLTAALRSQTHEHANQLH
+TALALLDSGRTDAARDVLTRHRRPDQDAEDVVSALLEAKAAQAAERGVELTYAVRLSAPA
+PLAALDLVSVVGNLVDNALDAAADAAEPAGRWVDADVTCDADGLLVQVADGGPGLDPDGD
+RVFEPGWSTKPAGIAGRGMGLALVRSIASQAGGVVEVATDSGTVFTVEVPPAGPEQDGEA
+A
+>MHAAABBN_01140
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRARLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVSGEASLAAGGRVLVVQQRVVRSPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLGNLVDNALDAAAAPDLSAADRWVDVEVVSDAAGLVVQVADGGPGPSDADR
+GRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVATDSGTVFTVEVPREPTPQEET
+>LFPAFLNI_01360
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRVRLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVGGEASLAVGGRVLVVQERVVRAPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLETARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLATWWTTPSTPPPHRTCPRQTGGSTSKWSRTPRAWWCRWPTAAPDPPTRTA
+AGSSTGAGRRSPSAPPDAAWGCG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001952.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dada43186076828aeb9bcb7fbf26340f12e7e9ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001952.fa
@@ -0,0 +1,19 @@
+>MOLHKGIG_01411
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
+>NAFOICDF_01395
+MSAERPYRVLIVEDEELTAQTCADHVTRLPGFTVVGAVGTVDAARRLVAAALDRDGRFPF
+DVLLLDMNLPDGHGLDLLQQLRAAGFQGGVLALTAATELSVVRRAIALGVVQYLVKPFGF
+EAFAQRMTGFRSAAALLAGPGRLSGQEHVDDVFRAGQRRGVEELPKGLSAGTLQAVLDLV
+HDADGGRSASEAAAGLGLSRVTARRYLEHLERIGRVRRRARHGGRGRPEQEYVWAPGAPS
+A
+>MHAAABBN_01141
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHADGRFPFD
+VVLLDMNLPDGHGLDFLHQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+>LFPAFLNI_01361
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTEGTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001953.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5950a66a7df8ab21b3c3183d8c84e6516aa940e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001953.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_01445
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGEFDRPHVLCGVCRTELSVTAYLALEATADPACPACGAPFNPGCADHAPLYFDVP
+ASGSPAGDADPAAQP
+>NAFOICDF_01358
+MVTPADPGPAVRGVDADPQTRCAHYRTERDVVALRLDCCPEYWCCRECHDELAGHPGRPL
+PREAFGLPSVLCGVCRHEMDVPAYRAAMAHADPHCPACGAGFNPGCSRHARLYFAVDA
+>MHAAABBN_01177
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGDFDRPHVLCGVCRTELSVAAYLALEATADPACPACGAPFNPGCAAHAPLYFDVP
+ASGSPAGDVDPATRP
+>LFPAFLNI_01395
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGDFDRPHVLCGVCRTELSVTAYLALEAAADPACPACGAPFNPGCAAHAPLYFDVP
+ASGSPAGEADPPAQP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001958.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cfa92d6f3c186bb0c19496909f13f430418a101
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001958.fa
@@ -0,0 +1,16 @@
+>MOLHKGIG_01506
+MLATTLEQISVAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRR
+RRPGRPIDFGEDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWL
+TTLL
+>NAFOICDF_00640
+MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIRVVGVKGRPRTRPERVIADKGY
+PSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFGRDQKRRYKGRNAVERCFNKLK
+QWRGIAARSDKTPRNFHAGLSLAATLQWV
+>NAFOICDF_01746
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
+>NAFOICDF_02236
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001959.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c158fe4414d9b634d93773862a77ddf9cd88ade2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001959.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_01592
+MTRTPPAVAPPAAETGGESLLTVLIALGVNAVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>NAFOICDF_01221
+MSHSDDIRPSVAAHPDDGDATSDPALAPPQAEDRPEGLVTVVIALAVNVAVAVVKSVVAA
+LTGSAAMVAEASHSWADAGNEVFLLVAERRAARPADARHPLGYGRAAYVWSMVAAFGLFA
+VGAAVSVWHGITAWSAPEEEGGGHLIGYVVLAVAFVLEAVSFGNAHRRVSAGAQEHRVSR
+SRFLARTSDPTLRAVWAEDSAALVGIGIAAAAIALHQLTGDARWDAAGSILVGVLLGAVA
+VFLLSKNMAFLVGEVADPAVRVRVLRWLLERPEVLSVSYLHLEYVGPGRLAVVGAVDLAA
+DEVESLAAVALQRVEDALLAHPVVAAAVLSLSNPSHAPLRLEDEEAAARR
+>MHAAABBN_01304
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>LFPAFLNI_01519
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001961.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9205e10aeb7e0a4dc99c72539162dadcaf77ea8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001961.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_01780
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLGAV
+>NAFOICDF_01021
+MDRHLLPAGPGEVTPRPRIALDPARLHAARAALSVFGPVHRQEPIEWAAEEPLAPDLAEF
+YREVGPDWVEIDTLGLPLLMFPLERLWDEQAGYRWNHRTGAMLADWNEDWTVVAKQGAEP
+FIHEAATGHVLMAHGEEGWEDRLGEPVPVFRDVAEMTLALCAAGAAWAGSDDPFTADWHV
+RPEVTSAVVDGLEQVLGDRARAVDVARRLGHLRAA
+>MHAAABBN_01487
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLRAV
+>LFPAFLNI_01709
+MTRVPPAHGHRPALRDSTGSAPGPGVEPGARPQLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNHRTGALLVDWN
+EDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPEPVFRDLAEMTRALAAVGTAW
+ARFDDPFTVDWHLTEEVTTAVVAGLEAVLGAHDRAVDLARALGYLRAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001965.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b53efed9e7751346287f0bb3ccb49fd8b5f65cee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001965.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_01913
+MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
+>NAFOICDF_00882
+MTALHGGTGPAEARERFRAGLVRPTAGIADGFAQANLMVVPQDLAWDVLLFAQRNPKALP
+LLGVLEAGEVRGPAVDGDVRTDVPQYVVYEDGVPVGRPTDLLEVWRDDLVTFLIGCSFTF
+ESALVAEGIRIAHQDAGVNVPMYRTTRRCVPAGRLSGPLVVSMRPIPADRVADAVRITSR
+YPSVHGAPVHVGDPAALGIADLSAPDFGDAVEVPPGHLPVFWACGVTPQAAVMESRPPLA
+ISHAPGHMLITDIPDRTFQIP
+>MHAAABBN_01609
+MTTTTPLPPLDAATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPKALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRNGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPIPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
+>LFPAFLNI_01833
+MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001968.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2041596b8d8b1f6b37d9d6276c22e66aa2bdd07d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001968.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_01917
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
+>NAFOICDF_00878
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG
+VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN
+TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL
+VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV
+RRALEDAGVTIASFA
+>MHAAABBN_01613
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVAIKAFA
+>LFPAFLNI_01837
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001971.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e2ecf88b8c732bd7d911a0e32052456e577490e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001971.fa
@@ -0,0 +1,32 @@
+>MOLHKGIG_02046
+MTTKDSRTRSLIDVDVLEYHRLLTPEQQEKLGEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>NAFOICDF_00734
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHVSGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTPGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKADT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADTGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>MHAAABBN_01752
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEELTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+RRVGELGYNHISGMTEDPLFRGHLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+TWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTLGYEATKIEHKTAVKIVQNADITFTDVRIPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERTQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEATGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
+>LFPAFLNI_01980
+MTTTDSRTRSLIDVDVLEYHRLLTPEQQEKLTEIRAALAEIVTPHVAEAWSRDEFPHEIA
+CRVGELGYDHISGMTEDPLFRGYLMAELARADISLSVYFALHNDLVGATLEALGSEEQKQ
+KWLPGLYAMEYTGCFALTEPEHGSDVAGGMATTARREGDEWVINGAKRWIGNGTMSRIAI
+VWARDEEDDQVKGFIVETDTSGYEATKIEHKTAVKIVQNADITFTDVRVPAENKLEKANT
+FADTNVILLGSRNGLGWQAVGAQQGILDAARRYALERAQFGRPIAGHQLVQSLLVQIAAN
+LAATLGMAHRAVQLEAAGEVSMTQASLVKLKTSQMCRESAALGRQMMGGNGILADVGLGR
+FFCDVEAIFTYEGTYEVNSLIVGRGLTGHSAFL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001972.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e34d11c28545fbacc72e407b95a15c727d899be7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001972.fa
@@ -0,0 +1,56 @@
+>MOLHKGIG_02048
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SQRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEEGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
+>NAFOICDF_00732
+MTENTITWDQDAEGVVTLTMDDPTAKVNTMNGHWQESMRAAVERLEQERESITGVILTSA
+KKTFFAGGDLDQLGPSGPEDAEDVFAMTEHVKSLLRRLEKLGRPVVAAINGAALGGGLEI
+ALACHRRVAVDDPRIKVGLPEVTLGLLPGGGGITRLVRMLGLEKALMDWLLQGTQYRPAQ
+AKEKGVIDELVSSPEELLPAARRWILEQGAAAAKAREGGPEETDEALGAPSYAVKPWDRK
+GFRLPGGTPQQPQLASRLPAFAATLVKTLHGADLPAPRAILSAAVEGAQVDFDTASRIET
+RYFTSLVTGRVSTAMVQAFHTEMGAIRAGAGLGERVSERHTIATAAVLGAGMMGAGIAHA
+LATSGIDVVLKDVSKENAERGKAHCADLVGKAVARGRMDQSAADEVLGRIRTTDDYADIA
+GVDAVIEAVFEDFDLKSEVFAEVEKVVGRQTLLCSNTSTLPITQLQGPRERAADFVGLHF
+FSPVDRMKLVEIIRGEQTSQETVERAYDLVQQIRKVPILVNDGRGFYTSRVFGTLVLEAA
+AMVEEGVDPQRVERTARQAGFPGAPLAMLDEVSLTLTQHVRREAEKAAEAAGTERAEQPG
+ERVVDRMVEEFDRPGRARGAGFYEYPAEGPKHLWPGLREHFAAEVDVSDEDLKDRFLYRM
+ALETAACFEAGVLTDTASADIGGILGIGYPPHTGGPATFATNRPGGLADFVSRADALADA
+YGERFRPSDWLRERAAAGQGLA
+>MHAAABBN_01754
+MSEHMITWDQDTDGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMDWLLQGTARDARA
+AMEKGILDEVVTDPADLVPAAKRWILEHRDDADAAAKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMKLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGGTLRQLAERG
+EGPGR
+>LFPAFLNI_01982
+MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSA
+KKTFFAGGDLDSLAQAGPEDVESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEI
+ALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMVGVERALMEWLLQGTARDARA
+AMEKGIIDEVVTDPADLVPAAKRWILEHRADADAAVKPWDVKGFRIPGGTPAQASFASRL
+PAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQA
+FHSDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAA
+ERGRERVGALLEGRVAKGRMSREDADAVLARVQPTEDYQDLAHVDAVIEAVFEDLELKDS
+VFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHFFSPVDRMRLVEIIRGEQT
+SPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARH
+AGFPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQ
+GAGFYEYPEQGPKHLWPGLAEHFATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPS
+ANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADRYGERFRPGDTLRQRAERG
+EGPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001976.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce1d91d3ca6324166f7ff123b442505691a4e14d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001976.fa
@@ -0,0 +1,16 @@
+>MOLHKGIG_02171
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDAR
+>NAFOICDF_00507
+MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD
+NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD
+AGHRAGGTDGTPGNGR
+>MHAAABBN_01885
+MTDIRRTATALTLAAAVVTGLGAPAAVAQTTAPATEAATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVGGAHRDHDVHRVDDRAGDVRAEGADTR
+RPGTGDAR
+>LFPAFLNI_02116
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001979.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae21be5499b508cb353cd71c08ad134ea9722d50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001979.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_02224
+MTLMWGAVAASSLLVGAVLATLHRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKRRRHLLIQWSLVTVVCALATWGGGLIADVAS
+PALTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
+>NAFOICDF_01229
+MTQILLWGVVSASSLLLGALLALARDWHRPTIGRILAFGAGALIASVSLELAEEGVNTGG
+AVAVGVGLALGAAAYFTANRVVERRGGGSGGGSGAALTVGALLDGIPEQVVLGVGLAAGG
+EISLALVVAIFVSNLPEAIGSSADLLRAGKTRRHVLTQWSVVTVVCILATVVGGLLAELA
+TPGMTAGVQGFAAGALLVMLIDTMIPEAREQGGETAGLVTVVGFALACGLSLLG
+>MHAAABBN_01939
+MTLMWGAVAASSLLVGAVLATLRRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKTRRHLLVQWSLVAVVCALATWGGGLIADVAS
+PTLTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
+>LFPAFLNI_02162
+MTLMWGAVAASSLLVGAVLATLRRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKTRRHLLIQWSLVAVVCALATWGGGLIADGAS
+PALTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001990.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72c967b24611d4e0c5d3e14408788613409784a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001990.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00210
+MKPGWTTVALGDVAEVRRTSVHPAHMRPDDPYLGLENIERGGRLLSVSTVAGEGVKSTKF
+RFSPGDVLYGKLRPNLAKILKVDFEGLCSTDILPIAVNSGTLSADFLAYYLSQPQVVAQA
+ASRASGANLPRLAPAEFLALRIPLPPLDEQRRIAAALDRATVVIGGIGDLRRRTRSIGES
+VVQQSSTGAGRWSTIGKSLTLRSGSTLPATRRRPGGVPVYGANGAIGEHDEATHEQPHVT
+IGRVGAVGAVNVTAGRAWISDNALIVVKAPEHLSNGYLAIALAMADLGRFASQSAQPLIT
+QRKVADVPLWIPSQAEALRIDAILDRLAEVERANVERVARADALFASLQSRAFRGEL
+>MOLHKGIG_01621
+MTLPANSIRIIEANNWVSAETAARMKLKLTPPGAVAFAKIGEGLKAERLRRITVPTAMDN
+NMMAAIPKPAVVDSGFLIYLIESVHIAEWAQGSALPYLSQKLLADIPVHVPSLPEQRAIA
+ATLGAFDDKIESNRQAMATGESLIRAVVESTLDASEGEDGTLGDYCALVKAPVEIDKIDP
+DDNYIGLEHMPRGSIFLTEWKKAKGLGSNKTAFKRGDLLFGKLRPYFKKVGIAPIDGVCS
+TDILVVRPKSPRDIALVTAVAASDALIDSLSASSTGTRMPRASWKDLAAWRVPVLTATER
+IELSARVDPLVERLTQLTFESHRLVALRDALLPELLSGGLRVPVTS
+>LFPAFLNI_00189
+MKPGWTTVALGELCELKYGKSLPAKARSGEGFPVFGSSGLVGAHEKAIQRGPGIIVGRKG
+SIGEVHWSEDDFWPIDTTYFALPRRANVDLRWLYLALRWLPLKTLNKAAAVPGLNREDAY
+RLTLALPPLDEQRRIAAILGTSLHSIGCRVRACIWIDDFLDNVYNSTLRSGDIPRRPIRS
+LGEVSTGKTPATSKADYFGGVIPFVAPGDLGGLVSAKRTLTDLGAQESRLVRAGATMVCC
+IGATIGKVGIVAEQSAFNQQINAIEWGPDMDDLYGYFTMRAQSDVVAARGSSTTMPILAK
+SKFEELLIPVAPFEVQEEFARVASIVSRVRSNLVAAWEAERQLFASLQSRAFRGEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001992.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..563b6858bb68ac58a32d1a8f7e57903daf90b54d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001992.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00268
+MATRLRQRLLSAAALTAAGALLITGCAESQRDSGGSAGGSGSNGDAAQVDGSFIFAASSD
+PKTLDPAFASDGESFRVSRQIFEGLVGTEPGTADPAPLLAESWESSEDGLTHTFKLKEGV
+TFHDGEPFNGEAVCANFDRWYNFTGIQQAETVSYYYGKLFRGFADAPENAVYESCEANGD
+AEATVTLAQPFAGFIASLSLPAFAMQSPKALEEYKADEIGGSAESPQMSEYARAYPTGTG
+PYKFDSWSVGEDIKLSAYEDYWGEGGDVTDITFRVIDDPVARRQALEAGDIDGYDLVAPA
+DTQALSDAGFNVVARDPFTILYLGLNQQQEELKDVKVRQAIAHAIDKEALIGQTLPEGTE
+PATQFIPKSVNGFSEDVTKYEYDPEKAKQLLAEAGYADGFTIDFNYPTGVSRPYMPTPEQ
+VFSNLSNQLSQVGIQVEAKPAKWSPDYLNQVQGTADHGLHLLGWTGDYNDTDNFVGVFFG
+QEKPEFGFDNPELFSALEEARGVPTLEEQTPMYEEINKQISDFVPAIPLAHPAPSLAFDK
+RVASYPASPVNDEVFTEIDLTE
+>MHAAABBN_02132
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
+>LFPAFLNI_00124
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001995.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03a4f10cb40630c778033e3c037a36f9070fb84b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001995.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_00526
+MTQNAPALTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADVAERISGRKNIPVV
+VFPDGEHQVEPTNEETAQKLTALGLL
+>MHAAABBN_01928
+MSQNDLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI
+>LFPAFLNI_02154
+MSQNVLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001996.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1d31527378cc29f9177f44e9e7006634e60a17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001996.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_00532
+MVGIKDVARMAGVSAATASRALTGSGPVASSTRTRVQEAVAALGYVPDAAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRRRYDLTLYDVGQDHDRRSAVLTDLLPRRRLDAL
+VTLSFRLSPFELDGLARLGRPVVAVGGRLPSGEALPEWFTAVQVDDARAARMATGHLIEL
+GHREIAYMGRVADDIEFQVSTERTRSFLDALAAAGLRTPADWMLPADFTIGDAYHRARAL
+LADPEHRPTAVLCISDEMAMGTLMAAQSLGLRVPEDVSVMGLDGHPDAARLGISTVDQTP
+VDQGRRAVRLALGALDGTPTRPASSTTWPCNPGRAPRRRERRAGSRPRRRRPPSTPPSPR
+IVGHVPARERTPPWPP
+>MOLHKGIG_02212
+MVGIKDVARMAGVSTATASRALTGSGPVAAATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSVFEFAGLERLGRPVIAIGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
+>MHAAABBN_01925
+MVGIKDVARMAGVSTATASRALTGSGPVAVATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSAHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSMFELAGLERLGLPVIAVGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001998.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..528ecdb337139ab3ecb26696320e1c302ee17405
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001998.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00534
+MSTSSTTSARPDAPHEDPADAGRRGLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLF
+QLAAAGDWVVFAVTLAVTLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFT
+NYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLEQGGDLHLLTVRDGQAVLGGADEP
+LAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSRAYV
+YSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPS
+LRDPLLRVLVWTFAFAFLSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLS
+GLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFSVIVVNLWLGFPYMFLVTTGALQS
+LPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGGPRF
+ADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEI
+DS
+>MOLHKGIG_02210
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>MHAAABBN_01923
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002003.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e4f387f5fe6889519a590eb35ecc0bc92d80bec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002003.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00689
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADADIDAAVDGSLMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRYGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
+>ACLBLIBL_00823
+MTETLTYADLLAAVVAPEGAGTEIKDPATGDLIGYAPQSTTADLDAAVELARTAQRDWAK
+LSHAERSAALNRAADAIEANSAALAELLSREQGKPVKNGPNAAFEVGGCVAWTRATAGFE
+VQPETIVDDETGRAELHWMPIGVVGGIGPWNWPMMISVWQIAPALRMGNTVVLKPSEYTP
+LSVLGLVHVMNQALPEGVLQVLAGDGELGRAFTSHDGIDKITFTGSTATGKAIMKGAADD
+LKRLTLELGGNDAGIVLDDADPKAIAEGLFWGAFINTGQTCAALKRLYVPDSLYDAVCEE
+LVAVARRMPMGPGLEEENVLGPLQNRAQYEIVERLVQAAKDGGGRVLLGGDPDPERPGLF
+YPTTIVADIDNDNPLVAEEQFGPALPIVRYTDLEQAIEWANGLDVGLGASVWSADPERAK
+EVAMRLEAGSVWINKHGTIDPRVPFGGVKHSGMGREFGVLGLKEMAEAKSISV
+>MHAAABBN_01797
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADANIDAAVDGALMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRHGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002004.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..599cdd8b55de742e959d07aefc5a2f94c9e13af2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002004.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00693
+MVSNRLEAESGWRRSQLHGVRADDALTTTTLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFAADRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALNVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRHLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPAVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAALAAQVHGASAPTFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTAAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+>ACLBLIBL_00810
+MAPEPPQADPERIRRARHELAARGLIAGSVPPALVGEQIEQSWRRSVAHEVSLDAVPQGG
+ADLDPALPLRRAAETVVRRWAEGLGQLRVSLVVADATGRILVRRALDTRDEDALDAARAA
+VGYGFGEQDLGTNGLGTPLQVKGDVYISGAEHFTDGLAGLTCAGTPVLDPVTGRAVGALA
+VASRADEAHPLMLGVARQAAAEVMEALRDETAGPDLEIARAFRGLRGPDRAVLVMSADTV
+MTDLPGLARIDAQTQAVLWETLRRRSPGEEPVRLSLPGLEGEALARRLPGAEAAYALEFD
+AVPAPEPALGRAAAAPRSGPPAGGGPERGAGTAPSVGVHPSEMAVAYDGIGDALTAAAEQ
+TGLVELTGPRGSGKRFQAVRWLRDRALAAGTADAPDPLHVELADVTGPQGEDLLRRVAAR
+GRAVVVAGTLPTAAETAQARAGLRTTVARVVLEHPEAPRVVLLRSVDASAEDDVAGQVRL
+PALAEVPQDIPALLARLSERLHPGAPPPRFSPEALQRILAWPWPDNMAGLSRLVSLLPGL
+RRGATVQVEDLPAALRAGPGSRLTRMEQAERDAIVAALREHGGNRSAAAAALGIGRATLY
+RRLKALRITV
+>MHAAABBN_01795
+MVSNRLETESGWRRSRLHGVRADDTLTTATLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFASDRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALSVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRCLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPPVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAAMAAQVHGASAPMFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTVAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002006.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2045adcde640338e708afb015fab7e478c3039c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002006.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00737
+MEDVHARAVIDASGTWTTPNPLGQAGLPAPGEAEALAAGQITAPLPDVLGADQARFAGQH
+VLVVGAGHSAANTLLELGTLAQDTPGTRISWAVRSADVARVYGGEDRDELAARGALGTRL
+RHLVETGTIQVHPSFTITAFTTTGLGMMVQASTPAGEEHLVVDVVVPATGFRPALGMLSE
+LRLELDPAVEAPRQLGPLIDPEFHSCGSVTPHGEKMLAHPEPGFYIAGMKSYGRAPTFLM
+ATGYEQVRSIAAALAGDRTAADNVELQLPETGVCSTDLGGSCDAPAPATAADTADQGCCA
+PAPQTLPAPASRLPVLLPVQAATCC
+>MOLHKGIG_02073
+MLTTSTTSHPVAIIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEAAGWTAPDADVLPTGHELREHYLEPLAQLPQLAESIRYGARVTAVSRA
+GIDKTRTARREETPFLVRIQTTDGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+RAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIAVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLEPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GGCDAPATAGDACCSSPQLIELPLGR
+>LFPAFLNI_02001
+MLTTATNPHPIVVIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ
+YNLDAAAQRLLEADGWTAPDADALPTGHELREQYLEPLAQLPQLAESIRYDARVTAVSRA
+GIDRTRTTRREETPFLVRIETADGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA
+HAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTTIIWAARTADL
+TRVYGGGDQDELAARGALGSRLRQLVDSGRIEVLTSFTITRFRADDTLTVHAVTPDGERE
+VSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLGPLIDPEFHSCGSVEPHGERVLAH
+PETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCTTDLG
+GSCDAPAPAGDACCSSPQLIELSVGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002007.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4cf0fe96cd8dbb7086f6d54fbe613e377f0a89c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002007.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_00761
+MTLAHPASRPMPATSPATPGATPPDPAARLVPLRGADHAAVLAEAVRVRASGGIPVVGDE
+RWPAALMAAQVEHAAATLRDLAVRDPRAAAEIAWAAFTSGSTSRPRVVLRTEASWRAGHR
+VAADWLGLRPGEELLVAVHPVSSMAVHAASLCGALGARLRVTARARLSAADLAGPVVLDA
+TPSQLVDALDLLDDGAPSTLRVALIGGDRLPAGARDRAAAHGIRVAHFYGSAEASFVAVD
+LDGAGLRPLPDVRLRIADGADDAGPAGPNTPDPNTPRARTGLLELRSDQLAAPDDSRLSS
+GAPRWREDGWLTTGDRATWDPDAGVLEVHGRADDVILTAGATVAAADVEAELAAARDGSG
+RPVASGVLVVGVPDRRLGERVCAVVEPARGQDPEAALQMLKTAARAGLSPAARPRRWVLV
+DRLERTGSGKIRRALPAATRHAAGRQDHA
+>NAFOICDF_00724
+MSPLAPVPDPAARLAFLADADHAAVLAEAVAVRARGGVPVVGDERWPADLRAAQREHAVV
+QLRRLAARDPDLAARVGWAAFTSGSTSRPRVVLRTDDSWRAGHPHVAAWLGLAPGEAMLT
+AVHPVSSMALHAAAWCAATGHRLAVSPHARLTAADLTGPAALTATPSQLTDALDLLDDGA
+PSTLRVALVGGDRLPAGARERAAAHGLRTVHYYGAAEASFVAVDLDGSGLRPLPGVELEV
+AEPDVLADADGPRTGVLRVASPQLAVPDDSRLASGAPRWDAEGRLTTGDRVTWDPAAGIL
+TVHGRADEVVLTAGATVSAADVEAELAAVAGPDGRPVAAGVLVLGVPDPRLGQRVAAAVE
+PAPGVAPEDALAALQGVARARLSPAARPRRWVAVGRLERTGSGKIRRVTPPELRP
+>LFPAFLNI_01993
+MIPPVRLPPSDDDVAPAVSRLAPLRGADHEAVLRRALEARTAGLVPLVGDERWSVAQWQA
+GVGHAEALLAELTARAPDRAARIGWAAFTSGTTGRPRVILRTADSWRTGHRLVEDWLGLE
+PGESLLVPVHPVSSMAVNAADLCAHVGARLLVPSRARLRAADVTGGAAAVHCTPAQLADL
+CDLLAAVRAASAPAGPRVVLVGGDRLPGQLRERAAALGLRVVHYYGSAEASFVAVDPDGS
+GLRALPGVRLEIREGVLHVRSDQLAEPDGTRLTDGTPRWGADGWLCTGDRAQIDDDGVLH
+LRGRADDAILTGGATVIPAEVEAELLRATVRRESTASGGDSAPHAVPVCTAVLVQGEPAP
+RLGSLVVAHVEPAPGLPADVVLAALKEHARTHLPPAARPRRWQVVDRLERTGSGKIRRMA
+PDVAAIPDPPGGSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002008.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1204aca96e8bbba32c9b64f68c6cc5cdb460cb7a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002008.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00762
+MVASALTGGDPALPGIGPVAAVREVLDAAGIALAEVAVVEVVEAYAAQVWAVLDELGLSA
+EAGAARADDWGVDPRVNAEGGALAFGHPWGASGAVAATHAVRRLQSCPPGSSALVTCAVG
+GGMGVALVLDVA
+>NAFOICDF_00725
+MSAVGLDAAPVWITAVSRTPVTARSRAQAHLGAGELAAGPVGEVAAGTHPAAVVLGNGAG
+PGGNVARIAALAAGLGVATPGWTVDAQCGAGLVAVAQAAGHAVATGRACVGGGVESPSTA
+PERSIDGVSYAQAPMVPAGWDDPGMTAAADALAAARGIGRARQESFAARSHVLALAGGLR
+LPDDDGPRRLDAAALARFRAVTPGADPATAVTGATAARIADGAAAVLVTPHSAVVRETDG
+VSTASVRGVDVLRPCRVLSWSLTGVDPALPGLGPVSAVRDALDAAGRTLEGVAVVELVEA
+YAAQVLAALDDLGLTGASGTSAPGASGPATAHDPWGVDPRVNAAGGALALGHPWGASGAV
+AVVHAVRRLQAEPPGAVGLAACAVGGGMGAAMVLEVA
+>LFPAFLNI_01992
+MTTTPGLWITAAARTAFTARSRGQAGLDAGALSAQAVAAVTGPAAADVAAVVLGNCTGPG
+GNLGRIAALAAGLGEHTPGWSVDAQCGAGLAGVLQAAQHAAFTGRPCVGGGVESPSTAPQ
+RSRDGVPYTQAPMVPSGWPDPGMTAAADALAAADAMPRARQEAFAARSHALALAAAGLRR
+IERVPGAPDDDGPRRLDARALARFTPVHPDADPAAAVTGGTAARIADGAAAVLVVPCERS
+PVGRDEPAGGLRPVRIVGAEIRGGDPALPGIAPVAAVERALAAADWRLGEVAVVEVVEAY
+AVQALATLDRLGLTDHARPGPASLGSDRQGLDDWGVDRRVNAAGGALALGHPWGASGAAA
+VVRAVHRLQGQPPGARAVVACAVAGGLGITMLLEVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002010.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a11d5ad4f9f742ca87755f772a810d244a1f4a97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002010.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00776
+MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY
+RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG
+ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS
+VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG
+ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL
+SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT
+TAHTIGVKRLG
+>MOLHKGIG_02042
+MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY
+RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA
+ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG
+STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS
+VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG
+ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL
+SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT
+TDHTIGVTRVG
+>NAFOICDF_00744
+MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY
+RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA
+ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS
+TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG
+ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL
+SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT
+TDHTIGVTTVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002011.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72ebcebbe6d6510c77e8f754ee357b242b72af6f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002011.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00777
+MRMSRGVEATWTDYLRAIQSLNPSGVFSHATAARIWEMWIPGRLFEDPRVHLAKERGRGG
+RTSRPGLVMHQLQPDAPVIEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAE
+ARRLGHLPPRATTVDEMRRLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAG
+FPEPQVNPPIRLSAGETVRVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDW
+AVTWVAGEVFTRGGWPRFVGDLSRLIRRQAARHGTVLPPRLPGE
+>MOLHKGIG_02041
+MPRPLAPLATSLPTILTVPEGREAGLSRARLRAPDLVAIGHGLRMSRDVEATWTDYLRAV
+QSLNPSGVFSHATAARIWGMWIPGRLLEDPRVHLAKERGHGGRTSRSGLVMHQLQPDAPV
+IEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAEARRLGHLPPRATTVDEMR
+RLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAGFPEPQVNPPIRLSSGETV
+RVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDWAVTWVAGEVFTRGGRPRF
+VGDLSRLMRRQATRRGAVLPPGLPGE
+>NAFOICDF_00745
+MADPSRATPPRLVTTATLRSRGVAPWELRRREYTGRGRSLWGAAGVEFTLLDHVRALQEL
+HPTGVFSHATAARLWGMWLPRDLLQEPSVDIAKVKGRGGWPSREGIRGHHLDPAAQVVRL
+HGVRVTSPAWTWVDLAARLSVEDLVVAGDSLLPDEHGATARSLGRLPCRASTVAELRRTA
+ATRKNVRGVVRARHVVGLLREGADSPAESRLRHRIVEAGFPEPEVNPALRLHDGRIVRPD
+LCWRALRMCLEFDGDHHRTERAQWQEDRARRRGLEADGWSVTWVAGEVFTRAGWGRFRGD
+LAATMRRQAHQEGVVLPPSLPGEEASLW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002015.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4f7d735ec71c2a42894e0b020d5102b151d046d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002015.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00824
+MSARTEFDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVASSEPPIV
+LIGSAGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAPEVDEFAAASLTPEPSVVV
+GPPRVAASPAALECRLHEVHPVGDSFLLMGRVVHVSVDTDVLTTDARGRTLPDPAALGPV
+SRLGRMEWGGLGEVFELERPSAG
+>NAFOICDF_00157
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRIDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA
+>MHAAABBN_02186
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRLDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002019.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfc43a17aa3912c167d404c5d38718470ba5bba0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002019.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00843
+MRIDENSERDAQGRLIPTPGQTIGPFFGYADGYEQVHLPFRDGQNLVPPGRADALRLTGT
+VYDGNGDPIPDAMLEIWQADAQGVISQEDGSLVRDGFTFTGWGRATVDNVGTYTFSTVEP
+GATGEGTARFISMVVFARGLLNKLHTRVYLPEDTEALAADPLLQSLPEERRRTLIAERLD
+DGSLRFDVWIQGRGEHADKETVFLQFPGIEYPQHD
+>MHAAABBN_01709
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD
+>LFPAFLNI_01937
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002020.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b6b09c27300b9d8c1ee4ad2f51c972fb987f2df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002020.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00898
+MTLTTRDAQTWEQMWLPLWPLASDDLRAGIYRTARKDARGKRYIEANPQALSNLLVVDVD
+HEDALMRALWGRHDWLPNAVVENPTNGHAHAVWALAEPVTRTEYAQRKPLAFAAAVTEGL
+RRSVDGDAAYSGLITKNPQHASWHTSWTSDRLYSLGELASRLEEAGHMPAPAWRRSRRQN
+PVGLGRNCSIFETARHWAYREAKRIRQRHEHATAEDSRDYYAAVLAHVHELNAAFSEPLP
+ANEARDIAASIHRWVTTRFYGWTDARTVQQATLSTLQAVRGRKGGTKSGEKRRSTVEDRA
+RLIVGEDA
+>ACLBLIBL_01314
+MDARETQAWGQMWLPLWPLASDDLKAGIYRTPRATARGRRYIEANPQALSNLLVVDVDHE
+DALMRSLWDRRGWLPNAVVENPENGHAHAVWALGRV
+>ACLBLIBL_01316
+MVKTIVRHALAEPITRTEYARRKPLAFAAAVTEGLRRSVDGDKAYSGLMTKNPEHTSWNT
+SWISNELYSLGQLAEHLDTAGFLPAPSWKRTRRRRPVGLGRNCSIFETARVWAYRELRHH
+WGDPEGLRVAIVERVHELNAEFSEPLPAREALDIAHSIHRWITTQSRMWQDGPVVYEATF
+TAMQSARGRKGGAKSAEKRRAVVEDRARLIVGENA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002022.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efdeb0d20faf84bffa53d5a060c5485340a8ebac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002022.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01077
+MTTATPRQPLIEDHAYLSNQHSGALLTREGDVTWLCLPRFDAPSVFTSLLGEPEHGRWSL
+RIADGEVRERAYLPGTLVLRTRWRGPDGEAEVLDFMPLTSHRGSGRAHDDDAGALADEGE
+AARADLVRLVRCTSGSVSVDQCLQFRMDYGEVVPWVSRQTDPADESFLAVVAGGDALAVH
+GPDLRPDSTAHRGRTRLEAGQSAAWTLAWYPSWSMAPAAPDPERALEATVTDWVEWLGEP
+LATGPRADRVARSLLVLKGLTHRDTGGIVAAPTASLPEDFGGVRNWDYRYVWLRDTALTL
+EALMAHNHTDDACAWRDWLLRAIAGDPRDVQIMYTLSGERRMPERDLEHLPGYEGSRPVH
+VGNGAADQWQADVIGTVMLALGRLRDAGVDEDRWSWTLQKRLVERVLEHRDTKEHGLWEM
+RGEPAYFTHGRVMMWAALDQALHAARDHGLPAEDEELAAWEQARDELREEILTEGVGPSG
+GFRQTYGSEETDASLLQIPHTGFLPHDDPRMLATVADVERDLVTETGLVMRYRASGMDGL
+PGEEAPFMMCGFWLVEQYARSGRLADAERLMARLDECSNDLFLMAEEYDDGRDRMAGNFP
+QAFSHLGLIRAVDALEEARGAAGGEG
+>NAFOICDF_01012
+MTAQTAPASPLIEDHAYLSNQHSGALVTRAGDVTWLCLPRFDGPSVFTSLLGAPEHGQWS
+LGIADGEVVERAYLPGTLVLRTRWRGPEGEADVLDFMPLADHAGSGVVDADDVGILMGEG
+EGPLRRADLVRLVRCTSGTVEVDQWIRARLDYGEVTPWVSRQEDPAGEEFLAVVAGGDAL
+AVHGPDLRPDGMRHRGSTRLEEGRSQAWTLAWYPAWTTAPAAPDAEHALEKTVTGWVEWL
+GDPRARGPRAERVARSLLVLKGLTHENTGGIVAAPTASLPEDIGGVRNWDYRYVWLRDTS
+LTLEALMAHNHTDDAAQWRDWLLRAIAGEPKDNIQIMYTLSGERRMPERELGHLPGYEGS
+TPVNVGNGAADQWQADVIGTVMLALDRLRDAGVDEDQWSWPLQKRLVERVLAHRDTKEHG
+LWEMRGEPAYFTHGRVMMWAALDRALHGVREHGLDATEEETAEWERVRDELREEILTEGV
+QEDGAFRQTYGSDETDASLLQIPHTGFLPHDDPHMLATVAQVERDLTTETGLVRRYRATG
+MDGLPGEEAPFMMCAFWLVEQYARSGRVEDAERLMARLDDCANDLFLMAEEYDDDRGRMA
+GNFPQAFSHLGLIRAVDALEECAEDARAAE
+>LFPAFLNI_01718
+MSAQPRIDDHAFLSHQLSGALVSREGAITWLCLPRFDSASVFTSLLGTREHGEWSLGIED
+GEVAERAYLPGTLVLRTLWRSPSGVAEVLDFMPLLDADGVGDAQGDDGGPDGTGASEAAP
+RADVMRLVRCLAGRVRVTQSVFARLDYGEVEPWVSRQEDADGESFLAVVAGGDALAVHGP
+DLEPVDGHHEGTTELVAGESAQWCLTWYPAWGMAPSAPRAEDVLEATVRRWRGWLEESTR
+QAPRADDPLADRVQRSLLVLKGLTHRATGGIVAAPTTSLPEDIGGVRNWDYRYVWLRDTA
+LALEALLAYGHVEVATAWRDWLLRAIAGEPHEVQVMYTLSGERYMPERELEHLPGHADSR
+PVVVGNGAADQWQADVIGTVMMALCALRDAGVPEDEWSWPLQKRLVERVVAHREDPDHGL
+WEMRGEPAFFTHSRVKMWAALDRALHAVATHGVPATEAETAAWERHRDELREEILTRGVH
+ADGHFTQAYGSDAVDASLLQIPHTGFLPPDDPRMLATVRRIEEELVTDTGLVLRYRPDGS
+DGLPGEEAPFLACAFWLVEQYARTGRLDDADALMERLDACANDLDLMAEEYDDGQDRMAG
+NFPQAFSHLALLRAADALALVRAGDGAGEAGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002024.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7423c5272ef608aeaa0e49f8ef3a194d21fafc61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002024.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01215
+MSKLRMLSRMPKKGRFMFIISGGDRARYMSRKGLVRGMGENVWFQPRALPNDPNLIRFHN
+NIVVASGVTFVAHDVINLMIGRKNGVRLPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAI
+IAAGTVVTKDVPPDSIVRGVPAKRLGDFSVLEAQRLADAGRFDGMTRAQIDDVLWE
+>MOLHKGIG_00888
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG
+>MHAAABBN_00610
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002030.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..877416fa1345b59c06843065c20e4b934184feac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002030.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01578
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>MOLHKGIG_01314
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>NAFOICDF_01474
+MARARLEGAVLDALWDHPDGLTAQELRVRLEREDGAPAVTTVLTALSRLTAKGHVRRVGA
+RRPQVFAAARTREQHAAGLLQDILGSSPDHEAVLAAFVGGISDADAAALRRLLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002034.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3fa44cfb7fc2b7b07a3bb46abf0283bf6fb8472
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002034.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01993
+MRRELTLTPVGEAEPCAARVPLFAGLEPDQLRRVSALARPFALEPGDVLHLPGARTERLW
+VVHTGGLALSLTSPTGRERVVRMAGPGDSVGEQEFLTGAAARHGVRAVAPTRLCTFSHEE
+IAGLMAEHPGIGRRVMRTLAVRLADAERRLAQERQPVAARIAGHLLELPAVHASGTPTVL
+LTAPKKDVASLLGTTPEAFSRGLRRLVDDGVVAVDGPRVRLLDADALEGLAAG
+>MOLHKGIG_00944
+MRMDLPLAPMDEPEPCAARVPLFTGLDLEQLRRVSALARPLVLEAGDALHLAGDRTDRLC
+VVHSGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVAATRLCTFSHAE
+VARLLAEHPGIGGRVMRTLAVRLAEAEQRLAREHQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLDPDALEALAAE
+>MHAAABBN_00663
+MRMDLPLIPVDEPEPCAARVPLFTGLDLEQLRRVSALARPIVLEAGDALHLAGDRTDRLC
+VVHTGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVVATRLCTFSHAE
+VARLLAEHPGIGGRVMRALAVRLAEAEQRLAWERQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLNPDALEALAAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002041.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45f7c08c494ae45fecc4a275836fd95e39ba4186
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002041.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_02431
+MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPPTPGQAGCAISHFRVLESFASS
+LGHEDGVALVSEDDVLMPPETEAVLEGILKDDSFEIAVLADRGPTNPSLAFQRLLMTEAE
+LSLLSRPIVCGGRIRRLGRFEGNPYMAALYLVTRSGARKLASGLVDDAGGPWTIADDWPL
+FRDRYGLDIRVLRPGLVTYMGGSTTRDAESLARDALSAAGDGRPLTRLKTAVGLRSRSRA
+ARLVVRATLRDIATR
+>NAFOICDF_02276
+MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP
+LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV
+LADPYGPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGFYLVSR
+DAAKYDIAWRLRHRRGGAR
+>NAFOICDF_02312
+MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP
+EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRGWGWTLL
+AQGLEDPFRDPFWAKSRDRAPQSLLAKPVGPPSSPWRYRLGNWDGELWGTGLYLVTREAA
+RALTDHATREGLSWAADDYVTWHAAAGVKVWILLPTIAGWVGESEINATTRPHLQIQSYA
+AHPMGRQAWSRRVSRFRAGARIAWKEMRGDTRPWAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002043.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0231910a286b20ffa615c3f7e5923b14889d0e5a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002043.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_02502
+MKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQKMLTQTLRA
+LEEDGLVMRTVYAEVPARVEYRLTEAGHSLRAPLEALEKWSITHLADVLHARTHYQT
+>MOLHKGIG_00455
+MVTMRQAGAKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK
+MLTQTLRALEEDGLVTRTVYAEVPARVEYRLTEAGHSLRAPLQALEEWSITHLADVLHAR
+NHYQT
+>NAFOICDF_00141
+MNRSWNPLLASCPSRTSLARIANKWTALIVIALAEGPLRFGGLHDGVDGISRKVLTDTLR
+DLERDGIVARTDHGGVPRRVEYELTALGRTLETPLAALVDWAAEHHDAVEAARVDYDERR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002047.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c548bf6d55db586d94fdd629e9ebdec9de88aa98
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002047.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_02653
+MTVSMRVMSAGDGYKYLLKSIAAGDGDRSLSTPLTRYYAEAGTPPGFWMGSGLGRLGHGD
+LVEGGQVSEAQLALLVGMGHDPITGEPLGRAYQQFASITERIKQRVDALDPELGPATRAQ
+EVAAIEAEEAERGTRRAVAGYDFTFSVPKSVSTIWAVADAGTQALIADAHHAAVAELVAF
+LEREVAATRVGATGPDGAVAHVDVAGVVAAAFDHYDSRAGDPQLHTHVVVSNKVLTVQDG
+RWRTLAGRPMHSVVVAVSELYNAALADQLTRVLGVEWEARERGRDRNPAWEIEGVPDELV
+TEFSTRSRHIEAEKDRLIAGYVAKHGRQPSARTVLKLRAQATLATRPEKQVRSLADLTAE
+WRQRAGRVLRRDANGWARTFTASTADAPRRVLRADDVPLDVVREVGQTVMETVGEKRSTW
+TRWNLHAEASRQLMGWRFASIQDREAITGLVVDAAEHASLRLTPPELASSPLQFRRVDGT
+SRFRPHASTLFSSEVLLAAEDRLLARAATTAGPVVPLETVERIARKPDARGRVLGEDQAA
+ALAAIAVSGRVVDVLVGPAGAGETTAMNGLRRAWEKEHGTGSVIGLAPSAVAAQVLADDL
+GIATENTAKWWQNHLMYGTTFTAGQLVIIDEASLAGTMSLDRLTHEAEKAGAKVLLVGDW
+GQLQSPGAGGSFAMLVHARDDAPELTDLHRFTNEWEKTTSLQLRHGRAEAIDALIEHGRI
+TGGDEEAMIDAAYTEWRADLAAGRASILVTETHATVTELNARARADRIIDGTVNPTRELP
+LRDGTAVSEGDLVITRENDRRLRNGRTWVRNGSRWTVTGVREDGSVIIRPAGRRFGGGIV
+LPADYVAEHLDLGYAITAHRAQGVTTDTAHAVVTATTTRENFYVSMTRGAHSNHAYVTVD
+REDAEHAVPHPGDNPNVTARSILYGVLQHIGAELSAHETVAAEQDRWGSIAQLAAEYDTI
+AQAAQHDRWATLLAASGITAEQIEDVLGSDAYGALSAELRHAEANHHDLDALLPRLVAAR
+SLDDADDIASVLHARVARATARPAGSGRTRKAPRLIVGLIPHAGGQMADDMRRALDERRE
+LIEGRADAVLRGYLTDEEPWTADLGAAPRGDKQKAAWWRAARTVAAYRDRYGITDDRTPL
+GPTPESTSQKIDAIRARAALNRAQAIAHEGTTADAVRPATTSRPAPSL
+>NAFOICDF_01772
+MVWVTVSMRVMSAGDGYKYLLRTVAAGDGDRSLSTPLTRYYAEAGTPPGRWLGSGVTALG
+NGEIAPGAQVSEAQLQLLVGMGRDPITGVPLGRAYPVYSSTADRVADRVNQLDPALGAVE
+RGRRVAQIEAEEAARGSRRAVAGFDFTFSVPKSASVLWAVADAGTQALIAQAHHEAVAAV
+VAFMEREVAATRTGATAGDGAVAQVDVTGLIATAFDHFDSRAGDPHLHTHVVISNKARTV
+LDGKWRSLDGRPMHAAVVALSELHEAVFADHMTRTLGVSWEPREMGRDRNPSWAITDVPE
+ELAAEFSTRARQIEVEKDRLVAEYVATHGRQPSDATVIRLRAQATLGTRPDKQLRSLAEL
+TAEWRTRASQQLGVDATVWARTITVGERQMLLRADDVPLDLIGQVGRSVVEVVGEKRSTW
+RRWNLMAEAARQTMGWRFATVEDREAITAMVADAAEHASLRLTPPELTTSPVEFRRLDGT
+SVFRPKHSTVFSSDTLLAAEDRLLQRTRATTGQSVDLATVEAITGRPDAEGRVLGRDQAA
+ALASVAVSGRVVDVLVGPAGAGKTTAMNALRRAWETEHGAGSVVGLAPSAVAAQVLADDL
+RIATENTAKWWTTHQHTGATFHAGQLVIIDEASLAGTLSLDRITQAAEEAGAKVLLVGDY
+AQLQSVDAGGAFSLLIHDRDDAPELVDVHRFTHDWEKTASLELRHGRAPVIDTYLAHDRI
+HDGDAEAMTDAAYTAWRHDRQAGLVSVLIAETRENVTALNVRARADLILDGTLKPGPEIT
+LSDGSAAGVGDTIITRRNDRRLRNRHGWVRNGQTWTITAVHDDGSITIRPPGTRFGNSIV
+LPADYVAEHVDLGYAVTAHRAQGITTDTAHVLVEPTTTRENLYVAMTRGRESNKAYVILD
+RPDDHATAHPGDSPDATARTVLYGVLQHSGAELSAHETITAEQDRWGSIAQLAAEYETIA
+AAAQHDRWTTLVRGSGLTGDQAQAVIDSDAFSALTAELRRAEANHHNVDTLLPRLIRARG
+FADADDIASVIHHRLANATTRPAGSGRTRQAPRLIAGLIPEATGPMTPDMQQALTERRHL
+IETRAEAVLDTALHTHEPWVTALGPIPTSGRERQQWRRRAVVVAAYRDRYQITDPTPLGA
+QPEDTAQRIDRARAETAVRTLTRPTMEDERGRPAAQATRHLDL
+>MHAAABBN_01105
+MTVSMRVMSAGDGYKYLLRSVAAADGDRSLSTPLTRYYAEEGTPPGRWLGSGLTGLGDGQ
+LAVGDQVSEAQLQLLIGMGRDPITGEPLGRAFPQYAPVADRIERRVDELPDELGPAGRAE
+AVAQIEAEEASRGTRRAVAGFDYTFSVPKSVSVLWAVADAGTQALIAEAHHDAVAEVVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002051.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e2e1e5bfce6797d60e25ea37297aecac533d070
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002051.fa
@@ -0,0 +1,13 @@
+>MOLHKGIG_00029
+MSHASTVPPAADAPSRWGRAAGLSGLVMPAVLAAFSLYLLLGSLTMDTDGADFPGPDFFP
+LILSVAGLVIAAALAVEVVRVRQAPEG
+>MHAAABBN_02047
+MSQASTVSPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
+>LFPAFLNI_00029
+MSHASTVPPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002052.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb9445b358c560c37e6e5f52aa2f3b215065b3c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002052.fa
@@ -0,0 +1,30 @@
+>MOLHKGIG_00031
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMAASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSVKRRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>MHAAABBN_02048
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTRFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGAERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMVVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>LFPAFLNI_00030
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002054.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f69b7dd8a096feef97efe2f074e93aa11e84c945
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002054.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_00166
+MEYTKKWLPLEAQVERLVQRGLEVDDLTRALRLLESVGYYRVTGYLYPFLESEKQVDDQG
+HTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEGVERIEVAVRMRIGYVLGRTSPFAH
+ENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRRDGSDEQFVAHFRQKYDDHMPVWAL
+TELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMMGSWLASLNYVRNVAAHHARLFNRK
+LQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALAIIAYMLRPIEAERSWAPRLAELFR
+TFPTSHALSVQSMGVPEDWHTLDLWRG
+>MHAAABBN_00353
+MGYYRVTGYLYPFLESEKQVDDQGHTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEG
+VERIEVAVRMRIGYVLGRTSPFAHENPTCFDDSFTRANTDSRDPRPSKQVLWLERVKQRR
+DGSDEQFVAHFRQKYDDHMPVWALTELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMM
+GSWLASLNYVRNVAAHHARLFNRKLQNAPSRPAAGMVPLLDHLREPAAPKGDFGTYNALA
+IIAYMLRPIEAERSWAPRLAELFRTFPTSHALSVQSMGVPEDWHTLDLWRG
+>MHAAABBN_02025
+MRYSKPHLPYDQQVRLLASRGLNVGREGDAVRALKRIGYYRLSAYTYPMRAFTTDDAGTV
+HRSDDFVEGACLSDAVALHDFDHRLRRTLLPAIQSLEIALRTKVGYHLGKHGPLAHLDRS
+GLDPQRCDAVSRGPDHTGTKYDTWRSEYDSLQRKAGREDYMVHFATKYDGDVPVWAATEF
+MTMGCLIGLYRMMQPKDARRIAEEVGVKNPQVLFGWLKALNVLRNHCAHNARIWNRSTVY
+PPDKINRRMVEEELHHLVSADTNKVYFLTAVLAYLLRHVDPDSRFASDLRTTMGKFPSVL
+GWTPGHTMGFVDGWSTEALWSIH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002057.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb33dd1c8b6cdb88e87d0501b1c3717e11b505a6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002057.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_00274
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVVGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARIE
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVAREVLG
+>MHAAABBN_02289
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGSEVGAKLLTLTPDNPERGLPAIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDAGRAAALAARIT
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVARVVLG
+>LFPAFLNI_00272
+MSTPISTAPGLPWIDGPAVRSALSPCAAVDALEAALAAGLDPEADAPRTRVATAAGQLLQ
+MPSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGAPGQAPRAVLDGVELTGLRTS
+AVSTLGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARI
+EAELGVTASTADSEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDA
+LARRATVAVESRDSAAREAGDVTLAVASGALAGIEDTVTLAELVAGTARRREGEPALFVT
+TGMPWQDLVVASAVARVVLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002058.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3438add78d6db7797dba2692a71821c66bcf7eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002058.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_00415
+MGTMPTSSALPRTTPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGTVVAEGDA
+SATALLMVRPIPVEALAAALAAHPHVSWVQFPFAGIEPFIPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYVRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDSLDEVLPGAQVVMIAAAATDETRGLFDADRLALLNEDA
+VLVNIARGTLVDTDAVVRALAAGRLHGYGTDVTDPEPLPEGHPLWTEERALITPHTADTP
+QMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
+>MHAAABBN_00135
+MGTMPTSSALPRTRPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGAAVAEGDT
+SATALLMVRPIPVDALAAALTAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
+>LFPAFLNI_00418
+MGTMPTTSTLPRTRPDDVPERLLILPAAQDVADTPYAHARRLAEQAVADVGGTAVAEGDT
+SATALLMVRPIPVDALAAALAAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLTAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002059.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a2f7d81b78409c17804069a7af95c59f04be154
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002059.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_00498
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>MHAAABBN_00219
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>LFPAFLNI_00497
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002065.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0fb62b23bda7dcc4a05d28a096019ac6de1b6d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002065.fa
@@ -0,0 +1,17 @@
+>MOLHKGIG_00600
+MTSPWVEDDELTDWEAPAAADDDGQTGTPLPYVDPEIAAELAGEGPPVWMGTRWREIEAE
+HQWEAWNTLRRWVDWFVAEYRLVTSVVPPCWYKHSDLTAELYAAMCMEYKVWEEQAPGLG
+PMMMWHPHVEMLTARLRRMVDEAGCAKIGQHKEPEAYGDRPAFNLDYDEDDFTAWAATTC
+EQHALERPEAGVKYVRARVFNGDGEEIALSNPVGLASRRTSTGVTAELMMTSSTPLAPGL
+RLTVPSATPGLEVGWQTSVNGHDWE
+>NAFOICDF_01802
+MSTHSPEPDDQYDDPGILDDQPDMFDTNALPEPPHPINWNLLSAQDLEAELLELNRWVDW
+LRHTYGLPASVIPPYWHRHPELLWELSALHLHWLCAYDPEQNGSAPLGWHRDFADARHRL
+RDWVTASGTRLDRDRPTRQTTWPGEEPQPTHGESVITDRDADFVQFIIDQVNERQAAEDA
+FYASLDDRIDPATGEVRDDVLGPEGG
+>NAFOICDF_02241
+MASPWVEDDEPDWSETAPLQDEGPTETSLPYVDPEVAAELAQEGPPVWMGTRWREIEAEH
+QWQAWNHLRRWVDWFVAEYRLGTSIVPACWYRHPDVTAELYAAMCMEYKVWDEQAPGLGP
+MMMWHPHVEMMTARLRRMVDEAGCAKIGRHKDPEAYGNRGAYELDYDESDWTRWAATERE
+EELIERPTEGVKYVRAKVVDSDGNVLGHSAPVGLRPVPNVVGVEAKVRVTSSTPAEPRMA
+VAVSSGRDDLGIEWEMSPDGAEWSTRPNDDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002066.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..276f9ebb7ee67c1f636ebb5ff85890af84583367
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002066.fa
@@ -0,0 +1,11 @@
+>MOLHKGIG_00613
+MTMIKEPGVSPTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSA
+HLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHSGPAATG
+ALPHDAGH
+>NAFOICDF_00703
+MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVSKH
+VGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHTHH
+ASDTDKK
+>MHAAABBN_01773
+MSPAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSAHLACLAGC
+GLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGPDGPAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002069.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bb09993e74fc15f29c0fb28f0fe1fc776e95af0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002069.fa
@@ -0,0 +1,11 @@
+>MOLHKGIG_00808
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESHDVEGDELRAFVRFQSRDG
+>MHAAABBN_00540
+MTDSPIAADRDGIRYLSGVIPAADGGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIAS
+ELLRRVFARFGQVRQHVLLTDTEERQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
+>LFPAFLNI_00777
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002070.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bfed0aac8903a1d5d288101a818b8375360b86f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002070.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_00829
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHPESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDDAAAG
+RLELAGDYRHMWEAKPRWQGL
+>MHAAABBN_00561
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHPESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDDAAAG
+RLELAGDYRHMWEAKPRWQGL
+>LFPAFLNI_00798
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHLESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDEAAAG
+RLELAGEYRHMWEAKPSWQGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002071.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7d3f7c8511e52240e15a57064ed98a7ed8afb47
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002071.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_01038
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>MHAAABBN_00751
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>LFPAFLNI_00980
+MARHGRDEDEAHEAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVLGCAMMGF
+ALGIAWMYVERGRDGRDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002076.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d196bc2eb8292a98b42f6353213541de59d4cbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002076.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_01390
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
+>MHAAABBN_01122
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
+>LFPAFLNI_01341
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002077.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6cab1ae00bf7f92d44dab62cecca8fadb567620
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002077.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_01391
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>MHAAABBN_01123
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>LFPAFLNI_01342
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002079.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a0205a1e5f8c3a9e719aa814f5ea1131403b1c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002079.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_01396
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>MHAAABBN_01129
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>LFPAFLNI_01346
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002080.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6970a937d16956bd2dc02d4012619cfb9349291a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002080.fa
@@ -0,0 +1,10 @@
+>MOLHKGIG_01507
+MRESGVMSRDVISDEVWAVIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPER
+FGNWNTIYKNVNRWAAQGVWERVLEKTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRP
+TGGLDELQEISGRAG
+>NAFOICDF_01747
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
+>NAFOICDF_02235
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002084.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61ce6c361e76dcf9f837ae935a62998e38d056c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002084.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_01622
+MKTPVLSATDMRIVEQVLDMGDGYVLDFSNRTFADFFADLDVEIEPEDSGLSKAKRLRAF
+FRSASTSECARVLHALLEYRGEQDGDDESASIDKYRAIVSRLEGVAVPLSAAPVAPEVLT
+LAYVRELSDKAERRLAASDLEGAITVSRTLVEAVLEQLEIRLTGQSGNYAGDLQRQYKAV
+AKILRIDDKDDQVDEGFKQIARGLVQIVNGLAAIRNMASDGHARHVQPQARHARVAVNSA
+KTVASFLVEVYLAKRTGPTSPAAVRSGG
+>NAFOICDF_02204
+MASTSPTLLPFRIDSLATSLFAKETGFSGPQLHDFFARYTDVLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRAMLLSAGTPGAQAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS
+>MHAAABBN_00369
+MASTSPTLLPFRIDSLATSLFAKETGFSGPHLHDFFARYTDMLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRGMLLSAGTPGAHAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002085.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42886b9b56ca1f24e61eb4bc54878d647418af19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002085.fa
@@ -0,0 +1,33 @@
+>MOLHKGIG_01623
+MSTFNENVVELAALEHFAELGYRRVHAPEIAPGEPDAERDSYEDVVLWGRLRDALRRINT
+SADAALIAEAVKTVQRAGSQSAVDENARLHKLITEGVPVEHRGDDGLLRTTRLWLVDFDE
+PANNDWVAVNQFTIVENGKNRRPDVLVMVNGLPLALLELKNPAAGHATLKSAWNQVQTYR
+HDIPSVFVPNAVTVISDGTSAAMSSYSGAFEHYAPWKTIEGREVVSNRPALEVLIKGVFE
+PKRFLDLLKNFVVFSDETVTDKSTGQPTRALLKRVAKYHQYWAVNAAVESTVQASSPDGD
+RRGGVVWHTQGSGKSFEMVFYAAKIMRDPRMANPTLVFITDRNDLDDQLFGETFAPARIL
+PETPVQAATRSDLRAKLKRASGGIVFTTLQKFAPGEDGDANPVLTDRRNVIVIADEAHRS
+QYGFSETLDRHGRLKSGLAKHMRDALPGATYLGFTGTPIESNDKSTRAVFGDYVDVYDLT
+RAVEDGATVRIFYESRLAKIELSEADLAALDDLADEITESVEKDTATAAKSRWSRLEAVV
+GAEARLDLVARDIVEHWEKRRESLFGKGMIVTMSRRIAVRLYEKIIALRPDWHSDDPAQG
+KIKVVMTGSASDPAEFQPHIHSKDVRKDLKLRAKNADDPLELVIVRDMWLTGFDAPSMHT
+MYVDKTMQGAGLMQAIARVNRTFRDKPGGLIVDYIGVFANLQNALSEYSPSDRDQAGVPI
+DEMVQVMLEKHDIVRGLLHGVQFDSSPELTAAQRLNEYAKVLDFVMADPDRTSRFNDQVL
+ALAKAFALAGARDEAAAIRNDVRLFTDVRAAILKIQNPDSGRGGSGAVEVDTALSQLLNE
+AVTANQVVDVYMLAGIETPEISILSEEFLDSFAEKDRPNLQMGLLRRLLNDQIRTVQRTN
+VVQGRKYSEMLEETVNRYTNRSLTTAEIIAELVKLAKQMRDAQKRHEELGLREDEVAFYD
+AVVQNDSAVMELGDETLKAIAQELVTSVRQSATIDWNLKESVLAAMRSKVRRILAKYDYP
+PDAEAKAIELVIEQAELFARGVSA
+>LFPAFLNI_02203
+MTHANAPLTPTGRLRMVHRHLRDLLTQSNSGGIYFTTLQKFGLTQAERDAGADHPVLSDR
+RNIIVMADEAHRSHYDTLDGYAAHLKNALPNASLIAFTGTPIAEGERDTRRVFGDDIDVY
+DLHRAVEDGATVPVSFEPRLITLSRVDGVDDESLDAAADELTAGLDEADRDRIQRGVATL
+EAVYGAPHRLQTLAEDFVRHWEDRRDAMQPTMGVPGKAMIVCATRSIAARLYERIVALRP
+EWHDDADDKGRIKVVYDANPSDTGEIKKHMRRPSALAAVKKRLKNPADELEIVIVKDMLL
+TGFDAPALHTLYVDRPLKGALLMQTLARVNRTFRGKEDGLLVAYAPLAENLQQALAEFTR
+DTRTAGTKTLAQNTEEAAEIIETMVGMLADTVGVDWKATYQSDPKNGWRKALLEVTSRLR
+SPGTPGNTDPEDPTVRPVADTFRSQASRLHRAWALAGRVAAVERFRLDVKFYEEVRTWLA
+KLDAQDRIARGEPIPEEIARLLGEMVVDSTEATGVMDIYAAAVG
+>LFPAFLNI_02206
+MEEAAAPSKAELAIEGLRTDLLKEATRVTGGNEIRRAQFSERINAVMAKYTNQQLTAAEV
+IAELVEMAKEVVAEADRGRRFTPPLHDDELMFYDVVAQNEAALDVMGDDVLAQIARDLVA
+TMRRDIKTDWTVREDVKAKLRASIKRLLRKYGYPPDQQPEAIVEVMRQMEAVAPRMAEGQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002089.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..121f2110a0952f7d3427ec1f365fee2f4fd1f79f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002089.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_01962
+MTTAVRTCAASACAFNAETSCSALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
+>MHAAABBN_01655
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNVDLACTAEGIEVTDVATCATYTID
+>LFPAFLNI_01888
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002095.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f09d70b99ae25e3cbb051d2f845917083ef586ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002095.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_02166
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>MHAAABBN_01880
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>LFPAFLNI_02111
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002098.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2f9105dfb7966212862d8a0e77e7dea2451aa98
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002098.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_02205
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>MHAAABBN_01918
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETPLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>LFPAFLNI_02149
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002103.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36f44936e262e0fdeb95904b914896e5d5f1c2c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002103.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_02264
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>MHAAABBN_01959
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>LFPAFLNI_02195
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNALDITLRKVVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002104.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95954d0ea83bae51518ebb00998bbd9b3ed4ea86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002104.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_02269
+MGTIFLYEIAGTAILLLLGVGVVANVVLSKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQTET
+DQGAILGTFATGPEIRNPLWNMVTELIATFVLVFVVLLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>MHAAABBN_01962
+MGTIFLHEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMITEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
+>LFPAFLNI_02201
+MGTIFLYEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG
+AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET
+DQGAILGTFATGPEIRNPLWNMVTEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA
+SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002108.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12e836b71eb4c4cc574298395cb53733c00a31fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002108.fa
@@ -0,0 +1,20 @@
+>NAFOICDF_00320
+MTMMHELGHVIYDRDVSTPWRSTKSPEEERAFRFAGAMLIPANVMKKRVTESLTLHGYLA
+IKADYGVSVGALVKRAESLGIISKSRARSLYIQISSQGWRYNEPVPVAAERSLLIQQATA
+RAFGENLEGVAQSTGVPHRLVEHWTGFKRDLRAPMADVIPLRR
+>MHAAABBN_00366
+MTRISPLSAAGTDFDGTRLTVARRLRRKTKATLAREVGVTPTAIAQFEKNLSKPTQSVLA
+RLCLQLGLPREFFGAGRPLALLPASGAHFRSLRSTSATSREQALAYGELCLELVDLIGAY
+VDLPPVSLPELELPEELTDEAIVEAARLTRSTWGIAPGPLPSVVQTLEAHGIIALRLPVE
+TDAAVDAFSTYSGARPLVFLSPTKDDKARSRFDAAHELGHLVLHPDTEPGSKLVEQQAHQ
+FAAEFLMPRDEIIEDLPRRINWPAFHELKRHWGVSLRALVYRAHSLGRLSEASYRRANQQ
+LSAWGHPEPGPLGPAESPQVLGIARQLITDGGYDFEGIMAAGRIAPEVAEAVMDAASTVR
+PKLRFVI
+>LFPAFLNI_00171
+MSLEPSRIVRARRRAGISKKRLADLIGATPRTISNYETRGAPDALAATLADVLNVDPTFF
+SMPATSPLEEDRVFFRARRRTSAAVRHAASEAGRTGVEFYSLIAEHFKLPEVDLPDLVGM
+GPAIAARQLRAHWKVGAGPLPNLIQLAESRGLRVMSLPGTTDEVDAFSVWEKGVPYIFLS
+QRKTAERSRFDLAHEIGHLVLHSGLGNGDSVERDAEREADAFASEFLLPGEVLRGAMPRQ
+PSTEAVLKAKVSFGVSAMAMAYALFRNGLLSEWAHRQMCIDLTRRGYRSSEPGGIHRETS
+RVFGLTLSLARQRLGLGTEEIAQALGVCPQEIHELTFGHAVTPVASVGGSSAAPEPGPRP
+SLRVV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002112.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..490d5745ef40e02c043a9704b5b333d4301e1d69
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002112.fa
@@ -0,0 +1,25 @@
+>NAFOICDF_00671
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
+>MHAAABBN_00357
+MTAGVDRPADGKVAVERVDRPGRRGMRLLGPAFVAAVAYVDPGNVAANLTAGAQYGYLLV
+WVLVAANLMAMLVQYLSAKLGLVTGRSLPELLGHRLPRGRRLAYWVQAEIVAAATDLAEV
+IGGAIALHILFGIPLLAGGVIVGVVSMILLGVQSRRGQQPFEFVVVGLLAVITLGFVSGL
+FYGPISWGEAVAGMVPRFEGTQTVLLAAGMLGATVMPHAIYVHSALARDRHQGAHAHPGT
+LGRLLRATRWDVGLSLLVAGSVNIAMLLLAAANLSGVSGTDSIEGAHAAITTALGPAVGV
+LFGVGLLASGLASTAVGSYAGSEIMGGLLRWRIPQMLRRVLTLIPALLVIASGVDPTWAL
+VLSQVLLSIGIPFAMIPLVRLTGARAVMGRHANSTPLQTVAWVVVALIVALNAVLLWLTL
+TGQG
+>LFPAFLNI_02013
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002116.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b867e13f8ab66ee9c14e1bfe97a3554ebcdf0c8c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002116.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_02203
+MSRFQMLSDAQWELIAPMLPTHTGRPGRPFSDARMMIEAIIYRYRCGIA
+>MHAAABBN_00370
+MSRFQMLSDAQWELIAPMLPTHTGRPGRPFSDARMMIEAIIYRYRCGIA
+>LFPAFLNI_00110
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QRSVDLASALGRKRHMGHGAGHADRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002117.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..367026ae04fa553e456971a779843466d34d199c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002117.fa
@@ -0,0 +1,24 @@
+>MHAAABBN_00101
+MTTIPIHEAQVRHQPLHAYVEEHAQVSPDRTAIVCGGSQLTFGQLQSQVEQLSAYLSEQG
+VSHGDTVALFMQNSPQFVVSLLAVQRLGATAGPCNPMFKQWELEYQLNDLDTKVLITFDD
+LVPVFEKTDTGVQTVVLTRWSDVIEDVSQVPVEDGAEPVQQTKAPHTVRYAQIIGGERTV
+PPAAEIDLAQDPALIIYTSGTTGQPKGAMLSYRNVEFKTACTVQTYGFTSDDVFCAVMPI
+FHIAGMTVCMNSPLMVGGTMVIEPRFEPGTMIRDLERHAVTVTYTTPPMNLALLDHPAMA
+EADLSAVRLSPGTSFGIKITREISDRWEEVTGAPLFEWAYGMSETHTGDTQMPPEAIRYG
+SHGKPTFDTDVRISDPEDPSREMPQGELGEILVSSPSVFLGYRGREEATQKTMHRHWYRS
+GDLGRIDSEGYLHFEGRNKDLIKSSGYSVFPEEVERMLVRHEAVAQAAVVGYPDPQRGES
+VRAFVILEEGQSVTPKELIEWSRERMAAYKYPRDVRIIQELPTTTTGKLQYAKLRDLD
+>MHAAABBN_02299
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP
+>LFPAFLNI_00283
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002120.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9ae559a5685fa33d98fb0e083bef7bd0a4236b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002120.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00037
+MSTLETVAERVAADRALYAAAYAQGHADGLAEGLAQGAAHPAITDSVARVFAGWGGAEAA
+HARSVAAFRAWHTAARAELKEAA
+>MHAAABBN_02229
+MNGPTCRHCADWAYGYAEGYAQGHASGLAAGRVQGAAEGPAHPAIADSVARMFAGWDGAE
+AAHARSAAGFRDWYAQARQEENAHDIAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002124.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad4ae8aa3f5804806455197b7daa0b9643a3b997
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002124.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00078
+MRLAAVNPIPGLFTIAPADRDHEVGLRVGVTVLVPLLVLLAAGRMDLAVYAVFGAFTGIY
+GRNLRHGPRLQAQLRGGGLMLAVLAAATLAGRLGVSEQADPWGLVLWTTVVAGVAGVVAT
+LLAAPAGVHHNYWAMVAAVVPLVGHSTRYRVSRGLQRVIGTFLGLVLTAGIILLDPPVIV
+LVLIIAVLQVAAELYIARQYVIAQTVVTPLALLSTMLVGVTAGGAGSLMAAGGLQHLADR
+GVETVIGAAVGIVCVLFPWAWRRWVWGSPDPARAIPVVRGPGS
+>NAFOICDF_00062
+MTTQAPGIPLTMGRIRARRPRRKDPRPVRLADVNPFPAMFTIGPPDRGHEVGLRVGVTIL
+VPLLLLLALDRMDLASYATFAAFTGIYGRNEPHGVRLRTQLRAGLLMLGVLTAATVAGRF
+GISEAHDPWGLVLWTTVIAGAATVATGWWNLRPAGSLFHIFAFAAAASVPVKPPVVEGML
+MAVAVVVWAIAVGLSSRVLPSHRTPLTWPPSDRPDRGRRRLILLEAMWYVIAAGVAGSVA
+TLVAAPQGVRHNYWAMVAAVVPLAGHSTRYRVNRGLQRVLGTVLGLGLTALIVLLDPPAV
+GIVLVIAVLQVLAEVYIARQYVIAQTVVTPLALLSTMLVAVTVGGAGSLAEAGAFRNLQD
+RAVETVIGAVVGIVCVLYPWAWRKWVRRSPDPTREIPIVRPEQIQRPVGGRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002127.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..045d2c204bc6f095cfd3be20a80ea97581cda4ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002127.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00091
+MGESRSGGIIRYAHLQEPHCVYGGWIQEDFTARQVLDSLTSQNEQGEVVPWIARAWEVSD
+DGLAWTFHLREGVHFTDGTPLDAQVVVDNFQYWADGGNSTAAVHLGGFFESAEVADAHTV
+RVHLLRPNGVLPSTLSQTYFGLQSPTALRTRSKEDNCRQPIGSGPFTVTEFQRGSHISYA
+RNPDYQWAPADARHQGPAYVDGIRWSFVPDNTSRYGALLSGEADAIGEVPAVNVAEAQER
+FAYQQYVTPGRPVVMSLNTREGIFTDVRVRKAFAHATDRESIVRSAFLGTVPFEPNGFIS
+RTTPGYDPTLADALPYDADAANRLLDEAGWTGRDPDGVRTKDGRRLQSRIVYGAGSILNP
+DGATAVASVAEQARAVGFDLGIRPATQSELFGGLFATPETRGIEVGYWTSPHAGILHINY
+RPSTPEEPNGANTSFLDSPETYSTVVDALSARSEEQRNALFAQAQHELNDLVPAIGLYDQ
+TNSVATSRGLTGVWLEGSQGAPVFHDAYFVAPAAPDGPPADARRTDQKD
+>NAFOICDF_00134
+MSRPPHPARRRRRALRVSVAAAAALVLASGAAAVALPTGPDGPSDGQVLRVALGSDQGCL
+DPQQVSSNDSIYVARQVADSLTDQDPETGQIVPWLAERWEVSEDARAYTFTLRDGVTFSD
+GTPVDSEAVAANLDSLAEGLGPRASLATGYLAGYAETDVHDARTFTVRFHRPTVQFLQAT
+STVSLAVVSPASIAAGAEQRCAGVVGSGPFVVDAYSPGAGSTLSRRDDYAWGSSLWKETG
+RAGVDRVEFSIVQESGVRAGLLQSDQVDLIGSIAPQDEDPLAASGARLLQRANPGTPFGL
+LLNHEHEPFTDPRVRQAVSAALDRQEIVDVAFFRDSQPATSMVSRTTPGYADLSGRLQHD
+PQRAAAALQEAGYTRDPDGYWTKDGTPLTFTVTWSAVSPHNAPALEMLQQQLDDAGIRVR
+LREISTDQAGQILAESDFDAFWTNTTRADVDILRTSYHTGLANRSNAAASPTDGLLEQID
+ATTDSAARDRLAARAQDELLTSLPVIPVAELDTQLAARPEVSGVLFDSGSRLILHDARVD
+AEQKEQKEQEEH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002132.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9f888b128476bfdbe104626887865fcf4d948a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002132.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00117
+MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPAAGADGFRVLPYLMEPTATSM
+DLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIKGL
+AQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIAFS
+DTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQDV
+ALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLGNW
+ETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTILT
+LDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGSTP
+ADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQSG
+VAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYAKD
+ASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEMTL
+TPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR
+>NAFOICDF_00085
+MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT
+SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT
+GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA
+FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ
+DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG
+NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI
+ITLDSTNGVPDESVNGPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGST
+PADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQS
+GVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYAK
+NAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEMT
+LTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002140.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c72289a1fab29a6d86b5a58f3084ff258f984039
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002140.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00290
+MADMGNKFDKLKGDAKEGLGKATGDDRLRAEGKTESTAAGAKDAVQNAGDKVKDAAAGIK
+DGLSKDR
+>NAFOICDF_00236
+MADMGNTFDKLKGDAKGAVGEATGDSHLEAEGRTESAAASAKDAARSAGDAVKGAAEGVK
+NAVSRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002141.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5145487300edc0175418a161017fbf0af92a0674
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002141.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00340
+MSAEEKNLPHGEESTTVGEMNDTVATGLPEEPRTEEGADAPQGARAENPQSDAAAGQCPV
+AHGGAALPHPTSGDANQQWWPNRLNLKILAKDQPVQSPHEADFDYPAAFEALDLAEVKET
+IAEVLTTSKDWWPADFGNYGPFMIRMAWHSAGTYRVTDGRGGAGEGQQRFAPLNSWPDNA
+SLDKARRLLWPVKKKYGQSLSWADLIVLAGNVAHEIMGMPTFGFSGGRIDAYEPADDVYW
+GPETEWTNGGAERYKGERDLDNPLAAVEMGLIYVNPEGPEGEPDPLKSAKDIHETFSRMG
+MDAEETVALIGGGHTFGKTHGAGPVEPHIGPEPEAADLEQMGLGWKNTYGQGKGRDTITS
+GLEVTWTYHPTRWDNEFFHILYAYEWELMESPAGAKQWRPVNGGGSDMVPESDFQGRREP
+RMLTSDLALRFDPVFGEISRRFKDDFAAFQDAYSRAWFKLTHRDMGPRPRHRGVEVPQEE
+LLWMDPVPAPESVPGDAEVKAVKDAVAQAGLSVTDVVKTAWAAASSFRSSDFRGGANGGR
+IRLEPQRSWEVNEPAVTGPVIDALEKIAQEAGVSFADTVVIAGNWAVEKAAADGGVQVTV
+PFTPGRGDATAEQTDVTSFGHLEPKVDGFRNWDPRGSKTFPAEFALVDRANLLGVSAPEM
+TVLVAGLRVLGAVHGDSQDGVWTDRVGVLSQDFLTAVTDIDTQWEKVAEGRYRGVTADGR
+ELTGTRNDLVFGSNPELRTLAEVYAADDAREKFVQDFVRAWAKVMDADRFDAK
+>NAFOICDF_00280
+MHGKGASLPHPTSGDANQQWWPNRLNLKILAKEQQVINAHDADFDYPTAFAALDLDEVKK
+TIAEVLTTSKDWWPADVGNYGPFMIRMAWHSAGTYRSGDGRGGAGTGQPLTARPAADDGR
+PPHRVGARSAFPPGAGPCLQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002148.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40fc1f0d47f601acae5c40d74a9288c14e7e327e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002148.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00391
+MPPIDQWVTFEPLTGSPVGIAALLFAALYLRGAIWMWRNRRRWAIARTASFLIGCALIFA
+ITMFGVNRLATESITALVFQQITLLTVVPPLLIAGSPGLLLLRSTPHTGLGRLVLRAAHG
+GLRSRFWSAALHPVVAIVIAILLYPVLYLTDAISVIMRIPFGQDALLFVILVLGIVSATP
+LWSSDPLPRQPSFAARFIDIAVEIQIHAIFGLILLRTATPLFSAYATPTGSHDPVIDQAT
+AGTLVWTYAELPMFVVLIVCLSRWRARDVRTSRQRQKAEDAELDSYNEYLASLSRRRNES
+>MHAAABBN_00330
+MPPIDQWVTFEPLTGSPVGIAALLFAALYLRGAIWMWRNRRRWAIARTASFLIGCALIFA
+ITMFGVNRLATESITALVFQQITLLTVVPPLLIAGSPGLLLLRSTPHTGLGRLVLRAAHG
+GLRSRFWSAALHPVVAIVIAILLYPVLYLTDAISVIMRIPFGQDALLFVILVLGIVSATP
+LWSSDPLPRQPSFAARFVDIAVEIQIHAIFGLILLRTATPLFSAYATPTGSHDPVIDQAI
+AGTLVWTYAELPMFVVLIVCLSRWRARDVRTSRQRQKAEDAELDSYNEYLASLSRRRNES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002158.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da5986687d7b4ca28689c18f18049849535d1253
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002158.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00507
+MTLTAALLSFALLALLITITPGLDNALVLRYAGRQGSGAAFAASAGICAGLFVWALAASL
+GISALLAASEVAYTALRWIGAAYMVYLGVRMLISAIRGGYGAPGGSSVATVRSRDAFRTG
+FTVNLLNPKVGAFYVALIPQFMVTGVAPAAMGVLLAVVHIAVCMAWFVVLIALVGVVSGW
+LQRPSVQRGLDGVVGTALVGFGARLALAKA
+>NAFOICDF_00443
+MTLTVALLSFALLALLITLTPGLDTALVLRYAGRQGSGAAFAASAGICAGLFVWAVAAAL
+GVSALLAASELAYTALRWIGAAYMVYLGVRMLIAAVRGTSGDHDGDAAPALVRRGQAFRT
+GFTVNLLNPKVGAFYVALIPQFMVPGVAPAVMGVLLAVVHIAVCLAWFVLLIALVGVVSG
+WLRRPAVQRGMDGVVGTALVGFGARLALAKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002163.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1f5c124b9f3aa62ead0b00b21093d8f24c74c22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002163.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_00523
+MSLFETADDRVSVDVWSDVMCPFCLIGDRLLGQAADRAGHPVQVRYHSYQLQPDLPADRT
+RPVLDMLVDAKRMPREQVEEMDRQITARGAEVGVEFRQDIALAVNTRDAHRLSHVAAEQG
+LQHAMVQALFRAYFTQGRNVADHEVLADLAAEVGLDRQAALDALASDAHADTVDADVEAA
+RRLGIGGVPFFVVDGKYAISGAQPLEVFERALAAAWADKADGAPPAG
+>NAFOICDF_00072
+MKVTVYSDVACPWCYIGKRRFETALAGFEHAEQVEVEWRSYQLDPTLPERSDLTEVEYLT
+RMKGLAEPQVRRMLDHVVMQAAGEGLTYDMDAIVVANSFPAHRVIQRARAVSAEAASALE
+EALFAAHFERGQDIGDAAVLAELGAAAGLSAEQVEEALTDERWAEAVRADLAEARAVGVT
+GVPFFVLDGKYAVSGAQPPELFAQALAQTWAERAPLRAFTPAAAADDDDAPLIGQACGPD
+GCA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002164.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..755fb37e088a9394405a091b84251ab2afb05163
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002164.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00529
+MLRPRHTRPALLLTAGLTSLALLTGCADGDPAPGAAATTAAATTAAATSSAPTTQAASSS
+PASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASREAEAEAEA
+ARAREAEESAAAEAEREAEAAATVEEDSSTTAGEGTVSSGQAVRAAKNYLEVLPFSRDGL
+VHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQLIAGDEYSD
+ADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQAEYGVDAVGL
+>MOLHKGIG_02215
+MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSAGSPSAASSSSGASSSGRVSDGA
+APSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAAEASRSAEAEAEA
+VAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLSFTAFSRSGLIDQ
+LEFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQLEFEGYSNADATA
+AVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLMFEGYSASQAEYGVDAAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002168.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cae124176773b733b2504541dad8864174af713
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002168.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00581
+MNKDAQPSTELLSSIPEGHVEFGLHTFGDVTLDAEGRRLSHPEVLRDVVAEGVLADQAGV
+DVIGIGEHHRPDYAVSNPEMVLAAIGARTERIKLISAVTVLSSDDPVRVYQAFATLDGVT
+GGRAEVSLGRGSFIESFPLFGHDLKDYERLYEEKLDLFMKLRTEEPVSWTGTVRAPLERQ
+SVFPTTAHEHGLPAWVAVGGSPQSVVRAASHGAGLELAIIGGAPRRFAPYADLFRREVAE
+RGLEPRRVAVHVHGFVADTDEEAMELYYPHWEAAFTKLARERGGPLPTPEQFRQEAVHGA
+QHIGSPETVARRVADTVRAIGASRFGLKYSNATLPHGPMMRSIELYGSRVIPLVRDMLSE
+G
+>NAFOICDF_00799
+MDVKFHIDTFGDRTSTLDGELESHAQGVRHVVELAETAEQAGVDGITIGEHHRDDYTVSA
+PDMVLATIAGRTERLTLGTGVTVLSSDDPVRVYERFATLDALSSGRAEAIVGRGSFTESF
+PLFGYELSDYEELFEEKLALFAELRAEQPNPVSWTGKLTQNLEDVVLYPPLEGAEPLKAW
+VAVGGSPQSVIRAAGHDLPLMLAIIGGPSARFAPFAKLYRDAREKFGHAGETQVGFHMIG
+HIAETDEAALEQFAPHYLEHHKRLGAERGWGSMGMEGLMHEVRHSLMGVGSPETVAKKIA
+RGIADLDATRVNFKVQHGPIPHEYNRRSVELFGEKVIPLVKDMLAAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002171.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71023f5731dade45597ebfb2d9690c176d926c18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002171.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00639
+MAARGGTPADHAPAARRLLDRAPVLLLAERAGSNSPRVVGRSGATLAALHPGAQPRWLTA
+GLTVTPEARRTGVVRRLLHAVIGAVADRGGGDLHSVVNAGNAPSLALHASLGLEIVETGP
+RFAGIEFASGVGVLLSRPTCPESAPACA
+>NAFOICDF_01983
+MIASYARWQPEDHGTPRADVLIRPVRPHDVPALARVMAARGGAPETHTDAAALLLDRAPV
+LLLAVAEDGGGDALGWSGALQTSVHPGEHPVWLTAGLTVVPQARRAGVGLRLLHAVAEAV
+RTSRIETGPLHSVVNTRNRASLALHARAGFQETASGPRFAGIEFDGGDGVLLRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002172.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16abf22afbfbdd7655cf8556a3aa02b302d2c3dc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002172.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00644
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR
+AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS
+>NAFOICDF_02224
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR
+AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002177.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b6d1f0ae149a55440bedc4f4a918f54fa258fbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002177.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00735
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>ACLBLIBL_00745
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002179.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b49b1159f25ddf6026d5ccdfa80f1c8c0f0e105e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002179.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00759
+MPVRLRPAVLDDAKALTALARSQREHLAPWEPERPARWFTEAGQREALEQADCDRAAGRS
+YAFVITDDAGHLLGRLTLASVVRGAGQFCSIGYWVALEATGRGVATAAVEQALQIAFGEL
+GLHRVQAEILPHNHASRRVLEHHRFQRYGLGHV
+>NAFOICDF_01982
+MEITLRPASPGDAEELAALTLAQREHLAPWEPERGPGWFTVDGQRHALRAADADRAADRA
+HAFVIVGASGAIVGRLTLASVVRGAAQFCSIGYWVAHEATGRGIAGEAVRRGVALAFGPL
+RLHRVQAEVLPHNHASIRVLEKAGFLSYGRAPEYLRIAGRWQDHLLYQRVNPDWRPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002180.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dfc851ad78ca6ee72e6464c15df2b05d9326d2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002180.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00773
+MAGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRFWFKRPHAC
+LRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRAREDGPSHYVELARSL
+ARVQKSLTAADVAELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHPAQCTAAERERAIE
+GMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEGVRLSDWGDTVLAHPFASLR
+ALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVGDVLDLAMMLAVPQRLSCWSALADADAW
+AEYAEYIAPLWREIGTPVAEVEVP
+>NAFOICDF_02404
+MTGTGVLDVAGRTAARDWIAGVLDLPAAALTVRVVRERSWGDVWRLSSPAGVHWFKAPHP
+RLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAPRPGEVAR
+LYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHPAHCTAEE
+EARAVAVRAALAMRWEDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSDVGDAVLGHPGA
+SLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVPQRLRAWGALRS
+PETWAAYAEWITALWRDIGTPVDQLTTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002183.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5792ee177f590c5d24564528a780c931c717bb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002183.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00852
+MALFRKTAAWGATAAGAVALAAAAMAATWTGPGYTVVNDHSNIFDYKGSIKTTSCVRQSD
+GTHLIGGYIRYVQGGRDTGRLWTPTATSCGQTVSRSTTFKDSLALNAPKTQFYYGLNKAP
+YGALSEPLGGN
+>NAFOICDF_00789
+MGDSRCGQTVSCSTTFGDSLGLNAPRTYFNFDLNDVPYGALSEPVDGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002186.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7556ab9dd2db3cead0707b4b20c22d70b1d2e613
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002186.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00897
+MTSTPTRAKRKQTARELAERFGVSPRTIRRTVAQERADYLADAAARHERIRALRAEGLSM
+RAIAAKEGVTVGTVHYAIHKDD
+>ACLBLIBL_01315
+MTSTPTRAKRSQTARELAERFGVSPRTIQRTVAQSREDYLNEAAQRRARIRALRAEGLSM
+RAIAEREGVTVGTVHYALHKEDQQP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002189.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..038ff58268aa95f6f580799bf174f359cefc29c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002189.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00910
+MPSRRPPERPVVGPAAPDVAPSRPVPGSCQRALVRRSPLILAAVVLLVSAAVLAARGETE
+AAGLSVQIAMVVPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDAL
+VHFYSGVPIALGCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALG
+AQTQKGNTDTMTDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGA
+>LFPAFLNI_01867
+MTPHLDTHPDARPDPGSRQRALVRRSPLILAAVVLLAGAAVLAAQGHREAAGLSLQIVTV
+VPVPIALERAHRVRLPTALHAMYAALLLVAPWVGAALGGYDAWPWWDALVHFYSGVPIAL
+GCVFLLGVAAARRGLVLPPGLEALLVMALHSLVALAWEIAEFTADQALGAQTQKGNTDTM
+TDMIVGTLGALIVAFALYAHRTRGRFAWLSRFTGARTDLAGGPAQPPPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002190.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..431004825780b3ff6e979afb7753718875bfb4a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002190.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00933
+MAAGGFTLGLGQPLTMSLVTQAVPADWRSSALAVRLMGNRAGQVVLPATAGLLAAPLGPA
+AAVWFACAVLAASGLERTAAARRRR
+>NAFOICDF_00864
+MTESRTGAAAGERTTAGPGAGWLWALIGAAVLTQAATNLARPVTSYHLLSLGAPDAAVGL
+ATAAYALLPLVGALWLGRVTDRLSSAAPLVVAGAAVVAAGAAGLALATDVAAVLAASAVL
+GVGHLAFTIAGQAAIARRAPAHLLDGAFGWFTAAFSLGQMLGPLLSGGILTAVGGTPRDA
+TTLALWVSAGLALAGALPVLLAPGAPPGTRDPAAREASAESGAAPGDDAGRPTVRAILAR
+PGVGSAMLASLALLAVLDILTAFLPVVGERHGVSAAWVGALLALRGAGSLVSRVFLPRLR
+RRFSRELLLAVALWASAATIAAVPVGMTSGLLWLAAAAAVAGGLTLGVGQPLTMSVISEA
+VPHAWRSTALAVRLMGNRLGQVVLPAAAGLAAAPLGPSAAVWTACAVLAVSGAERAARSR
+RRRPPRSVRSGGGRGGSASADQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002194.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b43a1dcc51eda407db5c69869f982e0c7f692c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002194.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_00978
+MGPGQHAKLTMEGIAARAGVSKQTVYRWWKTKVDVLVEAVGAGYLVIPLPVIPDTGDLRE
+DLAHWLREMQEEIDGGGATHLSQSLVAAIATADSQSRQIHGMLVAPVREQLHARFRSARL
+GDGVDREMLAETVGAQLVMRVLFAEPTDEEWVRRLLDLVAPEGS
+>NAFOICDF_00942
+MTSLTPPRAGTIRPGGRTARVRAEVLRATRELLTQQGASAMRMELIAERSGVHRSTLYRR
+WKRPAGIIADLADDIAGTIAVPDTGDLGQDLRQLAGRLAHQLDGDGGALVRALLGWPDQE
+VQQHLEDFWRDRRADVGLVLQHHGIDADPALVTRLLASPLHYRSLIERHPVDDETITAAV
+ESTILAVLRTPRTSHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002195.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34bb35d0c2638b34a882b3d1a3d3b3184c9d342a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002195.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01005
+MDPVSTPTDPHRHPAPDARVRVQAGDAVVADGPLWARAALFAVPAVWLGLLIGISLIEAP
+LKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGPGRLWLG
+GLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVALIVAVA
+RHLLVRTTAA
+>NAFOICDF_00949
+MSVPPHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGISLIEA
+PLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGPGRLWL
+GGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIALIVLA
+ARHLLPASPGAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002196.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da2e2598d5003b35337b601f8bbd9accc727efe7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002196.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_01011
+MTDAGPQGPAVPVRTRRVAHPGRVTAVVLVVAALVAAAFLAGRFFQPPSTAADNEAAATP
+IDVWAHAEERVIDDGSSYVATVAAGRTRTVTVAADGPAVVLRQAAEVGEMVRPGDAAGEV
+SGVAYVFLPEPLALYRDLTEGDRGEDVASLQRALRQTGRWTATDGVFGDSTARALRETFR
+GAGSPLPEDEPVTVGWRQFIPVSDDGAVVTAAATYGATLTEDRPLLELQVSAPTIRFTAD
+VTQATALEKGQEVEVSGAFGSLHGTIAKIGEFAAAEGSERAGHPVTVAFDATAEDAPPVG
+QSVTVSTTAAEDVPAMLTVPQTAVRVEGASSYVVVQVPASAREGSASSAPAERRVPVTVE
+RTGGGYAAVSGDLAPGDRVKVS
+>NAFOICDF_00954
+MLVLALLAASFVAGRFFQPPTTADPAAVARPIDVWAAVEQRAVDTTASFAGTVAAGKTRS
+VAVQAEGPAVVLRQTAKPGESVRPGDVAGEVSGVTYVFLAEPLALYRDLTEGDEGEDVAS
+LQRALQKAGHATDTDGVLDSGTARALRELFAEAGDPLPEDAPVTVSWHQFIPLGKDGAQV
+TAAAGVVSALYPAWVASRQRPADALRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002198.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f46dfa89ef14238c15ca5e273e5cd9c465d2b46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002198.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01023
+MSPREPAPLPAAFSDLPFGAADLRRAGVSVERTRRADLRRVSQGLHRAREAERGEWADLG
+YPVDPLPWVPEEAAAVVPLTGGVVSHLSALLLHRLTVPPWVRPDGRLHVSRRHGRGVCDR
+SGVATHGRSVPQEDVVALHGIAVTSVERTWLDLASLMPRGPVDPLVIAGDALVNRPWIAG
+DGRRGEPVTSVESLRAALRRAGRFKGVRAARAALDLVRVGADSPPETELRLALVDAGLPE
+PELQVSGDPGDRFAPVADLGYRDWRLALQYDGGHHRSREQQARDARRDGWFHDRGWRSLR
+LTADDRLDGFRRAIAWVRRHRP
+>NAFOICDF_00964
+MAPRAPLPLPAHLADRPFTRVDLTTAGWSIERARRGDLVRVVHGVHRSWEAETGDWADLG
+FPVDPVPWPPVDAAAVVRRARGVLSHQSAALVHGLVVPAWVRPDGRLHLSRPHDRGLSGL
+PRVQTHARSVPPVDVTSIHGIPCTSLERTWVDLASLMPRGPVDPLVIAGDALVNHPWAGE
+GQARGAARTTVVSLRAALERAGRFKGVRAARLALDLVRVGADSPPETELRLALLAAGLPE
+PELQARIDPADPWAPAVDLAYRPWRLSLQYDGAHHRTREQQGRDARRDGLVQDAGWRSLR
+LTAEDRHDGFRRAVEWVRRHGSP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002201.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d31ae05690e6e63729dac268a44e2382f467920
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002201.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01080
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
+>MOLHKGIG_01796
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002202.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52cafdee5a48d7ee8d382d575e108374813ca9eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002202.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01082
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNIIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR
+>MOLHKGIG_01794
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNVIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002207.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c4f9854d1568f190e66eb2a62c010a3bb87e25a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002207.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01138
+MTARRGPLTPFFDSVRTTGFRRTRPRLVGGVAAGIASGTGVNVWLVRLALVLAGLLPVLG
+VGAYLAVWALTPWEDGTVPAERALGGR
+>NAFOICDF_01067
+MTPVSRPRPGGARRTPLTPVFDGIRALGFRRTRPRLVGGIAAGLAANTGVDVWLMRLVLV
+LVGLLPVLGLGAYLVVWALTPWEDGVIPAERALSGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002210.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f8428359dcb04ae710d6dee93d6d1c26ea7c3b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002210.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01272
+MVKKLEQNMGADAMRAATGRDHAGWRAVLQDAGAQQWSHPRIAAYLVEEHGVDGWWAQGI
+TVDYEQAHQGRLPGQQADGTFSVGLTRTVPGERLEALARVEAAVSAVHGEPHGRNLTASQ
+PVVRWRLPDGGRLAAAAQAPNKTGTPVNLTMQRLPDAAAVEPTRRALEELLEAARSGEGP
+VATPGR
+>NAFOICDF_02055
+MSTSPARGANLNAIAEATGLTFEDWAAWLDARGARDLTVHAEIVGLVLERMRSGETAEVG
+SPEWWAQGVTVAYEQHIGRRRPGQRADGTFAVTASRILEGTREEVHARAVGAVRAALSDG
+GALRGVGLAKEPTESATATRLFWRAVLADGTRAELATEPRPQTAGKPAKAAVVATHSRAA
+SAEEAAAWKAFWRNLPAAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002220.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88b238c70e58a95fb9c18b2f197c2ca7590e64a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002220.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_01924
+MTDLAAEHPRTDAVDSVSTRTHDEPFAVVGPWKDDPAAAGTAEKVKVTDEMLELVEAVRP
+TLLADGMFLVGLDIVGDKLMEVNVFSPGGLGSCQSLYGVDFAPAIIEDLERKVSVRKHYK
+GQIGNANLATI
+>NAFOICDF_01875
+MKIGFVVNDVATEKPVYTTTRLAMAALQAGHEAYLVGAGDVAYEPDGSLSVLAHGTQKKH
+RSLERLLEEVQDPANAAQMPVDELDVVMLRNDPADDATERPWAPTAAVSFGQLIAAAGVL
+VVNDPHTLANALSKAYFQHFPELVRPTTLISRDEALISEFIDERGGKAVLKPLQGSGGSG
+VFLVDRKESPNLSQIVEAIARDGYVVAQEYLPEAKNGDVRMFVMNGRPLEVDGRIAAFRR
+RSSSDDVRSNMSAGGTAEKVDVTDEMLALVEAVRPKLLADGMFLVGLDIVGDKLMEVNVF
+SPGGLGSCQSLYGVDFAPAIIQDLERKVATKDHYLGRIDNTRLAAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002221.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f909927682f6902291147b7718cbe2940bf7249
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002221.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_01933
+MATISTRTSKKGVTTFRVGYYEGGRFRQMPAMLSETGARRIKAIIEDPAQGPDVARRLLE
+AHADGAEDVPTLAQCLDRYVEARAVRCSEGTLAGYRREAARTFLPRLGQLPVTAIDRPAV
+QDWIRWQMTQPTARSRAAAERAARAGTPAPSLEPVSPKTVRNAHSLLSSILYLAVQDGLI
+PTNPAHGQDLPADDVEEEKDIFTRPEWDRFYRAMTPHFQPLLALLITSGARWGEATALQV
+RDLDVDAGVIHVRRAWKKGAQGVVLGTPKTQRGRRAIMLPDHVVAMLTPLAAGRPPEDFL
+LTSPTGRVIHRTNFVERHWKPALAAAGITKDLSPHSARHTFASWALMEGVAPQIVQHRLG
+HESLETTSRRYAHLLLDAQRAAVDAIGWRPSPGT
+>MOLHKGIG_00954
+MATIQTRTNKAGRTTYRVGFYEAGRFQWLPALAREAGAQRVKAIVEDPRQGPTVARRILE
+AQVDSAPGMPTLAEFFPRYIEHRGLRCTPGTLAGYEAEAARTFLPRLGELPVDMIDRRTV
+AEWIRWQLQQPTARWRAVAARAAAATPPRPEPPLATVSPKTVRNAHALLSAVLGLAVQEG
+ILPANPARGADLPDDDVEEERGIFSRAEWARFYAAISESYQPLLIVLLVTGARWGEATAL
+QVRDLDVAASVIHVRRAWKKGKEGAVLGVPKTARGRRTIMLPDWAVETLEPLAAGRAADE
+FLLTVPGGGVIHRTNFVERHWKPALAAAGIAKHLTPHSLRHTFASWALMDGVPAQVVQHR
+LGHESLQTTSRVYAHLLLDAQRAAVDAIGWEPPPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002223.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05a354cdc119401d7eb222cc2855d3f02a533595
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002223.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_01935
+MFHPWRALRTLTHVVVVWARPHPAAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLSAALPWSMSLDELADELWVTPLVLTDRLAGLTR
+AEREHLAARIPEHRDTV
+>MOLHKGIG_00951
+MFHPWRALRTLTHVVVVWARPHPTAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLADALPWSMSLDELADELWVTPLVLTDRLAGLTR
+TEREHLAALATEHSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002231.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5923d58157e4941ac9a77acebdc312547b922e15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002231.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_02203
+MAQPIAAIVVASPTRNASRLIAYALNRKQGQTTDRFVAASGLNGAIPEIAAHQFRDNRKR
+HGKNGERQVQVPDGEGGTVTVTEGVYVQGYHVIQSFARDGDGALDPSDPDAWEEAHRLGR
+KLCRRLAGDGRMAVVVTQIDGATGCIHNHIVLDSIDRQTGKSFASSNVKHKMLAATHDEV
+LAEAGYVQQNELQSTAAERREPSEDRALLKHQQWVAGGRQGPEPYSVAIVKHRIREAQGD
+PRSVSFDTYAGVLLEHGVRVEKRGEKGAGLTYEMVLADGGGGVLKAQPAHRRRASKLGRD
+FMLPAVEAACARNRAREVGRLRGLGAPVLPPREESAVEALLRELTEARAKGRAGRRPGPT
+EAPAAPPRTPEPREPAEASQAAQRAAQAQQAAAVAAPVQSSAWRSRLWDLPPSNRTVRTQ
+QIIDAVAEWEPSARERLQSGERLDEPAIPKGVGARFLESYGQYLDPAVRTELEAREETRA
+QRREQFELEREHEEALQAVGRRPEAERTIYERGVRAQLDTARLRREAIEAAIAEGRYGRA
+DVDGIVSEAEQAEREASARRREQVAERAAAMRDEDRESDDPQPGD
+>MOLHKGIG_01495
+MAAPIAAIVVASPTRNASRLLAYALNKKKGQTTDRFVVASGLNGAIPEVAAAQYRDNRKR
+HGKNGERQVRVPDDKGGMRTITEGAYVQGYHVIQSFARDGEGALDPNDPEAWEEAHRLGR
+KFALRLAGDGRMGVVVTQIDGRTGCIHNHLVLDSIDRQTGKSFASSNVKHKVLAQTHDEV
+LREAGYAQQNELQSTAAERREPSEERARLRHEQWGANGRQGPEPFSVAVMKQRVREGMSD
+PRSVSFETYAEVLAERGVRVERRGQDHPGLTYEMVLSDGKGGTVDPQPAYRRRASKLGRD
+FMLATVEQALERNRTKQAVQPTGHRPLLDPSKYVALVGRADQVPAPAVTATPNADETERP
+LLWRTYERMGLDWREARKVAPETEVEPAPTPDVAEPLPAPSAPAAEPIAAPTEPEDEAEA
+QDEAQRATAPAYRSPVRDRTVKRERSREFRERLAAADEHVVARLEAGEPVDDTVLKGLGP
+DKIRSYRTSLHPQTQRALRRRQSMQGAAARAYAAGQRELAQRIRAEVAAGEYRWIEPAPD
+AVAQHEQDEPELGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002234.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65aa5ea7f9ae27adb433960772bcae386899c7b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002234.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02214
+MTTTPPPVDRTRRPVATYRAISSRDASSTQRDGEAVLEVRRFAARDGHAEAEVLFGDGQW
+QLCDPERDLIPAFEFDAFPDHPFLAVEYGEDWNGWATPVVTRETLADVLAALELAHRWEG
+STAVLEIEDYEDRIEARADGLYDLAQAGWTVQQVEL
+>MOLHKGIG_01509
+MTTPQFSVDRTRRPVATYRAISTKDAASTQRDGEAVLEVRELSSRSGQREAEVLFHDGQW
+QLCDPEHDLVPGFTFDAFPEHPFLAEAYGETWNGWDTPVVRREVLADILTALELSHRWEG
+DVTVLEVDDYEDRIVPRLDGLYDLQQAGWTVQQVELG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002241.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92753e37f7179fd87ab8c15d299970ef3c331953
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002241.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_02367
+MSAALDRLKQQNAHEQPPQQLGSPATMEVLTSILTAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERIAAPASTSSPSSDVSARIASIESRQNEIASTLGEFARSLNGESLNAASR
+SLVAEAQKNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVEKAVEQVTGEA
+SATMTANLDASNERAERIIAATAKLETRQLWSAAAAMCLALLPVVVVIAGLWMGIAGLIT
+GAQWALDVNGSVWLGIGRWLVVGVGLAGASYGLFASVRWVAGLVETWKDRGLPKWPRWRK
+>MHAAABBN_00299
+MSAALDRLKQQNAQSGSQQQLDSPETMEALTSILAAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERITASASTSSPSSDASARIASIESRLNEIASTLGEFAQSLNGESLNAASQ
+SLVAEAQRNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVVKAVEQVAGEA
+SATIAANLDASNERAERIIAATAKLEARQLWSAAAAMCLALLPVVVVVAGLWMGIAGLIT
+GAQWALDVDGSVWLGIGRWLVIAAGLAAAGYGVFASVRWVAGLVETWKGRGMPTWPNWRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002244.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54f90b5e364d0befc5f8a5d6f2316f92bb7d905d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002244.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02370
+MSANSAAFDHVNGFRWRLGDPTLADAEAHLYDLGVLRSVLEEAVEIAVADARADGVTWAR
+IGDALGVTHQAVIKRYRRGGAR
+>MHAAABBN_00302
+MSANSAAFDHLTGFRWRQGDPSLADAEAQLYDLGVLRSVLERPSRSPSPTPEPMG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002247.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8341e1ac55abbdf44f723e8b61f7f87a338ae7af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002247.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_02434
+MDLLSPARALKHRAFLARKDAELRAEARRLRADPVFRAQYSAAEAGLKVPPLEDHPGPWA
+IAMVRNEADVIETAVRHLVRQGVDHLLIVDNLSEDDTPQVLARLAQEFPHLHVGTDHEPA
+YYQSAKMTRLADLVSAAGARWIIPFDADELWFAPQGRLVDALTRSGVPVRRAHLYNLFPT
+PDGQQWHLDTARHFDDKVAFRAWDGAVVVMGNHEVSRPGPRDGEGLRILHLPWRSFEQFA
+RKTRIGAAAVAQAELNEGEAYHWRWLGSASEDELRAVWRRLLSGEAVANAAWYPRGTLRP
+IGDTLPSSWADVQALLGPGPAEGNALSR
+>MHAAABBN_00239
+MPSPLDLARQAKHRLFLLRRAREVVRQAAAVRGSERFAREYALASAGFDLPGLPAMSGPC
+AVAMVRDEADVIERSVRHLADQGIPHIVVVDNGSKDATPDILRRLAGEIPGLVVGADREP
+AYVQSAKMTRLADLASAAGATWVVPFDADELWFGAEGTLAEALAAADAPVLRAVMHNAFP
+AADGSGPLLDTIAHFNVKVAFRPRSGAVVEMGNHEVLRPGVRADGLRILHLPWRSFEQFA
+RKSRTGAQAIALADTPEDKAYHWRRLGALDDDALRAAWEALLAGQPLTDAAWYPRGTLRP
+LRSDTPTRWDEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002249.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7fb175223f104262d0e5b136ad818229c071289
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002249.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_02638
+MSDTLRVVASRRYGTLSPLRYPGGKAALAGFFGDIIDALRVERARYIEPYAGGVGAGIAL
+LREGIVEELVINDIDPAVYAFWKSAVGDNASFVEMVASVPLTIAEWQKQREIYRSRDERD
+ALRLGFAFFFLNRTNRSGILNAGVIGGQRQEGRYKIDARFNRETLIERLTAIGGLADQIT
+VSDLDGRTVIQRYAQDDRAFMYIDPPYVQAGSQLYLNAFDGRDHTALAAIVNTVEKAHWL
+MTYDTAPLIEKLYREHFQCRLELTYSARYPGQAEELLVASPAVAGVVKALQGQTVMADAT
+SA
+>NAFOICDF_01769
+MTALVMDSPLQVRASGRNAAFSPLRYPGGKAALANFFGDVIERLGISNARYVEPYAGGVG
+AGIALLRQDRVQELVINDIDPAVHSFWRAVVEYPDKFADLVVNTPLNVDEWRNQKHVYRE
+ANESNYLALGFAFFYLNRTNRSGILNAGPIGGMDQSGNYKIDARYNRQQLAERISRIGEL
+SSRITVISLDGASVARQYAGDPSSFTYIDPPYVEAGGSLYLNSFTYRDHAQLAKSLDRCP
+DGNWIVTYDPSDFIRRIYAKHDVREYELNYSANRTGKARELLIASRPVARVLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002251.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..335c59888549bbae2814ce1db6292645ece80582
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002251.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_02652
+MATLAEQVQGERMARVALSMIAEPNDPITGYVLARHGGVETLRLIESDDEVPGLARADTL
+MWRERLTARVTPGLLDQMAQAERHGFGTLIPADKEWPAGLNDLSDRAPYLLWTRGAVSFL
+MTALSDRATITGARAATAYGEQVAGELAAGLADEERVVVSGGAYGIEGAAHKSVLAASGQ
+TIAVLAGGLDRPYPAGHSELLNRIGDVGLLVSELPPGAAPTRHRFLARNRLLAALSGATV
+IPEAGPRSGSMTTVIAARELSRGVGAVPGPVTSVASAGPNELIKQGFASLVTQPSDVIDL
+LDADRTPDRTVTRPEVGREFGHRHPSPGTPGRSL
+>NAFOICDF_01771
+MSGVAGLGVDERRARVVLALLAEPDDPVTGGLLRRLGAVETLGLLDTDTTVPGLGRVDGQ
+VWRDRLTSQGRLDGLDQRLRVLEESGIVILIPGDAQWPRALDDLGERAPYVLFVRGAASF
+LARPMQDLVTVTGSRAASAYGEYVAAELAGDLANRERVLVAGGAYGVESAVHRAALAAGG
+DTIAVLAGGVDRPYPSGNRDLLDRVGDVGALVSELPPGSVPTRHRFLARSRLLGAMSAAT
+VVVEAGARSGAIGVAAEAHQLGRQVGAVPGPVTSVTSHGPHELLRAGHARLVTSAADVEE
+LTANRATHRPGLSADFTRHTAPAAGPPERSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002254.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4170ad3749ddd120c019b7944461ec59f4f57a8a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002254.fa
@@ -0,0 +1,4 @@
+>MOLHKGIG_00164
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
+>MHAAABBN_00333
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002260.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdbc1e1dee7cdb6481cff6a030b9007f4b96d62e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002260.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_00502
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
+>LFPAFLNI_00501
+MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW
+RHRALRKARSTKFDLHWRLRMSQQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002261.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce9b328521ae74ef75ea566b462d1d0c7dea5a42
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002261.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_00587
+MNVHSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRAPASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKNRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVEGESQAEIRSTLRDAVDDLDEVLKKIEEGTR
+>MHAAABBN_00321
+MNGYSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRALASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKGRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVDGQSQAEIRSTLRDAVDDLDEVLKKIEEGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002262.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c37c4c1152b61a02a49fb5fa6743a5b9d43a0c19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002262.fa
@@ -0,0 +1,8 @@
+>MOLHKGIG_00593
+MLNGINPDGLSGWSQISGWVVGTALVVLILAVGAGVALAVWGRALFSPGGMRKGWTMVAL
+AAVGATVLGAGTAGTSWGAGLGTSELMPAGARPQSVAIEKNAPKQTCNRQAVRDFDKEEP
+SPDRAERERVISTLLGGQPALDGYEWGKEPTGTESSYTVVTSVKWYATGEVNGSGEPDCS
+AQNEATAECSPVEVHVARQSLTNGAQTGRTLTLTRGQNCS
+>MOLHKGIG_00594
+MSNLIHAATTVAAGVPDIAPRFDGPWMPTIQNVTGLALGTFLVVLIVAVGIGVLVWIFGK
+LSSSGRAQDVGISFVVWGIVAAALIAGAASLIGWGAGLPLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002265.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a8258a1281ae75e209c3a22181f6eabf8fa7118
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002265.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_00598
+MRRERGNNSVLEGDNPAETALIWLIGPAVLLYGAYLLAGFLAGRIHCGAATKPDSLFAPL
+GFLVGEHDPAAFGATAQGCTATTGGVIGWLIGLGVLALVLIGVAVTAWSRYQQSDKKFIK
+ELREREGLARSAEITKTVGRKSVLSRVKKVRPSIKKPAITDGAMRLGKAEGVDVFASYEE
+SVVLIGPPRSGKGVHLLIGAILDAPGPVITTSSRADNLGATAELRKKKGPVALFDPQGLT
+GQPSTLKWSPITGCEEPRVANQRAASLIGASGLGSSSSNAEWQAPAITIMECLLHAAALG
+ERTVDDLMRWGNNPAEAKEAVKILTEHPKAALNWNLVLKGIIEGDPKLLQSKWFGVEGAV
+KGLSVPEVRDVLRPNRFEETLDIDKFLTECGTLYIVGTKTGGSSAGPFLIAMMDAITERA
+RELAAKSPGNRLDPPLSLVLDEIANISGAWPGLTQLMADGGGVGISPFAVFQSMAQARNE
+WGEQQAQALFDAATVKVQLGGASNVSDLEQFAKLAGQRKIMRTSKSRGKDHTSVSEQIHD
+TEVVSVAELRRLPFGWGVLLNRNGRPILMQMTRWWDRKDGKQIKEAAGRYSKALLAELES
+KDPAPSTPTDADRAEDSVAALDPVPETAPAIPVR
+>NAFOICDF_02243
+MLEAIARTSKSCGKDHTSVSEQIHDTEVVSVAELRRLPFGWGILLNRNGRPILMRMTRWW
+DRKDGKQIKEAAGRYSKALLAELESKDPAPSSTPTDADRAEESVAASDPVPEAAPAIPVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002271.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20ea456105bc2a2e6d01e9d6385dd54e42718385
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002271.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_00890
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
+>MHAAABBN_00612
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002277.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0472b30f4253e2d234690c77c0b9f50d81f93de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002277.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_01388
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
+>MHAAABBN_01120
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002281.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e38b51bda09c1814089c3395e3218b2a329c6f8a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002281.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_01606
+MCHGHDREGSDAGQSVSGRPAAHRAAADEGAERLHRSLTVLTTTGFLGGVEITIGLLAYL
+LTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWAVTL
+VMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTRMQA
+GTDSPTAMIVASVAGAIVLAGGSLFHSVMDSILIIGAILSGAHGVGWLEWLSWVWWVIPL
+NILGGLALTTAPRLLRSKEVREETGR
+>MHAAABBN_01318
+MGPVCHGHDREGSDAGQSVSGRPAAHREAADEGAERLHRSLTALTTTGFLGGVEITIGLL
+AYLLTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWA
+VTLVMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTR
+MQAGTDSPTAMIVASVAGAVVLAGGSLFHSVMDSILIIGAIPSGAHGVGWLEWLSWVWWV
+IPLNILGGLALTTAPRLLRSKEMREEKGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002285.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d0b93cc8aa81adb22fb5908b548518178e2461e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002285.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_01949
+MVPASSIHTAATARTGTTYSGPMPVSAQGPRVTVVGDSSALGSTSLMNLEMPGITVDAKE
+DRTFAEGLTRLGQLKAAGRLRDIVVLGLGVNTGGTAAAQARQAMDLVGPDRELVLVTASG
+PVAWRAFTEQAMRDLAARYPGRVAVTDWEAASRYVTDFRADRIHPRAQGLSVDAQLVRLA
+ADRATGARTVTVQAGQTLSGIAVAYAVPGGWSAISRATGVPLAQLPSLNGPTLSTVLHPG
+QVLRIRCPLT
+>LFPAFLNI_00704
+MNRSTLGTRLGASVLVVAALVSAAPAAPAVTSASGTTTTTATTGLAPGTYLAQSGDTWAY
+IAPRVGVELADLLRANGATTSTAIRAGQPLVLPAVSKHLPATSRTGTPYSGPMAPSSAGR
+RVTVVGDSIALGAASLMNLEMPGLTIDAREGRTFAQGLTRLAELKQAGRLGDVVVLGLGV
+NDGGATATQVRRAMDLVGTGRTLVLVTASGPVAWETSTNTAMRNLAATYPSRVVVADWKR
+ASAYVTDFREDRIHPRGQGASVYARLVRLAVDTAPVLRSTTPRTVTVQAGDTLSLIATRY
+GVTGGWQALATLNKISDPHMIRVGQTLLLPATSTTTTPATYTVLPGQGWYAVSRATGVPV
+TQLLSLNGATLSTEIHPGQRLRLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002287.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89485913bdfcc4c4eb1efc8158c63f19c76ac7ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002287.fa
@@ -0,0 +1,8 @@
+>MOLHKGIG_02059
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPAYGPLEDIAW
+TGLDHLEGPQPVVRSENP
+>NAFOICDF_02219
+MTPPAAEGHFSRATLTDLLCEKFIACRVKSSLHLDSDARRGTTRDVELEPFEMAVHPLHD
+RSTGRPLTPLTWFETINLCNELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEY
+ACRAGTTSPAYGPLEDIAWTGLDHLEGPQPVVRSENP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002291.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b2583b03d2091f6c3d323496b50febc25d4f2b0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002291.fa
@@ -0,0 +1,34 @@
+>MOLHKGIG_02235
+MNVNDKAALTVAIDEFDEFFAAVNHGREPYAWQRALLRQVVTTGRWPDAVVAPTGAGKSS
+VLEVHVFAVAMTHAPGWEGARAPRRLWHVVGRRALVDDMASRAEAVFDQLAEITDVPIEA
+PLSRVAAALRRISPAGQPGSVTTLRGGIAPERGWQDDPVSCQVICATPDMAGSRLLFRGY
+GSTAGMRPREAGLIAYDSVLILDEAHLNRQLLTTARRVASLAGESPLAAHVPVLQVVETT
+ATPAGLAPAQTSIGVELSDIRTGAVGEALLRRLDRPKPVHLHLDGPWLAGGIARETTQGA
+QEIARMVTDAVQAGHTPVGVVMNRVASALAVHRALRGLNGGLDVVLVVGPRRRWEQALER
+SRTPDVYVATQAIEVGLDLDFGFLITDIASGSALAQRAGRLNRTGARESAPMHVLCPSAD
+PTAKTAAPYEVQDITDALEWLRDRAEDPKGVSPAALLENPAPSSTPARPVLSEIEAARAA
+LFSRTSEALAVEPDLTLWLRDSLDAETDVAVVGRRLPRLGEDAGEDWSGLDQAESAALLA
+TAPPQPHEAYPVTLSRLRLLLAGGRRGRATPAFVRRGRQWTLVDPDASGHGIVPGDVVCV
+PHDWAATHHHVLVEDGREPVGDVLDPRSADGTMLSLEPVKASQRRVVFMTGVASPGVQDH
+LRCSLLEVCADLQEADVPLTLLSVLDALDDRGQSAWLTAYLGQWADPDLVARFDVRVHVG
+GRAPGSPQQAAWVVFELLDAADPDDAQLSATTGRSPVSLAEHQRDVADRAGEFAQVLGLP
+EGLKRTLTVAGAHHDDGKSDDRYQAWLTQGVAGVDEPMAKSLLSALPFRQSRFLPAGWRH
+EQLSAAMLHAHADGADALAVRLVGTSHGHGRGTFLMGAESLVHPEAPPHVRMAAEELFDV
+GVWDALVLSVEQTWGLWAVAWLEAVLRAADVTISKEGR
+>LFPAFLNI_02167
+MNVNDKAALTVDIDEFDEFFAAVNQGREPYDWQRALLRQVVTTGRWPDAVVAPTGAGKSS
+VLEVHVFAVAMTHSPGWDGARAPRRLWHVVGRRALVDDMASRAEAVFGQLAETTDVPGDA
+PLSRVAAVLRRISPAGQPGSVTTLRGGIAPERGWQDDPVSCQVICATPDMAGSRLLFRGY
+GSTAGMRPREAGLIAYDSVLILDEAHLNRQLLTTARRVASLAGESPLAAHVPVLQVVETT
+ATPAGLAPAQTSIGVELSDIRTGAVGEALLRRLDRPKPVHLHLDGPWLVGGTARETTQGA
+QEIARMAADAVQAGHTPVGVVMNRVASALAVHRALLGLNGGLDVALVVGPRRRWEQALER
+SRTPDVYVATQAIEVGLDLDFGFLITDIASGSALAQRAGRLNRTGARESAPVHVLCPSAD
+PTAKTAAPYEVQDITDALEWLRDRAEDPKGVSPAALLEHPAPSSTPARPVLSEIEAARAA
+LFSRTSEALAVEPDLTLWLRDSLDAETDVVVVGRRLPRLGEDAGEDWSGLDQAESAALLT
+TAPPQPHEAYPVTLSRLRLLLAGGRRGRVTPAFVRRGRQWTLVDPDASGHGIVPGDVVCV
+PHDWAATHHHVLVEDGREPVGDVLDPRSPDGTMLSLEPVKASRRRVVFMTGVTSPGVQDY
+LRCSLLEVCAGLQEADIPLTLPSVLDALDDRGQSAWLTAYLGQWADPDLAARFDVKVHVG
+GRAPDSPQQAAWVVFELLDAADPDDAQLSATTGRSPVSLADHQRDVADRAGEFAQILGLP
+ESLKRTLTVAGAHHDNGKSDERYQAWLTQGVAGVDEPMAKSLLSALPFRQSRFLPAGWRH
+EQLSAAMLRAHADGADALAVRLVGTSHGHGRGTFLMGAESLVHPEAAPHVRMAAEELFDV
+GVWDALVLSVEQTWGLWAVAWLEAVLRAADVTISKEGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002297.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88d81ee11c747a3496a482474514b8464886f907
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002297.fa
@@ -0,0 +1,25 @@
+>MOLHKGIG_02279
+MSTFQTPQYTIVELLQKARSGELQLPDFQRPYRWDDERIRSLLVTILRGHPMGVIMTLRT
+GGQNVRFKPRPITGVPAEGLKDPELLLLDGQQRTTSMVQALTGDGIVDTEDVRHHKLRRR
+YFVDVVKALGDVREQEDAVVSLPDTGIVTENIGRDVVLDVTTEEKQWELGLMPVTVLFDS
+ADCFAWMMKYQQALPERMEITQRFLSSVAQAVQTYKIPAIELDKDISKDAVATVFEKVNT
+GGLRLDVFELLTATFAGDRAYYEETGEDFRLAEDWALTEEVLRTYPVLTDMKSTDFLMAV
+SVLATLAKRREALAAGKTGQQVPQTSARREDILGMSLEDYRVWAPRLRKALPTVARHLRD
+LHIHDSRGAPYSSQVVSLLIITTLLGDRAEEHAVRARLNQWFWCGVLGELYGSTITTQLA
+KDAEQIPEWSLGKSAETPEAIIRASFSESRLGSLRTRLSAAYKGVYALIMAQQPPAKDWM
+LDQTLDFQSYDDLQVDIHHVFPRKWCDENGIEPWRRESIINKTPLAKKTNIRLRGDSPAV
+YTERLDDKGLTPQQVDAQISTHAIDPALLRAGDFDAFFNDRRRRLVSMIENAMCKPVVRD
+WEVDSESTDAPENFNDPAEMEADEPAGDEEAANVAD
+>MHAAABBN_02021
+MPDTFGHHPWTVQDLVSAVDSGHVRLPDIQRPFVWSNAKARDLMDSMYKGFPVGELMFWE
+NADPEHSRAIGTLEKSQSGSMQVIDGQQRLTSLYAVVKGKRVVREDYSQENIVIAFNPLT
+ERFDVPDNRIKRSSEWIQDIKTVFASPIDARSDYLDGLEKARGGERLSREDERRIEEAIN
+RLSRVLAYQFQVVQLKKEVSRETVADVFVRINSEGVKLSSADFILTWLSVFWEEGRQQLE
+DFARGSRFTPQELARMDETTVRWTPKNPYLTLDPGHVLRVVVAVGNRRAPLQDAYNALRG
+RDPRTREIVPANRERELAKLKDGQARALDPKNWDEFLKVIERAGMRTSAMVTAKNAVIYG
+YALWLIGRTEFGVPVDDLREVMARWYFMAQITGRFSGSAETRAQEDLNRLDGLERTPEAF
+TTAIDSLVSTTLTEDWWTVTLSEDLHTSNMSGPAYTGYVAALNILDADVLLSTLKVKDWI
+DPNRRPVKGVEKHHLFPKDYLKGALGLKSTRQINQVANQALVEWSDNIDISNEAPSAYWP
+AQVTEKAIQGERLAKQTWWHALPEGWTEMSYTDFLAARRKLIAGVTREGFRKLSDPNYQP
+SPPAHPVPASEPVLPTFEQLVLAGALPVGTHLLPTDGRTDSIAEVTPDGTILLDDQEYTS
+PGLAAKADGAEDEDGWLYWSADLAGQATILDEVRRRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002300.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77c110d28dd4c24176edac3adf54e868027bf5d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002300.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_00053
+MRLIALPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE
+VAGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHSQGRYPLED
+TVSAFHQLVEDGKIRYWGVSNFDHRDLADLQDVPGSSGLATDQVLYNLSRRGPEYDLLPW
+CADHQLPVMAYSPIEQGRILHDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ
+HVRDNATALDVELTRDDLDALDRAFPPPSGPRPLEML
+>LFPAFLNI_01995
+MTLPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEEVVG
+EALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHWQGRYPLQDTVA
+AFHQLVEDGKIRYWGVSNFDHRALAELQDVPGSSGLATDQVLYNLSRRGPEYDLLPWCTD
+HQLPVMAYSPIEQGRILDDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQHVR
+DNATALDVQLTREDLDALDRAFPPPSGPVKSF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002303.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c52938e7e4bb5a2875b94097990948d58c2c01db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002303.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_00306
+MSDQNAVLVEYVDPDAVSLPLRVRARSEVWLPAFVVAVVLWVLFVMILLGLPPVLFEDPS
+AMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEAIWLNP
+THGLAPDKKTQVGFAVHERAWTDELRRGNRWDSGFPFGLGGMKPRDGMIMTQFATEPPIQ
+SLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
+>NAFOICDF_00334
+MTVSDQNAVLVEYVDPDAVSLPLRVRARSEVWWPAFVVAVVLWVLFVMILLGLPPVLFED
+PSAMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEEIWL
+NPTHGEAPDKKTQVGFMVHERAWTDELRRGNRWDSGFPFGLGGMKPRHRVIQTQFATDPP
+IQSLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002305.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62b920ee4e1c9417c435cc3dca5c3e208d0157c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002305.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00323
+MTQTPTPHLAGPSPVKVGLLVLAICAVGGVIIGAVAGLTDGGSVENMFIGAVYAGFIGFF
+LPGLPAALIAGLVAAARGRRRG
+>NAFOICDF_00343
+MDQDVATEAEQTVSEDGAVYAGVIGLFLPAALIAALVAAARGRRRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002307.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c88b2c8141bc7bc42fd25a10fe6d5bd6f93f095
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002307.fa
@@ -0,0 +1,14 @@
+>NAFOICDF_00327
+MGAPRELFAEHALRGEIVVLDYAAGRTRSGLPVRRHHVVVRAGDRLVHSFRWYVGAAREV
+FEVTLTFDEEWLPHRLWEPVAEAVRSARAPLAGEVDVPAVVPGAWDERPETVVVESGPGL
+DVAESLVEGLEVISASRKRWRSWSEADEVEQAVVRSMAPTLSARGGLRGRRTEVDVYAVL
+DEAVVVRRRWWGDQGTEIIEREVLRVPGRVAPWAMFVGMDVRAGWMREVSARRPVDAEAR
+SSDAEWEVIAGGERALGLLHGPRDVWAVSTGGGGLVAEWWQLPGEGLLGVFRDADSAQMM
+VGPVDGWTIYLLVLEAWLA
+>NAFOICDF_00333
+MHPTVALRHFTEPADGNVASASFREAFLGGQEVVEGFLLLSYEAFFTGRGLPGRRHHVIG
+WEEDLVWHSVRWYVGSGAEIVELTLTAEAGADLEIWGGQCDRMIRNVVCQGAPEPASNLC
+WPEVPADVRAQDSWEVVTEQGLNPPWLESLRAGYDAVQEQAPWSAWAREPSLEQRRVLEQ
+ELPILSGVGERSGQGFRIEACLDGRGGAVVVVVPEGEGDGTNVRRGVRTVPVSLVVPVLL
+TWAGLRADWLRDEVMEAPGDVAPTEMAELWRGRRGADGVGSEASADWWRWWNQEGEVVAE
+WVQPLHRAPLAVFRDESRCVGVPVMPGVLYSVLQATVQEIAGSPHM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002310.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..855f34f95129b558f60ed9129051c05e7b10dd3f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002310.fa
@@ -0,0 +1,20 @@
+>NAFOICDF_00425
+MGKVRGDQAVQSLQPHKVLDSDSSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASE
+SSLEGRTIGEWFSEDFFESNFWTYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSAL
+KFNRYDQYDSMVKPLLAYLEPHGVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQ
+EVGEDDLVSVTNGSITESTTYGDHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRG
+LPERSWFVSATATVESREVEEHIERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPH
+FPTQRPDQTIVWIHALYSDTEGAYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQES
+VNTVLVYMPFITSYFMPRRAGDRPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAM
+EAVYTLFDVERGVPEVFASATDLRELI
+>NAFOICDF_01186
+MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI
+AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN
+YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW
+MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH
+GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG
+DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKWESATVTTLDERIPAYI
+ERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDGD
+YVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAATGARCVPVMMPYVTSFFMPRRAGDRP
+QVVPEGAANFAFLGQFAETGRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYDVRD
+LLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002317.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..061c981f87a0d87286d585b93540ca7eb2158aac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002317.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_00637
+MSQLMGDAGGGPATPWSHLEFSTPEGPVLCHPTDPLPDLGTIMSVRTPRSHALSRHVPVQ
+TFSATNTDVVAVESGLEQELVLVLDRDPAQDRLVGQPLTVTWARQSGGTRRHTPDLLTLT
+HEGAVTVWDVRPEGRRDPKFWEAARCTRAVCEHNGWTYELFGGLPEVHAINLRWLSSYRH
+SMPWYADLRDTLERLACTNSATIGTLLGADDGSGELISAMWHWAWDGRLQLDLTRPLKTS
+TPVRWEPR
+>LFPAFLNI_02219
+MLSLDRDGQVCLWDARPSRRQDEEFLEAARTTEACARLLGWDYRVHAGHGPAYEANLRWL
+SAFRALKPWYPEAEQRLGQLLAHGERSVQEVFAVDDGTGELISGLWHHVWAGRVETDLDS
+PLCGASILRWVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002319.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a4034435b2a2ec3050132cfeaa15ef5549139fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002319.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_00666
+MSAEPDGMRPHSPSAQEAYAARAVEYADLLGRMDAVADADKRLVEAWAQRTGGVLADVGC
+GPAHWTAYLHSLGHDVRGIEPVEEFVAHARRAHPEVRVERGSFETLPTAAVDGILAWYSI
+IHTPPAEMPHLFEHAHRSLRPGGSMLLGFFAGDEVEPFDHAVTTTWHWPVDALSRLLTTA
+EFTVVDRGTRQDPGARLHGWIEADRE
+>NAFOICDF_00938
+MEAGTLDAEGGTTITADDVHGENISSCAAYGARAAEYAELLGTMAAVADDDRLLVEAWAH
+ETGGSLADVGCGPAHWTAHLAALGHDIVGVEPVDEFVAHARRVHPGVRVETGSFRTLPAS
+TFDGILAWYSMIHTPPPEATLLLEHAHEALRPGGSLLLGFFAGDRVEPFDHAVTTAWYWP
+LDDLTSVLTAAGFTVTDRGTRLDPGTRRHGWMRAHRN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002320.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bccb2925471ddef91f9720b7006eeff4e39e18a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002320.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_00667
+MDLAPSSSPTIELSWHADLTPGQLDDLNRLFAAEYLEDFGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSITVGDHHVTIAGVGGVLVTPSGRGHHLGQRLMRAAVDSMRAHSDA
+EFGYLGCHESVVPFYVSCGWRRIVAAERYIGLNGQPSESAQGDPLLVMPLRNAKQPWSAG
+EIDLQGRPW
+>NAFOICDF_00699
+MDLVPSSSLKIELTWHTDLTPGQLDDLNRLFAAEYREDYGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSIAVGARPVTIAGVGGVLVAPSGRGHHVGQRLMRSAVDSMRVHSDA
+EFGYLGCDESVVPFYVSCGWQRIVAAERSIGRGGQPTQSTQGEPLLVMPLRGTEQLWPAG
+EIDLRGRPW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002326.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c07bc716007bccad1a8e3beca5c23947b6ea0f78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002326.fa
@@ -0,0 +1,16 @@
+>NAFOICDF_00837
+MAFLGPGEHFRDLPGAFRTLENALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKDVTA
+RPLAPLRDLPPQRASALRETALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDW
+HTPPRSLDLHLALLSAARDDGGAPGAPPVRSQPRRRAEELRRPRSPAARC
+>MHAAABBN_00093
+MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV
+DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL
+RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI
+GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV
+LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP
+CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM
+QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR
+GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR
+AMAALNITGVADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHTAWS
+FLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLALRLHRVQSASR
+TG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002328.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..656254b5f588c0869f380b8c6f0d05220600e14a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002328.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00939
+MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA
+RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG
+DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE
+LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH
+>NAFOICDF_01294
+MAVLPSRRGQGMGRRLHALGLAELARRGARKYIGSTGRKKAAMVAVSRANDCIVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002330.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe247c1b9bf9d5e5577e9560f1c4ed705115d60c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002330.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01194
+MQPPSPGGPAGAPPWQVDLDWLWGTPPGNDGSPATLRLDVVGPGAARAAAAWLGSLPGDE
+DGGRGRGGWRADPGEQPDADDHAVLLLTSAGEDVADGLEDAADDAHAALAAVEGLTLRWT
+PLPRDPSR
+>LFPAFLNI_01535
+MQPPSPGGPAGAPPWQVDLDWLWGTPPGNDGSPATLRLDVVGPGAARAAAAWLSSLPGDE
+DGVRGTGGWRADPGEQPGEDDHAVLLLTSAGEDVADGLEDAADDAHAALAAVGGLTLRWT
+PLPRDPSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002331.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d8be442bf9c62d525c80ce10dff7640748b460e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002331.fa
@@ -0,0 +1,18 @@
+>NAFOICDF_01195
+MGVLKDLKERFERERVELHLDDIQGLVLRERPEPYVGAHAMLTVEEAEGGRDFVRRLAEH
+VTSAQDWADDLQSWTGVAISFAGLRALGLPEDPLASFPLPYQQGMAARAQQLMDTGPNAP
+EHWDEAFTQDACHIALTIYAADADALDAALDQAQQVLDHSTGVTLVATHRFGVDELNKNP
+FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV
+LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEALGNDPERR
+NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVTSAD
+DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP
+AEPARKRINGITTFNRMAGGEYLFMPSLRALRWIGEAGWTSDQSDAEA
+>LFPAFLNI_01534
+MGVLKDLKERFDRERVELDLDDIQGLVLRSRPEPYVGAHAMLTVEEAEGGRDFVRRLAEH
+VTSAQDWADDLQSWTGVAISYAGLRALGLPEDSLASFPLPYQQGMAARAQQLMDTGPNAP
+EHWDEAFTQDACHIALTIYAADADALDAALDQAEEVLEHSTGVTLVATHRFGVDELNKNP
+FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV
+LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEELGNDPERR
+NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVSSAD
+DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP
+AEPARKRIDGITTFNRMAGGEYLFMPSLSALRWIGEGGWTSDQSAAEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002332.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bb8c4598561835f73ce8750887fd8a14e52891f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002332.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_01196
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIRKHNPNLSGTAESAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDAISTPEAVDY
+>LFPAFLNI_01533
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIREHNPDLSGTADSAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDTISTPEAVDY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002334.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..068e7dbbc4077cb811b4da05fe29f99c027c47b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002334.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01211
+MSVTKGLLVRFDALPGKEDDVKDFLDSGRALVAEEPATIAWFAIRLGPSSFGIFDVLPED
+AGRDAHLSGPVAVALGGQTGAGALFSEPTIEKLDVLGSKLPA
+>MHAAABBN_00374
+MSVTKGLLVRLEALPGKEDEVQEFLGIGRGLVEEEPATVAWFAIRLGPSSFGIFDVFPDD
+AGRDAHLSGAVAKALGEQTGKLFSEPTIEKLDVLASKLPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002335.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4288c37a9f93e452a0c4deb212caaa222823c220
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002335.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01295
+MSTDLLTLRLPAAHAADHVRGDFEFRGLDTGTTDDLARCYLMGYPPGVAASGLAEAREEM
+DATFRGDYGELRADASATAWVDGRLAGAIMVVTRSIWDADLAGPFIIDLFTDPAVRGKGV
+GRALVQHAVDTCSAAGDAAVSLRFGEGTSEAAMGIYRRLGFRPRTGTQRGG
+>MHAAABBN_01782
+MADDLAQCYLMSYPPDVAASDLDEAREEMNATFRGDYGKLRADASTTAWVGGRLAGAIMV
+VTHSIWDEHLTGPFIIDLFIDPHARGKGIGRALVQHAIATCCDAGDHTLSLRFGQGTSDA
+AMRIYQRLGFRPVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002336.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e252f05baa51f024df3df32160e0dc5791db8d25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002336.fa
@@ -0,0 +1,11 @@
+>NAFOICDF_01518
+MDSDDGRLWLATLPALAAGASGVLIGREAAAEFPSADWRVMFYGTLGVTQVVMYVVYLWL
+TLRRFHGLDARTLERDLRTVSRGPRPGSWAVRMGLPYGSTLGWMTSVSVVALVIVVVVML
+DPATAGQPLLRVLCALVVVSSWAVLWVSQALAYARMAAQHGGIEFTGEEPPVFEDYLTLS
+AFVSALFGTGDVTLTGRRTRRAMRSHVMVAFGFNSMLVASLATLLLSRG
+>MHAAABBN_00686
+MQNTEQTPRDASTEAGGRLWRHRIVENDTLRMTVLSMLAAAVAIGLSTLLIATPLGDALG
+VGAARRASWMTGLMTLCLMWSIYSALDTVVLYRWLGRRDSTDLHALLRTRSRGPKESVDP
+VGWRALMLGASSTLGNTATFSVMAMLVVVISMWMPEVRSVPAMRLLAVATVLASWASIVL
+AQALRYARLAAQHDPKRSRPEGESPAPPIRFRGSDSPVFSDYVALSLTLSTMMGAQDVVL
+SGRAARTAVREHALVGFLFNSMIIAALASLLLTVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002337.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e2bc8e5598050246430799688cbb09e985214dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002337.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_01785
+MRIAVTTPMGHVGRHVTSMLIRSGVRPLLLARRPENVTPGLRKHADIVKANSTDPAQVTA
+ATQGVDAIYWVDPSVMSSDPLADYTLATEALVKAVTANGIGRVVFQSSIGAEKRHGVGEI
+DGLAGTEVALDTLDVDVTHLRCGYFFTNLLLDIDAVRQGQLTTVLPLDQPMSWVAPRDIA
+EVASLTLLNTQWHGHRVQAVHGPQDLSWRQVAETLTAHVGHQVHAEQITDTEMLQRYLAA
+GMAPMMADAILGMSTGLRDGFRPEQPRTLATTTPTTLTSWIHEELIPVL
+>NAFOICDF_01821
+MRIAVTTPTGNVGTHLTGMMIRAGVRPLLLARTPSKIPIDLLTHVDVVEADSTDPEQVVK
+ATRGVDAIYWVDPSTASADPLADYARATQAIVAAVEANTIARVVFQSSVGAEKRHGVGEI
+DGLAATEVALDRLDADVTHLRCGYFFTNLLLSMEDVRQGRLRTVLPLDHQFSWVSPRDIA
+EVAALTLLNPSWHGHRVQAVHGPQDLSWNDVAALLTDLTGRHVQAEQISDDLMRQQYLTA
+GMPPAMADAVLGMSTGLRDDFHPEQLRTATSTTPTSLAGWMQEELIPAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002339.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fe864185feecbed1897e04cb91054c14d29343d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002339.fa
@@ -0,0 +1,14 @@
+>NAFOICDF_01823
+MEGLERVGSVLGMMLQVCVNGARDIAEHPALSADPVRVAAECAEAVAAGADAVHVHPKDA
+HGQDSLQNPDVGRWVREVRARCAGVPVGVTTGAWALPSVEDRRQAIVGWQTLPDFASVNW
+HEPGADQIAATLLDRGIGVEAGIWHQEGLTAWLASPLRSRCLRVLIEVQDIPAEEVESEA
+LVLVQGVRRAEPAMPLLLHGEERSAWPALKLAGRLGLDTRAGLEDMVTFADGRPAPGNAE
+LITVASHLRGRSLEEEPTVMKPYSVPLAEARTAFLAALDAFEEGASSLDDLTLLGVSHVH
+GWSRLDCLVHVRLGLQEMLAGLAARTDDTPDVDAASYWTTYEPEKDPVPGILMTRRTASA
+YARPRNALEHLNQVSAGLRHAADTLIEESIAFQGHVLTAGDMLATWAVELAVHHHDLALP
+AGAPAPAPAAVHIGRLTAEALGSTSGARAGAEDDLAVMLAGFGRR
+>NAFOICDF_01870
+MSVAGEAERFAQQAHQFAEAASGLDDLALLDPSLCRGWSRLDLVVHVRLGLEEMAAGLGV
+RADDAPDHDDVTYWSSFAADEQDPVPGHMWLRRTASAYARPTDATAHLRDAAERACAASA
+LQDPRPVRFQGKVLSVMDFLRTWSVELALHLVQLDVGVVPSAAGLARRTLEALTGAPLPV
+RLTDHSALRVALGADPWPADEPGGGAYPLGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002340.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b45dedcda3923263c82fbaab14e833dd2b999df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002340.fa
@@ -0,0 +1,16 @@
+>NAFOICDF_01885
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLGETLLVLGPQVATAFAGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+TECFNETLPEELNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+VRTWLVEHEGQQQSAATPARQTKTREAWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGEARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
+>LFPAFLNI_00900
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLDETLLILGRQVATAFGGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+AECFNETLPEEVNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+ARTWLVEHEGQQQSAATPARQTKTREVWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGVARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002341.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f07afede29ee1014196a0a88fb8e58f10d781e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002341.fa
@@ -0,0 +1,16 @@
+>NAFOICDF_01888
+MWALVELGKRATSEPAAQLRLETLDDIEFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALEELLKAARTSTSKAT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST
+>LFPAFLNI_00897
+MWALVELGKRATSEPAAQLRLETLDDIVFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALDELLNAARTSTSKTT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002342.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b483c5014e08925de7055288ed225c0aea6e01ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002342.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_01889
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRPLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAIPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
+>LFPAFLNI_00896
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRSLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAMPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002346.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..637d861a023816eb809ea796b08ac6a1c5e234bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002346.fa
@@ -0,0 +1,28 @@
+>NAFOICDF_02315
+MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT
+GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT
+FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV
+APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA
+PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV
+DTIVRDGKTGWLVQPSGAVDATARVLTTLDAAAVTRASAAALADARARLSWRAWAATADE
+VVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVIAERSELTMLS
+SDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVASADLVD
+LQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQAAATML
+EAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLRDGTGAPFLLFVAYM
+ARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVLGFVHDLEP
+LYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVADEPAAFAEA
+VTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR
+>LFPAFLNI_00517
+MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR
+GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT
+FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV
+APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA
+PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV
+ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA
+AVMESVEEAVAAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGARVTLVST
+PGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRTADVVDL
+QWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRRAALAVE
+RLVLAMADDVVVLSDKDAALLSSRGRARVHVVPPPIPGSLRPERRDLQPTAEPQLLFVGF
+MARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVLGFVEDLE
+ALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVADDPQDFAD
+AVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002349.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78842360e1a2e9c33efeef18b5975ae280039863
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002349.fa
@@ -0,0 +1,34 @@
+>MHAAABBN_00766
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMGAEVFGPPAVANDVAARQMDLDGAARRAFDALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDVRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGITASTRDLVRAAVAAVDDAAEPPGPDGAARTWGEAHA
+LTPFLFTHEHPGGPDEPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASGLGGGHVTDQLDAWAAGRLLPVPSRPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRDV
+R
+>LFPAFLNI_00994
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMSAEVFGPPAVANDVAARQMDLDGAARQAFNALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDLRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGVAASTRDLVRAAVAAVGDAAEPPGPDDTARTWGAAHA
+LTPFLFTHEHPGGPDVPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASSLGGGHVTDQLDAWAAGRLLPVPSGPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRAV
+H
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002350.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62e018b381157b7032037e0ac576faaee33a4892
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002350.fa
@@ -0,0 +1,24 @@
+>MHAAABBN_00767
+MTPVPPSSPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLT
+LGGVRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEE
+LASTFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAP
+EGGRALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPE
+AYTLIPVHPWQWEHRIQVAFAPDLAVGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLK
+TALSVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAF
+HAVGSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAA
+QWLHGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGV
+PLTEQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEY
+TALGLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVSAPLRR
+ALAELRQDAAA
+>LFPAFLNI_00995
+MTPVPPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLTLGG
+VRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEELAS
+TFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAPEGG
+RALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPEAYT
+LIPVHPWQWEHRIQVAFAPDLAAGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLKTAL
+SVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAFHAV
+GSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAAQWL
+HGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGVPLT
+EQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEYTAL
+GLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVAAPLRRALA
+ELRQDAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002353.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..862424e41852a7f3d202d093d0c28a78c910f536
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002353.fa
@@ -0,0 +1,20 @@
+>MHAAABBN_00770
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAEAVEREVAAGAVPMA
+VVATLGTTDRGAIDPLPAIADVAERHGMWVHADAAVGGILAASAATRHELPGLHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVVSLFAGARERTRQACGILRARPTFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAATHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEELVDVVEEAALRHV
+DAVRASRHRWRGVARTRPHGPSVAVSCTLPASAGPRPSAARVDEHGEQVCA
+>LFPAFLNI_00998
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAAAVEREVAAGAVPMA
+VVATLGTTDRGAIDRLPAIADVAERHGMWVHADAAVGGILAASAATRHELPALHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVASLFAGARERTRQACGILRARPMFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAAMHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEALVDVVEEAALRHA
+DAVRAGRHRRRGAGRNRPHAPSASVSCTLPSSAGPRPSAARVVEHGEQVCA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002355.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaf3c780309acd726d22da10eed2291af8c07f70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002355.fa
@@ -0,0 +1,12 @@
+>MHAAABBN_01649
+MLLAYIDEIGEPGAYVGPDHPRSRTSPAFGYAGFVMPESAARGFGAKFTALKRQLFASEI
+DRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDALVRSVVVDHGGKLFYYADEKQRGTPK
+QIGLDVEKREADAMRETLNRLARHAHHHGHNLMVIIDQINEKTRVERVASMYAHIFSRAG
+DFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTRAVDHQLNDSSKYAWVTDPQRLASMR
+GSFTYESKLHLWNRGVQDINHSELFHRERRLAPTPHGQLLGASVDPAAAEKMAKIWRSGR
+>LFPAFLNI_01881
+MPESAARGFGAKFTALKRQLFASEIDRAKHPGRWEFKGANLFRPDTPARFPQQLRVFDAL
+VRSVVVDHGGKLFYYADEKQRGTPKQIGLDVEKREADAMRETLNRLARHAHHHGHNLMVI
+IDQINEKTRVERVASMYAHIFSRAGDFPEMRCIVEPPMHVDSSLSSNVQFADWVAAAVTR
+AVDHQLNDSSKYAWVTDPQRLASMRGSFTYESKLHLWNRGVQDINHSELFHRERRLAPTP
+HGQLLGASVDPAAAEKMAKIWRSGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002356.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d97098f48a050a70ff86ba6c3935b9877aa28474
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002356.fa
@@ -0,0 +1,10 @@
+>MHAAABBN_01705
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
+>LFPAFLNI_01933
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002359.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a51f282c994a77b8cadffe699ce2845d50327c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002359.fa
@@ -0,0 +1,10 @@
+>MHAAABBN_01749
+MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV
+GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT
+GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY
+KGPQPVTLMDSLPKNGTGKIVKDLLR
+>LFPAFLNI_01977
+MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV
+GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT
+GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY
+KGPQPVTLMDSLPKNGTGKIVKDLLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002362.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2aa0cba7099dff8b33d234d343ba7677955d2ad3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002362.fa
@@ -0,0 +1,10 @@
+>MHAAABBN_01985
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFQLTLAPG
+VPWTEPKVSPCASTLFTNPTRLSVTTDNSAFYYRITNLRADSTVTDVTASVLVQKSVVDK
+LSNGLTWTSETKDWSNPTLDVSGAKYIDNGIEYYRYYSTLRTAVPAPVSGTITLPRIQWY
+SNCSTNLLTQAQSTGVMANGRGSAVVNGTPLVNVGTYVRLTPRPAG
+>LFPAFLNI_02233
+MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFSIRRATT
+AAVPGASVSACGSGSTRLSVTTDDVNTYYRIANVRTGSTVTDVTASVLVQKDMVDAMETG
+KNPTTFTWTSSATPSWSTPVREVSGTGSPVLYTNNGIQYYRYVSKLSTPVPAPVSGTITL
+PIIGWYSNCSTTLAGVSVNGRGSAVVNGTPLVNVGTYRQL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002363.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3046a05a8033f65573a876ed28d061c9a2a0183
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002363.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_02024
+MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR
+>LFPAFLNI_01147
+MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002364.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b056a86f024f3e9b4b4eea0544acf35cc3569935
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002364.fa
@@ -0,0 +1,6 @@
+>MHAAABBN_02300
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
+>LFPAFLNI_00284
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002368.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5110bff12a71e38e73b7092eb9b1c9226e4f016e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002368.fa
@@ -0,0 +1,16 @@
+>MHAAABBN_02305
+MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR
+STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE
+ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA
+GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA
+VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP
+GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA
+TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP
+>LFPAFLNI_00289
+MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR
+STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE
+ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA
+GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA
+VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP
+GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA
+TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002372.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31dadb5a35ff726b409c7685809e3f37dc3cde27
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002372.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00039
+MSTTTATPLTVPELIAAIRSISDEIRAIQAGLAADNAQERHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002376.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73b8302e9c0c5a3afedd73e35e75fb1713baac70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002376.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00046
+MTVMTPIGDSVREVRATSAGDLPLHAYELRNRDFLVVQLPTGAVLAVPSDSVPPIERDLW
+EDAELRRSLWRGFDDAVCGRVTPLEDVLAELDFDLSSED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002380.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1f782486014c8147f424a218275e3fc4f157c9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002380.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00077
+MERKDDRRAFLTWTLISAVGLALVIASFTWPAWLVVPGALLALVGVSQSHEYRGYSHWFG
+LLVAAVAIGGGPFHLLSLAGDLGSFLGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002391.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44622f6550ea9f33fe7a367f999d6fd16d705851
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002391.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00164
+MPGPQGTDRRAIPQRSTRWAARLADLMHAAGLTPNRVSVGSVLFAAVGAAALVAAGHAAT
+GDGARAGWFVLAAACIPLRLNMLDGMLAVEKGLHSPTGDLFNEVPDRVADMLLLAGAGYA
+AAGAWLVPGWGAGLDVGVLLGWTAAAAAVLTAYVRSLGAANGVGNFFEGVLPKPHRMWVL
+AAACLLSLLEPLLPVPRGTVLALALAVIAAGSVLTVARRLRLIAAALRERADAAPARPAG
+ERTAGLPTDGGERA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002392.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ba87f572583984ebbb22535f703a077f7f9646d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002392.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00165
+MPRRQPAADRSALLDHALAAAAGFAEATFFVVVPDVWTSRVAFERPRRGLATAASALAGA
+LAGGAVTHAVSRRAGAARTRSWLTALPGISDGMVDTVEARVGAGGHLALITGPSRGIPYK
+VFARCYGVDAARPGRGLGALLLASVPARLPRFLLVTGGVGLLGARLRRRAPGLGRRGRGV
+LFWTGWGAFYAWYLPAVTRAYRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002393.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..330e8af1c6f1a503550ea005da747c05ca8cd500
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002393.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00176
+MRKALPTAVTAAIGLALVAPLAAAAQEGDTAALSVLHGVPDLTVDVYVDGELTLDDFTPG
+SLAGPLELPAGDYEVAITAGDAEDDSAPVLGPVDLTLAGGGDYTAAAHLDAQGNPTVTAF
+ETDTTPVAAGEGRLTVRHIAAAPAVDVWADGAVAVPGLANPDEAALELPAATLEAAVSVA
+GTTDPVIGPADVEVAEGVNTVVYAWGSATDETLALATQTVEGLQSAPENVNAGMAPAAQD
+DTALYAGAGVAALALLAGGAMAVRRKAAVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002395.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2999f45084724021e297127e3c179d1a769a86c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002395.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00178
+MSTDLSELAHRFAAGHADAMADVYAEHARMVFSLCMVGLRHREDAEDAAQQVFTRAWRSR
+DTYDPRRPLGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002396.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..488dac749c215e4342a1a598c396265e4fd39e04
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002396.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00179
+MDRIVVHDALDRLGPPQDEILRLAFHKDLPQKEIAERLQMPLGTVKSHIHRGLAALRATM
+TRTEEVHDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002400.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4dfab69c2a3e65abeb7e1ef470260b8c5199b15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002400.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00237
+MVAGLPWFAWIAIVAILVWGTLQVVQLVTGRALPGEEMKKEVEELRTRLDANEGRRPAGE
+LPARADAEGSDLERRIERLEARADRREARDREHDDWDRRAGELG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002401.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a85a42be4d8b55ef4e15e0226c597a3c76c319e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002401.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_00273
+MPRPARLVAPPYERYADAIAALPAADRSRSLGVLDLDAFRANAAAMAARAAGVPVRVASK
+SLRIRRAVVEALEQPGFRGVMAYALAEALWWAESGQPDVLVAYPTADEAALDALLRSPRA
+RAAVVLTVDSAEHLRWIEDRVRAAGVHPGQGAADLPPLRLCLDVDTAWRPLARLRVGALR
+SPVRTPDQARELADRILRMPGVRLSGVLAYEAQVAGLPDASGPRAAAVRVVKSGSRRDLA
+RRRPAIVAAVRQAVRAAGAELDFVNGGGTGSLAETAAEGVVTELGAGSGLLAPASFDGFH
+GLGLRPAASYVRPVVRRPAPDVVTVAGGGWIASGAPGADRWPTVAWPEGLRLTRQEGAGE
+VQTPLHGPGAARLALGDPVFFRHAKGGEPAEHLDAVAVYSAQADAIVDLWPTYRGEGRMF
+T
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002403.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ea0ec3d7bb769c201e860d67bf776ed038295ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002403.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00308
+MGAPDEVPDRTDPGTTTASRPWAAVVGLAAFAVQVPLARRVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002411.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..912d622f259ffedde07a5f243de254cb9828cfe1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002411.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00364
+MTSATSSSPASPAPAAACLVLTLAATAALPDWSGSGVARPLWALLLPAALGLAGAGLALR
+ARRPGGGGGGAAGGLGAGPALIVVTTIVSGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002414.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..daa1ad240aff10581d750d0ed383e86c794ba0d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002414.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00390
+MPRTTLTFGGLLIAVGIISYAVTGFISWTALIPAFLGLLIAICGLIALKNTTIGLSIALV
+ISVLGVLGTSMNVLKVGELISGQAERPLAIVASTVTFVLLIVYIVTGVRLFLTARRGDKA
+EATTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002415.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37ccc2179e161574912259008446b1394f2cc6b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002415.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00409
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDEQVL
+GLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002416.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d7f2d928ce4340953f743107730aa4c831e9ba8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002416.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00431
+MSLRIHPHHCRRIVHRPILALSRDWLRRGGQGPGAGPGEWRTVSTSAALAAPRTPGSVGG
+ESRGRGSGRGGIGQRGCPARARPTGCRTDGWHAAYARPPRPLQARGRGVAQTARPPTGGV
+DGPTAPLMITGPCMLSAVIRQRRRGPSVVSVTTMSARSLASSGVGSQRRVAFHVKHSYGH
+ASRRIACSSAWMSTAGRVTVLGGVHNGPHTQRPHARPQPPHPRTEPAGGIAPTDGLRRRA
+RAQWPPQAACAGPQPFAAGAPRPAISAAASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002419.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69b0bc5a3b613afdb4e8f7e46538a0c1c1f0b70d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002419.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00457
+MDAMLTGAEVQATASADQLASGLLRNDESTKFLDGVVPMLLNFRLPPEAIASLVIGQTFV
+GNTHYGRQTIYCDGGHEVVLRERTRRAGPMSAKASTSRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002421.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ec6f52f7fed4a901bffa17f7786728e024f7b93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002421.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00466
+MTLSPFTVVAGTFYRAVDARFVDSALRGSRSAGRYSPPDAPTLYLSSSPEGVDAAMVAHT
+DATTPPRELLTFDVHAERIVDLRDSEALAALGVDLADAMAPWKPAVEVGEEPSSWAVRRR
+LEEAGAHGLIDPSRTAPGLWHLTLFRWNEGGAPRVTRAPGGVTAGSGASPRRTRWTGRGG
+S
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002430.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..073f401140bbc3b834e24174755424e2281fdd2a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002430.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00485
+MTRVHVLATGGTIASRSGEGSGATAGDSAEVLLEGMDATADVEVTSEDVMTVGSYRLGLP
+ELATIARVSRERAEEPGIDGVVVTHGTDTMEETAFLTDLLNGTDTPVVFTGAQRAADHPD
+SDGPRNLRQAVLAAAHPNARGLGALVAFDGVLLSARGTRKGHTMVSQPFTGGTLVGATHG
+DEFRLHARPHRPGTLDLPDSGLDGVRVDLITAYPGADPAVLPAAVDRGAHGIVLAGTGLG
+NAGPGHAEAVADLVARGVPVVLATRTLAGPVLGVYGHGGGADILAAGAVAAGELTPFQAR
+ILAAALLAHRPDPHEFAARFTRLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002431.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c5b7033d946bbf54e0210b2ddeeaf2a92bf083e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002431.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00486
+MAKKIYVSVGIDVDAVGGWLGSYGGEDSPGDISRGLFAGEVGVPRLLQLFQRRELPVSWF
+WPGHSIETFPEQFDAVVAAGHEIGVHGYSHENPIAMTRQQETEILDYCTDLIERRSGTKP
+VGYVAPWWEFSTVTNEILLERGFLYDHSLMHDDHTPYYVRVGDSWTKIDYEAASAHEWMK
+PLVRGEETDLIEIPASWYLDDLPPMMFIKSSPNSHGFVSPRDIEQLWKDQFDWVHREMDY
+AVFPITIHPDVSGRPQNLLMLERLFDHIQGHDGVEFGFMKDVAADFARRFPRERG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002432.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..746111ed35f86704a6043d9caee66fa248194255
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002432.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00487
+MCGACGRGVASPTTALLNEHGLKRRALARLRGELAPGCRLTLEGDAWTLIRRSGRGEHHA
+DVEGLIASLEGGAAGDWVGAEPPREVVAAVTAGMVARARRRSD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002433.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..603cc54a64639a87a83815d952603436e94757d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002433.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00490
+MPTPITSQASTAWDGDLFTGSGTTTLVTSGSGTFDVNWKARAEEAGSTTNPEELLAAAHA
+TCFTMQFSNMLKKNRTAPTHLDTTADVTFVAGEGITKIVLKVTGQVPEISAEDFERIAGE
+AKEQCPVSQALAGVKDVSVEASLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002435.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0740ca16d43beebe3adb1cdaf082f53be962d578
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002435.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00494
+MELAPAAPWVRDLGLGPVDAAMTMHDVGDEGSEAPRRVRARLLRVREARFDRRSAAGGQG
+RKLIPGSVRRPDVDGLPGRNEPEAEEAEPPAADTGTPLIGTVSYEASFNPPPGWVSGPDG
+WLLDLEVLEELGPAW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002436.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..579afe1d4ab23fd6a79d35b742bb02bfb9b644e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002436.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00495
+MPFDQVTAEHAAAEGDRTLASWRAEHERFWRAHAASGFAPDMPVVCEAFRVVHRRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002437.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c7f83310a63b43488670129ee254e011c4fe9ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002437.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00498
+MKFVILIHSHPQPWAHPTSEHTAEYQALPPATQERAEEIAAAFSCPGDTVELRPVWEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002439.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c938bb89666b4bff7553b9f6e7fbe9d68dc120
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002439.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00503
+MADLMGLLYRSDDHGTVELRRILPVAPADLWPELTDPERLAAWFAPVTGDLREGGDYRIA
+FEEDDDEPGSASWGRIEQCERGRGLRLTWQSAEDEPAPSTVQVSLRAVDGGTRLVLVHSG
+LTHGEDVGHAAGWEVYLRDLAAHIEGTPAEEGDWFERWERHRAAYEATL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002440.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68794d281e249361ebd3c0ff9a5b1662e323d9b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002440.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00504
+MGVYVAGGGLGIVVSGLALPWALNSFPDDVGWRVGWGLLGAVGLVAWAVAARAARRVPAP
+APRAAGSRAPVRGMVPLLVGYTLFGMGYIAYMTFIVALLRGDGATDQQVAVFWVVLGLAA
+VAGGFAWAPVVERLQGGRAPALLMVVVALGAGLPLLWAGPVPALASAVLFGGTFLALVGS
+VTHSAQRVLPAAQVADGIGLLTTVFALGQSVGPVLSGVLADSADGVRAGIALSVAIVVLG
+AVAFLPQRRVLPEAATTAGGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002441.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbbad3e3df953cd00ec9162f02fc6deb41a9145a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002441.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00511
+MPAATLDDLRRARRVLFHGVTGAGKSTAAVRLGAVLDLPVTLVDEELGWLPGWVIRTPEA
+QVALAEPILAGERWVLDSAYRFYREAAVARADVVVGLDYSRAATFARLLRRTVRRAATAE
+PVCNGNTETWGRALGPESILRWHAQTFEAKRAWIRAREADDAGTPVLRLTHPRQWERTLA
+ALAAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002443.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8d1efebabdc14da4faa3ab4e331185d33bee9d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002443.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00520
+MTASAPDPATTASPLTVLPVLRDAPAADPDGERGVVRRHHTGDGASLITFTFAPGQGWPE
+HQAAHPITVQCLAGRLDFTVGDRTERLVPGVVAHLPARVRHDVAAPADSPDAANVLLLTM
+LT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002444.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adabd54d44d7696ab16c6fafbe3cc69b2c7a2fd2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002444.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00522
+MSENAPDPRRRLSTAEIDAAGLTDWRLLAGRLQARFAPADYAAGLDLVARIGAAAEDADH
+HPETTLTYGHVVLTLSSHDVGGVTSRDVRMARRISALAAELGAGADVAGLTRAEFGLDTD
+RGDEHARYYAALLGAEVTAGGEVTDPALQAPTLWWQGSAGEGSASETPLPAPEVEQRWHL
+DVWVAPEEAPARLRAVLDAGGRLVSDAAAPSFWVVEDVEGNRSCICTSQDRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002445.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1440f46e085447fd8581cf5a712af6ef65178a32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002445.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00524
+MDTQETQDLPAFTFLAADPADGDAEGAVEDTDAAFCRLDGSC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002446.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b841ccb01fe8f38a7efaa01ff40456b10d85cb90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002446.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00536
+MDTADLPDLPAPEDRTATASRRVEAPAGVVFELIADPSRQPEWDGNDNLAQSEAGQRVTA
+VGDVFVTTLRKGVDRANHVVEYEEGRRIAWKPAEVGGEPFGQLWRWQVEGDDDGGCRVAH
+TYEWAQLTDPQRIRRALRTGPEQLRASIDRLAALAEAEAREA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002449.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..998882227a1449ac8682f415e58f1bf9ed1f71a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002449.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00587
+MSTASTHPTTAGRRPGGAAVAPGTAGPGRPEPRRTEPRRTPFWTAVGTVAAREMKVKGTS
+KPFIITTLLLVAAALAATLLVPRLGDLFAGDGTSVGVVEQTAPAVAALGEDYDARTLGSA
+EEARAAVERGDVEAAVLPSADAPGGLEVLAMTDVPTSLVQALSVSPAVELLDPSAPNPML
+RYFIAFGFGLVFFMAALTFGQQIAVSVIEEKQSRIVEILLAAVPARAMMAGKVLGNAAMA
+ILQVALIAGALLLGLQINGDVLPLDGLGVPILWFVLLFSIGFVMIAALYAAAASMVSRQE
+DIGSTSMPVMMMIMLPYFGVIFFNDNPDALRIMSFIPFSAPVAVPLRIYLQQGQMWEHVL
+ALGILVVSTALAIWLAAAIYERSILRTGKALTWRQALQRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002450.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e36272abec86e4b8999b7c970c01f124d3a93eef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002450.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00597
+MTGTTLDRPTPTSVSTSVEPRTGAHAVARTLADTAADAAPAVRTPVPPLPPTRPRPPSRP
+GATASASRSSSPW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002454.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..578112cde280a610196d11d63ae104c1a152b38d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002454.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00607
+MLDHPNAAPSPEDAPAASARPAGDAGVTRLPRLALRVWQATTCATALPIAAVLAAVALWW
+DHPVGGPVLWILVALTAAVALADLAVVNRVRHRSYSYTVDEDEVYIAKGALVRHTVDVAV
+PQVLSVHVVRGPLQRALGLATVRFVSVVDAESLGPVELAEAQRVKEVVLRGLAARRQESA
+TALVAAGEVAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002455.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a32f9de9d04b77edda2b1c0ce4ef7c63ac15edf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002455.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00608
+MTTPAASTESRAVRRTERTITFLLIALATAVVVVLGLTTELTTLPRLGITLGALVVAYPV
+LRMLLYPRSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002457.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f304f841ab2eda0f4bc1fbc4c38f8ddd4495bb24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002457.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00623
+MPKKFSPELRERAVRMVLERQATQGGPRSHSIRAVAPQLDVSEETLRMWCQRHGHEIAQA
+PVSETPAEEIRRLKRELAEARRANEILKAASAFFAAELDRPTTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002458.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91cb462aa253882d87b708ffd2d5731afac28039
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002458.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00624
+MIAFIDEHLDQFGVEAICRTLRATECGFITST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002459.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40dac590bb524acca94ffedc597ac7f8b302b2c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002459.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00625
+MGTVGDSYDNALAESVNGLYKAELIHAKRIWESVEAVELATMGWVHWWNTTRLHEALDYL
+TPAEVEAAYTHDQDSAPVAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002461.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bc04de9edc99632e9102ee2e441a25063e224df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002461.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00631
+MGAAHVWDASTVAALDSVLTKYAQHGIHAEVTGLNEASTAMHARLTGRLGT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002464.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d09f6eac365449bc67791421c30c6769513c059
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002464.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00707
+MPAPYPREFRDDVVRVAQNREPGTRLRRIAQDFGI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002465.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21b2ad689729497927e3191c5d897b6b3ad81f0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002465.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00708
+MVSRSSHPDTETAPGRVRIRTDDGVVLLRCARGAQGEPPRLGLEDSGSTFGLALHAERCA
+APVPGVRVEVTRSGLFAERSPAGTVLLPDDGGEPLWLSAPERSAAGQILLGVVEALRAEV
+LPGHVSVPPVPAPRARVERIARWDEVLAPNGLAGGLAPGERPSQAQQALGGAWRLVLDAA
+PDLPVEARLWLAHREQVAGEKVVRLTATWHGPGADVPWHVELHVSHRLGEGQTEFLVIDG
+STQEEWTIADAVHVPGVPLTWRVHPAPRPDTAGRTGEGLYALIDALAHACPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002468.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9adbe63807b9ca7ffa3fc09f338d511048e2409d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002468.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00717
+MVADSEAAMPGHAMKIGEVAGRTGLSLRSIRHYDDVGLVPPSARSEGGFRLYTEDDVTRL
+LRVMRITPLGFSLEETALLLEVLEGPAAEAPREDIAAYLERARKGRATLARKLRQADELL
+AELEALGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002473.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16806716eee89bae3bcccacf343e1c08d4f7152d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002473.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00748
+MGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLDYVSEKLPAVAEHLDAARADILAF
+TTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRR
+YLGLEVLHRCRLTPVSNTGDEVDTDTALELSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002474.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9834a853c9e05842bd5caf082894420d6fdf0901
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002474.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00751
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002475.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e91e3e6a2fdac3ca819cf0c8ece82706eb293b0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002475.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00755
+MGDKISVLSEIDLDGAYVRLIATGHLTETNQQGLHPLIQQARTLAPDGAISVDLSHAEEV
+ESATVDLLRWAIAHNDDTGSGAGPVHILVPDED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002477.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0be269a3e7cc916e0840c2fbc0034b76fb7b2890
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002477.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00767
+MVPSLGILTESIHFAVLNPEEPYVDQNTLIMLARSLPLEGRIVMLTVDVADPGADEAAMR
+ADAEATARAMVLEYRTGMPEDPPSTGPDGFPLLDPPWLMMTVMLPPADDDGALAPVVHLA
+TGTGVTPAPDLVSRLEADLRDARPGTEHTGALEALVRTAVEHSTPSEQVRAAAAEDSLFA
+DRPAWQWALVGALLLALAAVVATALRRRRRRADPARDAHAADPARFAHAGEDPALRLRAL
+TELLALAADAPGARALPQARDATAAVVEHTLALDALAPGSRQGRPDAFRRSVRPELEDRV
+GRAGATLRVLVAAGRDARPAVRFPDAVLEAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002482.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..175068d7bab0fdb81263531e2d268379a54bb5e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002482.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00801
+MGLAAAPRPSRRIDDGGRQVLDLGGLSAVVEHYGRAHTRTDLTVLVPEAGVLDAVLQRLE
+APAARSSRNEPCGMAPTTGEVGAIPQGSFHGEVRVVPGHGAVVDATLVRAQREALAAAPP
+G
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002484.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b82f37bb984c9dc2b49ee0ca40f2dba273bf8567
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002484.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_00814
+MLVAAPIAALVAVVFAGGPLLASYTQVFMPALGKFIVGFFPLFLAGAVFGKLMASTGYAM
+AIARWITGLIGARRAILATVLTGTVLTYGGISVFVVAFGLFPIAYELFRQADIPRRLIPA
+AIAMGAFTYAMSALPGSPQVQNTIPTRYFGTDAFAAPLLGVFAAVVMFAVGMAWLSFRAR
+QAARRGEGFETTWTGGGMAGELRGEEDHLTEDTAHLEQESARAARTRHGRPDPPVALAAV
+PLLIVILVNLALSRWILPTLDFGYLAEEQWGATTLTSVIGLWSVFVALVTAVAFVLLVNL
+RRVRVLVEDLHQGAKDAVLPVFSTASEVGFGAVIASLPAYALVRDALLGVSSNPLVTASL
+ATTSLAGITASASGGLSIALETLGADMLASAQAAGISPEALHRVASIASGGLDTLPHSGA
+VITLLLITGMSHRESYKDVAMVTVVGPLLATALVVVAAAAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002485.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c57c6158313ac7c780c8c11bc4f515ce43d521e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002485.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00815
+MNAALGFIGLGTMGLPMALNLAKGGFDVVGYDAFEGARTAAAEGGIALASSPRDLAERGV
+TAVISMVRDEAQNREVLLGADGVMAARPQGLTVVVMSTLDPDAMNRLAADVEDAGEATVI
+AAAVSGGQSGALEGTLSIMASGPQAAVDAAGPWFAAMGQETFYYGAEPGNSQVAKLANNL
+MLGVVMNGVAEALRFAAAYGLPQDELLRLAQASTGDSWVVRHWDAVRDWTRETALEVLRK
+DLKAAHLQGLEREIPMPFNALASTELIRAWDTLPAAADEETCR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002486.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee35d96c88f861049ec0a14dce747806907d78ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002486.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00816
+MTTHDLTASNPEQTERERFDRGMARMMELVGDGAGTFDHAKLVESYRDVDPELSDYIVSF
+AFGDIYSRTSLSKQQQTLVTISTLVGRGAEPQLKLHINVGFTVGLTREEIVGALIHCIPY
+VGFPHVLNALSLLKEVEAERAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002490.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aedbebbd26908124734e57798ee067238c16a289
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002490.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00821
+MFRRTVGDHAEWKELISRSFVPLESEPLRPSRSFSGRLDVSEFGGIGLTTLAAGPHAVHR
+TERLAAAGGGGMFKVSLQLSGRGLLLQDGREVLLEPGRLAIYDTSQPYTLSFDRDFTSHV
+LMFPHTALGIAPGQAAQVTATALDEGHRLGPAVSAFLTQAADAMPVLDPATGGRLAHNVV
+DLVGTLVADLLGLPPRPAEGARPAPAEGTDDARGRQRAAVLRHIDEHLADPALSPASIAA
+AHFMSVRSLHLLFEGTGETVAATIRRRRLERCRDELGDPGNAGRPVAVVGARWGFADPAH
+FSRAFRARFGVTPGGYRRQAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002491.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0a5ccefc51f8cad29da96da8d2eb84db44d44f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002491.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00828
+MGGVRDVAPALTYGEVGATLGELPPGYRHLDERRTVGHGRADFDRLAAQLLAWRLQRAAG
+FAVHPSTPTLDVGTQVRLAPGPGLVPGGGLLGRLVGGWQCRVVAVVAEPDRAGFAYGTLP
+GHPESGEELFLLTLEPRTGEVVLRIRAFSRPGTWWSRALDPLARAAQRRITRRYLRALE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002495.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bde0edaa65894fe8e921bbb048b5aff1be93d4f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002495.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00915
+MRADHRFEATLDEDLEAASASALHHRLVTEIPPLTDTQLRAFRRARIEIRADHVPSFDTG
+LTGLRLVVAAVALGLSAAALYNVAPNGIVLVWAVVALAVVLLLAMLGMTLLHGRNRRRSQ
+TLEMAVALAEIVEPLGARPRVRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002498.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a45ced85354f90109a640839aed5983e70395fc5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002498.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00965
+MGGVHVRAGREGRGGEHLAGGLAQGEQHVRGGVLVRGAGRRQHGVHEPLDAAAGGGALGR
+ALPRVRLHEGRVQQGLDRHGGALAGVGHAGGEPAAGGVEVADRPARLAQRARDAHRGGPG
+LRRRGGLRRGVGAADGGRGGQRTAVGADGRAQGLEVGGGGRRGGGGGGPADQEGALRLAE
+GEVAVDRRVVGAGGGLAGGRVGRGLAHGASFRDGGCGARPTAAGRGLDSTSGPRRDTVGA
+GVRRPRRGGLSGPAGGAGVWWCPRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002499.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8da9569018d69234950321055c37fb97724d0e7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002499.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00985
+MASQDWMDKDFYATLGVSKDASEADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FGGMFGGAARQTGGFGPGGFGDAGYARRAPRRARTAPPPPRSPSAARSRAPRCPCALRTA
+RRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002505.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91f94266e3048f2bbf825f9a031c4ec09ccbe11f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002505.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01057
+MRFAREAWHAAISWPSILLAVVLTALTLHGVSEAASDPGVNGWDVAVVQVSNLQLVPLVI
+AVVWAPVFLARHRALQREDELLRRGSWRKAVAAVVISDAAIIIGALTLSTAAVLAVSASL
+GLDGGWSDRVVGIVSSGGLDSEVSAAAAAAWVGQWHGAPWLFLAIQTAWTAAGLLAWAAL
+HAALMIGIGPRTAAAVVISGALWGVLSGAGLLVGRPFPDMSAWTNSLWAVSNPPSVAVTV
+ALWTLAGVGVVGAAAARDGVREDGRLRLTFPHLAVSLALSVVLLYSWYGAGTEGGTGLAD
+VAFGGQYSSLLGHLLGALPAVVMAGLLAVQLSDLEGGGAEQILLRHGAPHRWVGGLLGRF
+LVGSVAMTGLLVGTFAAADFLWHSEGTTRSAGEWTLLAAAYVSFCCLLGVIALVLFWVRG
+HVQEWIFVVLAILVLGYPTLFPPSPANPLVPYSLEPGTPFTATPLVASLSLLALFVLGLG
+VLLSRLPAPRSS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002506.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ef2810c34a4e480d487f64ac389d86390d5dc0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002506.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01075
+MLLVAEAEGRPLGVAAWAAPGQAVAQRRRSLLAAPALLRAAWPHRAALRVLGERGPRVDQ
+ALEARHAAEPHWYLGLLTVAPDAQVGGVGSALVRAGLARADADGLPACLECDRHLEAYYA
+RFGFARTHTVEIDDGAPAHLGMGRPAGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002509.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7813fce892053ff488147e3694bce4cf69c564f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002509.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01217
+MTFLQRVRRKAVGDGRLLRQVLTVLSGTTMAQLITIVGMIPLARLYSPTDFGLFAIAQSI
+VLAGTMVAALRYDIAIVLPESQSAARTVHRLASRIILLTCVVLAVILLLAHRVVSEHYGN
+PSFGIWLTVTALIVYAMAQIMNTQNWLIRMKQFGLISQNRVLAAALMLTAQLVCAPLVGG
+FEGLLIGMLVGQVLTLIVLNRRVPELRTSHPVDAPAIREMAVRYKKMPLLNAPNVLVDAV
+RDAGINILIGNIALGSLGQYSLANKATNAPVYLIRGAIAQVFLPLMARARPGELTPLVTR
+LLIRIGLVATPVFLVFYWLAPWLFPLLLGDQWGQAGLIAQALMPWLFMNTFTSPLANVYV
+TTERQGWLFGFAVVYAAAPLIFLTTSTLPLLPRVQVMAWIMAAALMCMLVMTLIITRQFD
+RRGQPAEVTPDMARPTKEPS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002510.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc5dd5949b1da4af3af36f7335507450f69f7028
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002510.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_01222
+MRILLSSVGRRPYLVRWFRDALAANGVEGTVLAADVDPDAPSRPFADGFVSAPKVVDPGY
+ESWLRQTLVDHDVDLAVSINDFELSTWATLPEDPAWAPLVRLDAGTQRLVEDKFATSQAL
+LEAGVTSPVTWLGSTPPSTEDAAGPFVTKGRYGSASRGLRFVDRAGLPGALEEASGEVTT
+RQGVPALQQDAVPPAELIVIQERIDGVEYGLDVVCDLEGRYAGVLARRKITMRSGETDRA
+VSVDAAPFESIARGIAEAIPHPGTIDVDVFVDASGDIYVIDINPRFGGGYPFSHMAGARV
+PECYVAWALGRKAGAEWLRCRPDVVAGKFVEITATSEGGTGADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002511.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5fee193894ec600c775be3555900d3cd6dd9b6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002511.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_01269
+MLAVLRNPTYARLFSAQIIALLGTGLLTVALGLLAYDIAGSDAGAVMGTVMAIKMVAYVL
+VSPVTTALVSRLPARRVLIGADLVRAGVAVSLPFVTEAWQTYVLIFLLQSASATFTPTFQ
+AVIPSVLPDEREYTRALSLSRLAYDLESLVSPLLAAALLTVMAYNNLFFGTVIGFLVSAA
+LVALARFPAIQAPEPAPFLDRLTRGTRAYWARLELRGLLGVNLVVATTTSMVIVNTVVLV
+QADLGRPQQDVALLLAAYGGGSMVVALGLPRVLDAVPDRRVMLAGAAALPVLLLAAVGAM
+SGLDAGAQWAGLLVLWALMGAATAAVLTPSARLLRRNSTERTRPSVFAAQFSLSHACFLL
+TYPLAGLLGARIGLPAVGVVLVGIGAAGLALTVLAWRRAEGQPPVDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002513.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0f6f0d71a6e6aea3ee926c408f6c1dc89c66f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002513.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01274
+MEFSRVGLTDMPRTLVHYTNAPAFMSILEGHALWASSIGYMNDSQEYHYLYVQARHFLEI
+GYGALRHYGDAHPEDLETFINGVGWPYANSPSVYVIALSTDDDDLNLWRAYTAPGEGYCI
+SFDSQKIRELAEKSGWRLAQVEYGASCIPVLEDLWVRAFTKVEEGESSQEVLTWVNSRLA
+EIAPFYKHESFASEREWRLVKVQANFDQEDLRFRPGVSFIVPFVVFDFGAPDQHSIVQVR
+CGPGPNQKLAFDSMDWMVDKIGWNPSRGVSNAPFRPW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002516.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c482cf92c58f802ebc9243d7764d8731bb19ae7c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002516.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01289
+MPLATPTLDTERLRLRPFTEADGDALFALMTDAEVLRYWDSPPWKDRGSVERFMAGNVRA
+AEEGTGARVAVECRSDGAFLGWCTFNSWDPDFRSASLGFCFTRDSWGQGYATEAARALLQ
+WAYSTLDLNRVQAECDTRNPASARVLEKLGFRLEGTLREDCIVDGVVSDSWVYGLLRRDW
+QMHGASAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002529.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..feccdd266d7d4f2a155f8278d79b92e21799fd1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002529.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_01341
+MTFHVAVDARSPRMSHCSCSSPRIGVSWVSSPGGVLALVGAHVQGEHVERRAAGDPAVDA
+GGLEAGAAAQGRGVGDGHVLLPRAAGAGGQRVHVTDLGVARVFEDLARPPVVGRLVVVPL
+GDDGDVRVQGAEVVVHHVVAVAAAELVQRLGDLGRLLRDEVAPGGLAGHLEGLRDGVVRV
+DRVAGVQEEVGLRGVHRRVAAHAADLRVDAVALPRGVRGPHEGLGGGGLPAEPRAGRRGE
+AGHGRLAQAAGLVLERVRHLEAGAGGQRVREDLRGVVGGPVDPAGVQGQPASEAAAQHLP
+VLVDRAQRGVQARTAGRARPQHGRVRGDVAGGDAGRQRQTGRGQATGGVAGRTGGGGVGE
+GGGGEHGGGRRGEHRTAGGGVGQGCGGLLHGARVGHAGEGHVASG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002532.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66e1765945513036887e2708dd4e1414fe916ef4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002532.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_01357
+MSTGRPLRASVWRHAVDVLRPAATPARPAVVRLGVGAFAAWNGHRRRDLVRGLHRQDPRR
+FEPVGVVKVLKRPLPPRVADGLFDAAQAVNALATLGVAHRVTGPLNAALQLWTLSYRNSW
+GMLYHNDNMLLMHQMVLGVSPSADALSVDAAVAGRGLAPAVLERRYGGVLPMVNAATCVV
+YLISGVAKVRSELGVKWAGGDVLRGQIAIDGLRKELLGSEMPAAGRALYRQEHLFTLMAT
+VALAVELGAPLSLVDRRLGRAFAVAAWGMHVGIRVIMGIKFTYNTSGVSYLGYFPVGPAL
+PR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002533.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dc9d73c9b0bf2a4f31fd45d2460dd635d1f5a73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002533.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01430
+MDPGPRLARAAPPLGPVPAAAHRRAGRAAHPPGRAGVLRTAHPADHAGPLRLPLRAGPGR
+GPPRPEPGAGHVRPDLRHGRPEHGRARHPDAARPRGRLRHHHPPPLPPGAAAGLGVRLRG
+HDLLDRPGPRRDPGGSAGGRRLRPRRLRRQRGPARRLRRHAARPRLRCPGGAPAGRRLRP
+LPRLRPLRRAGVPRLRAAGAARVRRRVPAGQRARVLVGLAARGAARAAGRPGRRVHLRRQ
+PGRAHAGARRGRDGPPGHLVQPDGGQHPGPDRPARAALPDAAAVRLGRLPRAAHPADHRA
+DGRGRALRLPRRLRPRQPPLHRAALPPGRPLPGHARRPARDHPVRRRRRHPGPRGDRHAR
+ARPRRRSHRPAAGGPDRRARLPGADGPGSPGRLRGVRGPAPHRAHPAQPGEQRDRARRGP
+ARGRARGRRRRGRQPGRGGPRHRHEPRGGAARVRPVLARRPLAQAHHGRLRARPGDRHRG
+HPPARRTARGLGRAGGGLHLHGDPAAAAARDRPGRRGARADRPVGAAHAPAVQHRGPSVR
+RGPHPARAAGPRRRRVRRRRPRRRGGDGRRRRARGGRGAASAARHAEQALLPPSRLLGTP
+AAQGDDGGRSGRDPGEDDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002540.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d767139d6abf8c195e8039fb8c27137d93621ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002540.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_01503
+MRAVEVQIHNFRSIHDARIRLEPLSLIAGANNAGKSNIIDAIRLFYGDLKWDDARDKPKV
+ASGDAEAWVEVEFKPTENELAQLKDDYKSADGTFRVRNYVSPSTGADGKARSGYYAYEND
+NLSNNLFYGAKNVGSGKVGHIVYIPAVSKIDENTKLTGPSALRELVAEVLNKVVADSPAY
+KHLTEAFGTFEGSIKAQASADGQSLESLEKEVTDEITSWEASFSLAVQSIQPEEILKTLI
+KPQLIDETHGGEIDQARFGAGFQRHLIYTLIKLAAKHANPPKVLSSEKKEFTPQLTWILF
+EEPEAFLHPSQEEVLHDSLLKLVRDGTTQVLLTTHSSRFVSRSMDDLTRLIRLRRDAGVT
+TSYQLTQPELDQLFSDALVADDSILPHGTSSADVNKAAMMASLKTELWMQSTRTTAFFSQ
+RVVLVEGPSETAIYSYLTSRGIMEPPVRGLAIIDCMGKYNIHRFVAILSAFGIDHSVLYD
+GDNGGAYDAEVTQAISGAKTTFTKRITRFVNDLETELGIAPLPRNQSSRKPQYALYNLES
+GLVDQVKLEALKQEFVDLATAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002543.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80a5740f303ffc203b6bb5cca92e2150f4bd0272
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002543.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_01509
+MHLPIRAQGTTLADEQAKILDDEFFLSNPLSHFSSRVSMLLETARSSYEASPENEPEFFN
+ALGLDSADTALKFDTQHRSVQVAIDALSLRHQAAEALTRFIYARVAATPRKGDAKSTYLA
+IADCPNPMIKVIEANKAAHDADPHRFLQLLFPPGIVVEGPVVGAAETAVEWANHAVWLLT
+SDELSINAAHNKLKHGLATSARGDVRIELITTPPNEDGTIPTSAFGEGKSLPLFDRPMLT
+YLSRPPKDLRQGLEAVSLRVDLPVVLAQTWMMANVYAAMFHIAAREHYGKSLPEGVAPFP
+TRVVGRLPEHVIGGRPLGYRSAATLPPDGTTAPRPSGVAFFKQFWPMTVDFESKTQGVVV
+DA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002551.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..402c1338b645d2792bac50c29f87d1c294e4887d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002551.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_01739
+MYFFLNDEEAGALVMAAGYYAADQWGEDEWLSFGRETGTTDIIKKHDRLLRSWSFGDPDY
+TDACIAVMGQILKEGPDPQAGQAGKMDLLRDSMPDLPDWVRKNGPGRTRRLFHEYISARA
+NSEIPKEWLPASAPTTSTSAGKPEILPKELDGLNSRSVPTQLENSSQSGPDVNDKWDSVN
+ELTDKEPAPREQVVPTYDPTSSPREVFIVHGHDTAAVDSLKVFIQERFGVMPRNLQSAPG
+IGRTIIEKFEDSGSRVDIAVILLTPDDIGAAKAAVDNGEEPQPRARQNVVLEMGYFIARV
+GRSRVVVLNGGVELPSDIHGVSYISYPGDSWKDELFHELKSMGLVASSD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002552.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5049dfb225a0cd91b1d8f807ac2c2eb87c1658d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002552.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01784
+MTAAPDAAQVADGGAALAARQRRVVRTLAASQVFSGLGNGSALAVGSVLAVELTGNAALG
+GTTTMMISAAGALAALPLARLALARGRRTALTVAYLVAALGAACMLAAPGIGGFGLLLAG
+SFGVGLGAAGNLQARFAATDLATPARRGRDLGLVVWSITIGAVAGPNLIGPGAVLARAVG
+LADTAGVFLFSVAGMLAAVAILQAGLRPDPLALRREAGLGGVASPQPPRLRAGVGAVVGD
+PRIRVGVAAVVVGHAVMVGVMAMTPVHLSRTHGAGAGGSDTLVIIGVVISLHIAGMYALS
+PVWGWAADRWGRLAATAAGFAGLLAATLVGAVGAASTGAVTAALVLLGLGWGAVTVAGSA
+WVSEVATGPRRVLVQGVTDSGMGAAAAVTAGLSGLVLARWGFTGLTVAAGLLSAALLVWV
+LRARWRYENADEVSPISDIVTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002554.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c88fd7dcdd68cea5beb0d3f7a5c73ee580c106ae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002554.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01809
+MTALASLASPAALAPLAAFPAPPPGTASRSAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002555.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..029ff7802bf3f2bc6f5f47d5e09a462a9009c82e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002555.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01838
+MAEDPAAAMAAAWRELTPAAGRLAVLMDNPRSDTSMPRCLEQHRDDPAACAYGKAEGIEE
+SGAPALQAAAASAAADPQWGLVDVNHLVCPGEDACAPVIGEALVLFDTNHFTATFARTLA
+PELGEQIEALLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002558.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f646a04517165db007ef4785a08381708b00b89c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002558.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01856
+MMMSFRSTGKGRRGACGAVAGFVLVVAAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002559.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d0aacb413b666947771ba3fc4605543206850f0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002559.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01857
+MPCPTWLDVVEARLPAAKDMLKKLDEGVDFIGVMPEAMKGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002561.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2e351b523db394c28616141b3e4564f72e46407
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002561.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01864
+MPSVLFVLSASGHWTLKDGTRYETGFWAEEFVVPHDVFADAGWDVAVATPGGVAPTVDQT
+SLGLTGGAPWKTARLKRDLERLAPVLDRPVDLASVDEAGHDVVFYPGGHGPLAERILADA
+EARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002562.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4da72ecdb3f06c3db564c744acb0d074d2634671
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002562.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01881
+MAHGGVIRAAVGLLLRHEGEAFAALERIDNARAAVLQGAFATDTGAEGWGDWTLEGYGI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002567.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7da93e68772836b04c572faa19c14c3165c991b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002567.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01940
+MTALTPFQYGATAVRTAVVDGEPHFVAADLCAVLEIGRQQDATRYLDADEKRGCLVDTPS
+GPQTMVVVTEAGMYSLVLRSRKPEAKAFKRWLTHEVLPAIRKTGAYSVQRELTEDEIIHR
+ALTLTVAKVEALEAKVAEDAPKVAAWESIVSSAGSWSYNDAAKVLCESGQIEIGEKRLVK
+ALVDWGYLYRDARGRPHVYQRYVEQGLFVVKARTYRDLVSGEVRESAAPQVRLTGKGLGV
+VRSRLTNQPAFELLGIRVVKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002577.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f0f665668bec409a1ef003c552e6ae2a2ad6e32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002577.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01951
+MGDCECGRRGVLLDRELDLCILCRNRLDSAPAKEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002578.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8951a734f811081fbebba760fb3f26cbb5b1b7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002578.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01952
+MSYHHINEDGTAVVCTAQESAWCRSRPNCDTEEWNEHGCAEHDREHALTPGHECWQARNV
+NAWGGPYPDDQPDLRPGAPVTLTYEGEGIVTWDYVNGARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002582.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a0c9a073955cab5e1b88b31943ba64ceea19335
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002582.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01956
+MPWLKVSDASAMHPIALAAMEAEDADERLVNELFGYVARCAVMSAQHEQDYVVTLATARV
+TAGGDARFKVLAAAAERAGYWTRTTVKDASGAERPAFRLVEEKDLFHMLLKKERAWETQR
+RADVANPELTVPVRLRDGDGCRWCGKSVAWRDRKSGRGATYDHVKPGQGAASPEDLVVAC
+RACNGARKDEENTSFSRTLMAPPFRPLYGPDTLAFLAEHDVVPEQQDTATAAERQSQRET
+APTPTTAAPATAAGSTARTATAAPRQGVRETADGQERRRGAQVRDVDGQAADAAAAHAQR
+EADARRAEAERERRLDAWLADHGISVAPAPATALSPLDVEEADWAPSEGDAGPPGGPDLQ
+IPADRQAEGSGFPGTGRDGSGREGPGLDVSGTGGARDGSGLDGGSAGSGRRRRRRGRRGG
+RGRGGEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002583.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6677b7966ebd6ec0d37f003e962ba6ddad58704f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002583.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01957
+MRQDEYVRMMAAGMSEDQLQRGVERLARSLGWLAYHTHDSRRSSPGFPDLVLVRGDRVLF
+RELKTEKGRATPAQKTWLAALTAAGMDAGLWRPVQWFDRTIERELA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002586.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27c31c363dd7f89fc07ecfb4a86aebb1d9a8facb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002586.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01960
+MATSRTGTSEYKRWRSYVLREAERSGQHRCPYCGVTLDYRTGRLPHSAEPDHVTAWSAGG
+TNTVDNGRAICRRCNQSKGARAAPRPRAVQAAAPLRVSRRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002590.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff5df818a72d44b2fa58e1ae8739b68f029e01b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002590.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01964
+MSVNPRYLLTPPADDVDETHADGAIALAAGYGLVLDDWQQQAVRAWLRCGPDGRFLASTW
+GLSAARQNGKNAALEAVELYLMTVLGWKIIHTSHKLGSARKAFKRLTKFFGRFKGDPSAP
+YPELSALIQEFRRTNSQEAIELTNGGLIELSARTSGGARGTSYDLLVVDEAQEYEELEQE
+ALEPTISASAHGQPIVIYLGTPPKTIGERGEPFIRVRSKAVSGQMERTAWVEYGASLEID
+RMTDVELQAAVRDDHHVRDANPAVGARVTWETVNGERGRWSARTFARERLNCFPLPRTSS
+EKAIEEDVWAARHDPDPDPHARLAAVGLDMDPARTKVTITMAYWAEAGVHVEVAAAAPYA
+DAGVASLVAWLWERCKARVPVVIDSFSPARAIEVHLLQKRMKVRVLSAREWADACMGLYD
+AVSAGAVTHFDQTQLSLAVLAATKAPVGTQGAWRMQWPKDDVDRAPAVAGVCAHFGAMKF
+GRRPREGAASQKQTGHSFV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002591.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d474d9ec4ef98a8db73fde616e9a332b5d253877
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002591.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01965
+MAVLNTQEETLFLRMRDQVRRHQPTNRHRENLFNARKQLQKIGFSVPESMRSFAATVGWP
+EKAVMVPARRLKPTGFVSSREEELADELNAHLDSGYAAAVEQYAIEASVRHGCSFVFATP
+GDQTAGDPDVVLSARSALEASAIVDRRTLRTIAGLEATDEAGVWLMHVPGEVLLVDTRTG
+EHVVRERYRAAPGEVGVVPYVWDRSLDRPFGRSRITNPVIDLSGQAVRIMLRQEVQAEHF
+SSPQRVLSGAREEAFTDETGQRRPMWQVATGAIWGIPDFFDEEIGEWRRAELTQMAAASM
+QPHTDHLRTVAMMFAGETSIPISQLGIVHDNPSSADAIRQHESAMVDLVQAQIPSYMASR
+KALGRLVLAVAHRGLSPATNTALAHVHARFADPGTITRAALADRAQKFAAAYPELRGSSV
+ALRAWGFDDVEVRELQDHLQRAESAGLVRQLLEAGPGVGMSGHAEP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002592.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b53968a81bae1c5e62c8edfd173e927e65e3ccb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002592.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01966
+MPSREQLEAFNRDQALLHDLVMGALDGMARRLGRFATPDQVLTALLEAMPELVGQFGHAS
+ATLAAEWLEEVYGIRAVLGETYPLEAVTQTLRRHAGQLWQGAGPEAVVAAMRDDVARWVK
+AAGRGTLRDSATANGLRWARVPSGPITCAFCLMLASRDAVYLTRNRALRTKSGEDRYHND
+CDCIPTPIRGPQDYPTGYDPDELYSVYSEATSAVGSRANTTAILENIRRAHPGRVRDGVH
+TTN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002598.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c04de88c982d14147f3f6f47a4dbe4db990f3d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002598.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01972
+MRWPRLTGPPRPPLTFFVDDYVAIAVYSGGGRDRFGEPLPESRVEIPECLIAPRSTTEPQ
+ERSDLDGSRGVIYVQSEHTFHGSDRVEVLTGSHRGLWEVDGVPTLWPDGWEIPIRRGDRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002602.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3338ef7dcb034b51d46262f5194273f07a0efe50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002602.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01976
+MSEKTTFTKGDLSITTTDPAEKVRLRSQGFAAADTTAPAKATPKRADAPATDQKN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002604.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d187b9668ce063b60a9b510a4afdd8c230a8656b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002604.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01978
+MFGVDLAAWVAAGRWLGVLELIHSLPRSSRLREAQLNDPDVAADLLELQEAQDEPEEWAP
+ALAETSLITDLLSALIGEVRSLRSEQTAIASGKKPRPVKPIPGPRTALETAKALRAEKYA
+AETLSRFGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002606.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..568c702f6d25893c52018b4a60e3229bd7ef6439
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002606.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01980
+MAWSGAGSWASVSGRRMRLIWSATMSPTTVTAATSSVSVTVTHTLQTSAAIDDPSTAFVL
+SGGLGASTTSPYVRIGSLSGGSQVVSTRTVSVPLAYGKAQTLSWSASMSGLAYIPTTAKV
+SGSVPVPARPLAAPAAPSGVGVTRSSDTRHVITWTRNSPGSASAPYQNQVIQRSADNAAT
+WKTVATVGNVSSWTDTTTTAGRRYQWRVAAKNTGGTSAFASSPVVYTTPAAPTAVKAVRQ
+GMDVLVSWVKSVSPHSRSEIAWRQEGGAWQYPGWTSTGTSYVITSPDPSKPLQYAVRAEV
+ESQGVTLGSPYLWSSWVQLLALPAAPTNLSPALADAALPITLSWRYNSTDSSEQSAREIR
+WRPLGADAWKGIPKATAADSTHVVPAGLWEPGTVEWQVRTWGAHADPSPWSTPQLTRVAQ
+APSVTITSLQDGPLAASQAKIVYSFFDPEGDEQTAGSVQILDDEGSIVYQRTWTSASRGL
+TPPVRLQDGRSYTIRVRARAASGLWSEWDQVTVAVDYPEPPVGVLTAEWLPDSAAVMLTV
+AVPPPAEGEVEATSAEIWRSVDGGDWLRIAAGLPLDTALVDPTPHTSRTTAYRLTTVSDL
+PSTAEAAPVLVAPDPQGWIWLNSGPGWSRQVRMRDNARTGPSWSRASERHHMAGAKLPIA
+VRGEQRERSVSVSVRLAPNPDGGCTYAELEQFLDDADLPILYRDAKGRRWFADVSEVSGS
+EERILEEASFTVYEIDHVEAEAEAVEQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002607.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dcb80dcc78dc69fba4e9cde8dc9b0e17f85be31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002607.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_01981
+MTDQLHLIDAPEWGPAAVDLLAGSRDVEWIYELVHARTNRFIRTLRGVRNFRFENNLHAT
+IRSGGSCIWQGAEDIDWMEHRLRAHQRISHRGQSLQWTVGTFIVESPTRVLTDKTRGAQD
+LQLFDAMYRLDVQTSTVSEWVAHKGSNIIGTVRHLLDRQGIKHALEDSDAVFASQMSWEA
+GTTYLRMVNDMLAAANFTAVYADPQGVLRAGPARAATSRGVAWTFRDDSTAMRYAPEVTH
+NRDTYSIPNEVVLIARSDDPDTLPMSASARDTSSPYGTMRRGMVITKVEEVDAASQAILQ
+ARADLRLKEVQRPASTFTFQHLPLPLEMSQVVRFVRTRHDVDVLAVVEKTGFDDGTGLAE
+TTVREVVS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002611.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e39357de98531069b9f4e38a477b9e8a9b25ee8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002611.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01985
+MPDRILRTSAGVLGGLIIILGLTYAWLGITWLISPTPTRLAGIEWAPIGAHTVGIWWIAG
+GLVALIGGAWSARPVAAGVGAFAAILTPAVVAGLFLVSVWHGNDRGLITAGSYLPYALLA
+AWVTWRSGRGSEDTARDMAATRHDSQEGRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002613.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978a289171e224fedc24f3fbec2b394cc1ba658d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002613.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_01987
+MPTPFLTGLGRVLTTAGVTWEGVPGWETRTGFASGYRDVYGATVHTTETHDATFAKGGDA
+PTLEWVVDADGSRRGAHTYALLIGRSGKVYLIAAGPGWQAGHGSWPSKLGPNPGIPDDQA
+NFHTVGVSMDANESQYPPTEAQLVSLVKVLAALRAEWAPDRFDVMMHGEWSPARRTDPTR
+VPGGWDAIRKAVAAGAWPVQPKPTPPTPAATSSRPAPATGTYTVRPGDTLGGIAKAHGTT
+WQALAKLNALADPHLIEVGQRLRVPALPTHTVAKGEGLWGIARQHGLTVDQLANLNGLTR
+TSTIHPGQTLRLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002614.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06476ba9666b1c00a5a6ec4db288095073f8316f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002614.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01988
+MTKNAILRYFTYDHLTRSPLRDVSKLFHDLAGTLDAQLPDGPEKSTALRKLLESKDAAVR
+SALDIEGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002615.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46728e90856e89933c41687dd0d39a6a2b7ab597
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002615.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01989
+MQTRRTPIIDTLTLWTGSVQAALAAGAGAAILSDLPGWVAFSLAVGLFVVGMVQAGLRWA
+AQNATVPVGDVVEVREGSDVVAGPANDQVAEGAFVRELGRSPRHRVAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002619.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1c2e6d986a88f8b8539ff604fcb496e39c18636
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002619.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_02047
+MVRAAIAGEKDAARLLDQVVDLVASALARIAGSDETYRRELFDRLTVDPSGWAVPWDRLR
+APASTLSVLYNFQPFADTGSSVASKRLRVFGHTSDVIACSFLHHKKVDPTIGMISRPYLA
+RRRYLEMRPSWASWHAFADFAVQARDQADAWIAAGTRYERLYTRANWAPSHYAGALIHEA
+HPELIWTAEFSDPLSLDVQGKRRGDLLDRSDPMLARLTAPVEADFGRIPDEHFSIFGLAE
+ILPYALADSILFTNEHQMAEMLDHIYSPALRERVQGRAEVSHHPTLAPEYYDARPVTYEV
+DPTMVNVAYFGEFYVTRGITDITLAMAMLPQHIRDRIRLHVFTNFVPEGGLATRPPGFSK
+AQFDALVRRAQDGVGAHGMEHLVRFNASLPYLDFLAVTRQFDYLVVNDAQSGSRHTRNPF
+LPSKWSDYRGSQAEVWALVEDGSMLSTMPTALQTPLGDPAAARDVLWDRVEAKQEERR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002620.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f686ce9607799c61690ae3d36d3c3ee7e6b03b85
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002620.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02048
+MKPGPSLEKALYVGCLAAMSIIGVAVAVLGLLGQFRLVVILLGLGAVVASVLIPVHARRM
+RRFMGVAIRRAGGRGRAAAPTSSPGPAASVEVGRETMAALTRINRQLVSLREETMGGQLR
+PVSGAGSTDAADDRSDSSMAVAEALVGVRHELSVLRAEVAHLAEAPRGGRQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002621.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b8cc67674c0adc870b8299713fa9c66dbccd33e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002621.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_02049
+MNPYQQLLYRGMAAQDIVTTPVLSVDGFNPLLAVRAETSGVGVHLHWLNPVLAGARNGAD
+ARARVDRFLERVDEFIDADGRVVWTVHNVLPHDAVHLEQERRLQQGVADRAHLVHVMHPD
+TADVLGESLRWDSARTVVAPHPSYAGAYPDTVRRDEARGVLGIHEDEVVYVALGAIKAYK
+GIDTLLDAFDQLCREDATPRRLVVAGPVDTSPHTRALVKRLRTNPRVLVQAGPVPGDRVQ
+YLLRSADMAVLPHLRALNSGGALLGPTYGLPVLAARVGVLPAVLQPEFTEFFQDHTVPGM
+TAGLRAADRLLGAEARDAASDFARQHDPDLIGERFAQVLRARLWAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002624.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7e0f12c5432bc491bc4c50fda1a218be66a2362
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002624.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_02102
+MADRGHYELPHSGHNGIELVGTFAYEDAILRALPRLPADGASVEAQFTVDLVPEPDNPHD
+RRAVSVRHRGEVLGYLSRDLAADYHLPVKRILASGARLQTGARVFAYLSWDDKPEVRVYV
+GLPAPDALTPLNDGYPATTAVLPYGRTYQVTKEDQHFEHLFDYVPRSGQGPVILTLHKSE
+AMLRNGTVRRTVEVRLDAEKAGELTAATSAHYLPVIEHAEALGRVVGVWGTITGSGLAAE
+LTIKGAKSSELTDEWLREMPIFPHLVPEAHSYEVPDAYQGEPKTKGRSRAMGGHSAARLR
+EQLDQRFVSTSPAELDTTPSPSTPSPEKKPGKPQPPANPTPVPLNRDVTRLGIGTGPRTP
+IYYTVKGKEVFVDDRDRSSAGKHPRRTAWLLIAGLAVLGLILSGVPGIGPFLTLLTLLLV
+LISGPDQLRKAKVLDIDPHGTGHPSRDWRDRERGDVGEENQDHDTEDGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002627.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c62d65248d695c1cca33a5d57c5eb3aab8ca9a0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002627.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02166
+MHSESLDPSPVPDRHGSDPDRPDPLVVVDGAEGRVVPAPTAAPSSTHDAGGDPASGGEGV
+DPAAAEPPTLVSVGVLADWLGLSPTEPLPEVPEAPAYAQPGRCRPRRLVLLDVRFRATGG
+GADHEAYLRGHLPGAVYVSPAQPTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002630.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4290aece867ff106065293aca92161d3909d99a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002630.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02204
+MADQNPTITDEQRGRLDQALTVVLTEGVPIQEVTAAQLTSRLDGGARKTVVLAYLREMKA
+KAPDTEDAIPAPPEDLATASVQALVRAVWEAAYTAARAEVAETVAEAVSARQAAEDAAAQ
+AQDELDTAREEFQRESSQLEARLNKAKEQVTRDAGAARDAATAATEARAREGEVRAQLAR
+EQERTAALEARMDALIVKLTEPVQETPEPKEAPTRSRRTGAKKTPASPTEPTKS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002631.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..391086ef31a05eb296856108366eb83f1687d789
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002631.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02205
+MPRVPIRVPLTIAACAALLTGCASGADSTDPGSTTGTTAGQGQSQSAQEGASQPADPQDK
+PKTGEQPEFASGNDLLASVNTDLINAGATACVWDIKSEGPKYNNPEAYFWAECDHKSAGE
+LEFEGSTDKPHGVEVIYWHPDPAVLKENVIGDSENPVWATGKNWVILTDSYISPNYPFYG
+ENAEASDEEKQSWRDRADRVRTETGQMLGVRFTDGRDAGNQLTTGIDGNGSGTSGSSTDA
+P
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002633.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4a6b83a5dcbb3e74440ee77fb2815b00a8e5280
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002633.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_02212
+MEPSATAPETVSTAAVCSRDERPPKKGHPPVEPLPPHEPMAPERDQELQAVLAWLQARPI
+QDELTEAVLQSVHYILDGASTGRVYLHDPEVDSDERSAVGVNLQYRVLHVLGLPKEAPLD
+TTIEGIPVDIKCTTGTGYGWMIPPEAQCELCLLVKIDAEHDRFAAYLMRTHRVWLNEGGN
+QDKKRTITAAARKQYAVQLFEGEWAPLPRNPLRDLTSDQRELVLNLHPDRQRGQETRIKA
+MFSYLPSTVVPRHVLETIGAGRTDPARRARAIRSQLRAEHGLILLCGKWKPERDAARSAG
+FDLTGRDWVAVPEADVDPHQLDLVLAQRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002634.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..879732db53ca1ad4e37f70cfe8f8806541e91ee2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002634.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02213
+MAQLNWTYEEVVLAADLVARNGWKGLRSADPRVAELSRLLRAATIHPLEGRPHNFRSPSS
+VQRKTFDIATRHPDYQGTPTRGGKHEAAVIGAFLDRPEQMHDLARYLHASLGGADPAAGV
+AEPAGVVADPEEEALAAWEGMTRAVRHLRRERDPKLRAAKITSMVAAGGRIACEICGFDF
+EQTYGAVGQGYIEVHHVRPLHDSGPVLTRLEDLALLCSNCHRMIHRARPWLTPGELAARI
+ADRGLVRGSRPDHAARLCDV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002635.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0abc910ac8e287df2a6bc25c312f50998b133401
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002635.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02215
+MTRRSGVDRNAIRRIARQIERDFNKEFERRPLRIPVEHEIAPGSPQPHPHVVNHYAGPVV
+TINGDHAQVAWNGGTNIGHREESQTVTPGFEQVAKVVSDVLAQADALELEEDERLELQQT
+GEEILTEVVKEEPDTGAIRRTLRTLKGFLAPALTAGASAAVSTEAQEAAQAAFDAIQALS
+F
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002643.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e76fa8ca0adb6812b4cbf1a8de97e9b890b77f1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002643.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02248
+MTAEQAREAGHQVKVASKPVATIAAMPRPKIEEDAHGVIEVVVDAATDLVLGARPHCVEA
+QGLVNLVALAMRADVMASALRDGIWTHPSATEALNEVLGELG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002645.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd774ba6e5e3a512ba85c9ba3c7ae8392dce2115
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002645.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02298
+MATGDTVAVGQELAVVEAMKMEHPVTAAVAGVVTVHVAEGDSVAAQALIAAVAPAGADES
+AEPAPHEASAQNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002646.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..baf0808b2a8daa3ef41201150b390573c0c6ca6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002646.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02325
+MWFLIALAVMAVIGFILRPISSLLAMAKFIAFAVAAVAGFAWYMGGPADMYAGPTILGAL
+AWIGLMFVPQPRFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002647.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cc5488607db4a95cddf89d1383380c9aea10a1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002647.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02326
+MSNQRHTTADVAAFESWLSVFRRPQTVNNRVHYATRLETWATAHGCTPWTLDTTQISAWL
+STVGK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002651.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b34a8aaa419e9bbdc7f98b102a6b8cd99948581
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002651.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02363
+MKVELLHIADCPNTGIAEANARAALDALGLGAVPVELVTIGTEAEAANTGFGGSPTILVD
+GIDLFPTTLVHSLACRVYVAENGFAGAPAATQIDEALRDRMQGGESDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002659.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a29b4055ccb5c722d7c8992cf15dd9cd093ddc1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002659.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02498
+MKTNIFAHGFSDNHAVSFGASRKGRVWSNEQARDIHDWVRWASQVGPTITDTSISLDSVM
+SGFLLPEPARERPPLVPLSIEWPYQLVSTFSDRRKVSHEDQAFSLLDTELSLTDHTADQP
+LRFEVKTPSWSLEFEFEFHEDGPPTIRPVSDDGQVVTPSGVGSLAAFLTGHGLLVTFEDE
+VVLVEQGFLLKPERERRLFPIDAVETIDWSGVNIRRESQGAERDPATIQHRAIQALSAED
+EWEVVLDDDGTGELADIALLRRTDDVLEVLLVHCKYSSSDTPAARINDLYDVCGQSMKMN
+RAKSMSELLTKRLFRREQERQNAGKSGLIVGDIETLAAIVFEARYRLLKVTVAIVQPGMS
+KSAASEDMRSLLGATDRFLAETYGMKLRVIASA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002660.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a02482faa2ce53b19a7cf4dc6a19040bd0cb461b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002660.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_02499
+MPVLRSLGPAYQEDLHGRNAAVLLDVLTDKSATAAKNIALAGHYGSGKSSVILGVQDGLD
+ERKIKWVNLSLSTLGIDDTKRARIQQDGSLAPLTNLIQKEIVKQLLYRKPPSDMPGSRYF
+RIDSFKPWPALMWGGVVAVGFFVIAVLLGLVSRIQDVAPASVINSHSWVAWATVGALGAF
+VGGVWFLGLRVLQNRIRVESVSAGGAAVKLSAKENSYFDEYLDEIVYFFQRTKTKVAIFE
+DLDRFKDPHIFETLRELNTVLNNSEQIKSRPIQFVYAVRDSIFEELQVDAESDGEGTKTS
+ALHASALESAPSANRTKFFDLVVPMVPFITHRSARDLLAAEFAKADHQPSTALVNLVGAH
+LTDMRVIRNIRNEYEIYRASVLGENGLKGLTADRLFAMMVYKNLHLEDFEAIRLGTSKID
+EAHRAFHKMVEYQTRHQAMRSKTTQNRVRTKALWDKHAQAAGERLQEVLPIVYRATGRGG
+KPVLRYQSQDYQLSDLTSGDFWKSLYENRDSVHLLRPGYGGIELSFDELISLTGNGTDGL
+DDAVDADVAHLQRDSRVALETKDFVMKATMAELIARTDLVMPTTDGDERNLDSIVSELLS
+PLGRDLLTKGHIDENFTLYCSDYHDIAISVSAMNFILHCVQSDRAAPHFHFDEASSIEAV
+EREMGSRFLDGESVFNVEVFDYYLPARPERLDKAMDKLAVRSGDDSSFLDAYLIDGKSRD
+VLISRLAPRWDGVFIHLAEKAPLELDVVATLVDAAITCAAKDTEYEASDQVAEFVSEHYA
+QMQAFVGETDAAKATDVMALLRRLGAQIGDLGVLGQTQRQAAVAAGLYPVTRMNLSVALD
+ESTGLALDVMNAADDSVYRHVLSNLDDYLDVLQDHEVTVDSPDAFVAVLGDVADAAEFAV
+RTVAARAADSCEVVDLTDLDDGAWGHVVSAGRFAPTVWNVSQFVSKFGVNEELIENLGTL
+NLTKAEEVDEEPRLGLAYALANSGALDSAATVRLLGQLNLPDGLDPERLSDVGLALLPTL
+LEKDLVPDTADTYALVSDRPFAFREEYFAASKQLASYVCELELSSDDLARVMRSRRLAPP
+VKRAIAHDVEFITDRLSRQSVIAFCEWASKGNDVSVELLVKLAEAGAPAEHVLGLLEPYL
+PNIELGLLDQILLGLGDDYEPLTRTGHHRPRLKDRAGTEELLKALQSRGRVSSFGREKLI
+GGIRVNMRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002663.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d4a0a12759d9278d96e11bd6ac8d044309c5b93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002663.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_02578
+MADAPLGPVPRLGSPPEGSGRRPTRTAGMLCLGGRPRRLWDHPTYPPEVLVDWSSVTKTV
+TAAAASHLAAAGALDLDAPFRTWVPEIGNVPATVRDLAVHRSGMPTMHPTAARGLLRDPA
+RGALDEEELLGHCPGLFRSLREDHGRPRYSNLGYAFLGLVVERASGEDWWTAVRRLVLPA
+DRLPTVTVDPAPDLQRRPGLGPLRVSPWRLSSSAYRPAGGLWSTLSDLLAHAELASLPTA
+SRLGWHRDPSGLLVHTGSGRYSSCCAVLVPATGDSGVAHSTAVPAPRLQRRLVKALLSHL
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002678.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e884f58487b201b215c32af04f91f164a3956bed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002678.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_02655
+MGKRAGLAPGTRSGLWSYMAAAIDALQPQLVVIENVRGLLSSPAVRAPLEEDDDAQSNPD
+HATPGDAALREVEPDPWGLGDLAARPLRAVGAVLGDLADLRYDTQWIGLPASLVGAPHPR
+LRVFILARSRGTVQDAARHGLDSWRRVTGTGEGEAGDDRALASDHRPRAKRAGWLAEQEQ
+RTRDAVVPDRGHLRRWGRYARAIARWEHVTGRIAPALLDRTSGPRPSPEFVEWLMGLPSG
+WITDPIHQLTANQQIAALGNGVLPLQALSAMRVGALVQADAASLAGVQHPMVSRGCTVSQ
+EEEGEDEKAGESA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002679.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..395db7a54124d21c4d0a4b52285d4be10c67a50c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002679.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_02656
+MPVAGVAGLAMDAAFPALGWWPLAFVSVTLSLVTLIGRRSWGALLVGTVFGAAFWFPHVS
+WSAQFLGEHPLSWVPWVALAGALTIYTAVLTVPIALAYRWLPRRRNAFAMRLLALPLLVA
+GAWTIRELIMGSWPYGGFPWGRVAMSQSESPIAPVASWVGVSGLGFLMVAVCAAAIEAVR
+WIVRAQPARGNATEHPRTPLASWAASIPVLGLAAVMVLVPQFPTSHAGTIRVGAVQGNGP
+AAYVDEHEPGAVLESQLAASAPLEDEQVDIVLWPEGGVDSDPLADEATAHALDDAAARYD
+APILLNAAAADGHLVYNTSFLWTSNGPTAAHAKRHPVPFGEYVPDRWFYGALVPSLVDLL
+EREYAAGVDTPAIEVDGVEVGLAICFDVAFDDVIHEGAHSGAQVLMFQTNNADFRDTDEH
+LQQLAFARMRAIETGRSVVNLSTTGTSQVLAPNGATLAALAADEPGLMIADLELRDGLTA
+AVMLAQSINTLIVSGTLAGFLVLAFLLLRDRASSRHHRVLDSSQRSSIGLHECADAHRRE
+RL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002681.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79091a0eb0bcaec034f46c6f595f3bc093ab071a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002681.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02659
+MRFTAGLIVLVSLLVAEFLWPESRFIAFALSAGLVVAALTGSCLMGRILSRMPWNKVTAS
+PTARSAIASIPVATQEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002682.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94cfabbe2ce3622d6e1d5f5971fafa5c55198ef5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002682.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02661
+MTPRRGRSSLALAAVAALLVTGCGASEPEPVRDPYPVDGSLPVVDTSGLQLPTPFEELEV
+VDPGWDITPQYADGVYLAAGERDGVLEFTAVDVYGDVLWAAQRPASCTGFVVTTDAHGRA
+LAILGDLQITADALAATTATAYDLTTGEQVWGPVEVPGPYQGPGLVFAAPPDGFMGETGP
+RVALDPTTGDVAADESSPEGIRIIGEYHGIVLLTHEDALIARDTADDHELWRIPLAEHGW
+TAASISASLRPEPGDGLALIATSETTGALLNLDQGSIVSSTARDAAVDPTTGTLVTLDDT
+GLHGYDADDRPLWSLPVAAETTIAAIGGVFLYLREDGAIRVHNVLTGDVAQAYEPDGQGP
+IIVPTHITINGAALLLQERRHLVATIAESPLNESFPTSSHAGMSIVGARVADST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002688.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..424b9881f86a68d669c7c37dda1afbb5c700e745
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002688.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02668
+MRTIGLLHGMSSVATVDYYRRINDRVNELRGGHERAELVLSSVNFGVIERCVRAEAWDEA
+GQYLAGKARGLQRAGADFIACGSNTMHRVAPVIEAAITVPFLHIADVVATTATDIGVTRL
+GLLGTAPTMEQDFYRRRLERAGFTVLPPEPVDRTTVDQIIFDELTRHVFRPESRETYIRV
+MTDLHAAGAEAIVLGCTEIILLVGPDDVPGLPLLDSTTLHVEAIVQTAMSRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002689.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48863f0118e4c0799272597bd95aa29f82f6bd70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002689.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_02672
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWGSSPS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002694.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b14bc3878601f4e8450821ca9f586b58ff26980a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002694.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_00036
+MTGQWEWTTLREVLVPQPNKKPLQQGWSPKCIPSPSPDSETWGVLKTTAIQPGRFDETQN
+KELPATLAPRPAIEVQQGDLLMTCAGPRSRCGIPALVRSTRPRLMMSGKMYRFRPVEGVD
+SAFLEKWLLSAEAQARIDAMKTGISDSGLNLTQDRFLALPVPMPGMEEQRRIVDIVEEHF
+ARLDVAEGSLDVADKRLEGLVESAIQLCLDWGSVRQVELRSLLAEPLANGRSVPTREDGF
+PVIRLTAIRDGWVDPLQRKGGDWSRNDAKKWLIRPGDFLLSRGNGSLGLVGRGGLVLDDP
+GEVAFPDTIVRLRPNREKIDLDYLSMLWNSRLVRRQIESRVRTTAGIYKINQEALKSIEI
+PVPSLEVQGRLASSIGGVRLAGRRIAGVVEAERRRTAALRRAILTAAFAGRLSGRSTDTE
+VIEELVASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002703.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edc06c195419bc62a3bc2f1ed6b7f44f1aa5da00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002703.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_00519
+MRITTREEALAAAGSRYAPVSAGGRSADDAGVMVGKPCEVAGRRQLDAANGVDSPVLLSF
+FCAGTPSQDATEVLLEREGIQRDEPLMDLWYRGRGWPGDFTALTRDGRRATVDYASSWGG
+ALGPTVQWRCRLCVDGVGEFSDITAGDFWDADERGYPVFDDAAGMSALIARTPRGLQIVQ
+DAVAAGRLHVEPMDLQALLRVQRYQVERRKYMLGRLVGNRLSGGHNPRYRGFGLLTLVSR
+SPRRVLHEVRGTIERAAKRRGGRGPS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002704.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa3c1762eb45e9ac149f847b88453f257626d09a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002704.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_00520
+MPNLNDFHRPALDDVTTVDPRTPLLPFLRQLARAELVVGSSLHGVILAERLGVPARVIRS
+DAEPSFKYEDYYEGTGRANVRLAADIHHALDLGGVDSGSTVDATLAAAFPRDLWER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002711.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bb34fa8f9cd67b10993bbe997aca6e504018d21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002711.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_00606
+MPGATPIGDEAEVPTLGAVDHLRVLTRVLLGPVVKGPIVRRPAAVGLAERLDADAAGVAE
+MQRLRSRYGAGPVQLRIPGRRIALLLDPADVRRVLNDSPTPFSPATLEKRGALNHFEPAG
+SLVSTPQQRLSRRPFNEQILETPRPVHSHAEAMKAVITEEVSTLGGHVDFTGTLDWESFA
+VMWARMVRRIVLGASARDDDQVTDDLRRLRARGNFSYLMPQNRRLRERFLRRLQHYIELA
+EPGSLAALVAQTPAPDEAVPHQQVPQWLFAFDAEAWATFRALALLTNHPGATGTARSEVA
+HAPDLPFLRATVLESLRLWPTTPLILRDSTATTHWRNGTLPPDTALVIYAPFFHRDDQTL
+PQAHRFSPELWLQERDDNAWPLVPFSAGPGMCPGRNVVLLTSSLVLGELLRQHDFTAQEP
+LDTGQLPGTLSPFSSHFTVRHD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002714.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d71714fc57ce9fdba98bd463c7a3d9839af00d0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002714.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_00619
+MGKTVHRSASTGRFVKTSTAKRNPRTTTTETIPSPGGATRSVGRSAITGRFVTTSTVARH
+PGTTITQQVSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002715.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be5c02cea9a8fd2e46a2b9ee830b7e443955bfa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002715.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_00621
+MVSAEHGPSGSPYGEVLPGVGGNDSAQDPLVTWWLVLYGLSNLVRYHPAAWRATLDVDKS
+TLAVPLEQLVSFASEKVPDLLFEAFVDLGGGRQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002717.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2bd27eacc893500cc905cebe72c212218bca3fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002717.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_00701
+MILADAGATGVARVRSRGGVYDVVVPDSGTDYIQGHLQREGSPYEEEMLDRMAAALLPGD
+LVIDVGANIGNHTLNLACVADARVVAIEPDSHLADALRRSVELNGAVDRVEVYECAAGAQ
+PGFGRLILHDPANLGTQSLSFEEGDAGQDVAFYTLDDLIQRQSVRMVKIDVEGFELEVLQ
+GGMEMITRDRPLIWVECLDYEAYEAVSSLLSPLGYRVVDVVNASPTLLFSPGGKQNDAGE
+RTGINAVMHRLYTERRIAESLRSKFQTITNDLEDPEARKLVTHLGALAELEIGQSAAEAE
+LKGALTDARRRIAELEARERLHLEDFRAIRGFVETVEDRLWSTRTVQAENEAAAERLRYL
+EDALELVTTEKEMALAEAGEMRATLRRIRSSRTFRAGRALSEAQSVSGASRALPRLLAII
+REEKKGRDV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002718.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3cd0e296cd07eaae39ff9db6561199b5d208000
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002718.fa
@@ -0,0 +1,13 @@
+>MOLHKGIG_00703
+MTARIAVVGSALTRSALVADPRLSVPAGHFLARVSMAGLGTPPVEDADLTGVASDFRREL
+VRRDVDRMLVADLVRLDPDAIVVDVADERFALDVLPSGAVVTVSPEYLESAPPQDGRRRV
+PSGDDEHFALWVAGWRTFLSTLDAVGLRERLILHHGGMAVRTADGTAARHEAAILAAARY
+ADRLADRAAQDLDPARVVRVDDAIRHAALADDGTADPLALAPAAAAALAAGVVAVLDGRD
+PWEVDGLVDVSPDAEPVEPAAPQAPAEPAAPEPSAEPAAPEPSAPYRDVVESDYANYGVD
+PVRWGSVEEFAASGFGPGLHILPLPDGNHLDLIIRGDLGGVGERESVVVFLTGAMSQRNS
+VAPPFFAGRRLSYELGIPWVAVSDPSMQLADDLLLGWYTGSPGSQAHATLLATLRALADG
+LGRDLLLVGGSGGGFAALRLNEELEGRSSVFAWNPQTDLLDYHPPTVRDYLRTLFPGKEL
+DPVAEREAVEARLAEEGIGHRVGTLDAGRRVVVFQNAGDHHVEGHLLPLVHRTPGMTGGP
+RRFATDAEHQVRIATWGAGHAALPAHVTARAVDAMRRGHSASTVATDIDALLAHERGDDS
+DGPDVLVTAEPGGLSRVDWAAFPGEADDGHACTLSRMHGEDVVDQVEHIGPPVVLPRLDD
+GEHWRLEAFDARGRRVHEIHVDGRGDPVLFGGTGGSARPRRARQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002720.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f89a6a75fee049bce3aa40cd33387507254d789a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002720.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_00840
+MKRPERPISSDWLDLRRPADERARAGSAPLLDALAEHFTETGADSPVDVIDVGAGTGANP
+AWLAPRLRFSQQWTLLDHDADLLELVPSQLQDARVRHVRRVTAGIEDLGSLDEAEQDRCL
+ITCSAVLDLLTMDQLAGFCDFLAERRMPALLSLSVTGDVVLDPGHWADAQITRAFNQHQR
+RGSLAGPDAVGYAAGRLRADGMRVEVAESPWKLGPADDVLLRRYLHDRAQAVIEGAPDMG
+DVVDSWLAEHLGQSDEGRLHVEVRHRELLCLPPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002721.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..505b42f6aad325f59b1a2dd1aa7a3efa5e598252
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002721.fa
@@ -0,0 +1,4 @@
+>MOLHKGIG_00842
+MYRLTVRDHVMIAHSLPDPFFGPAQALHGATLVVEVTWRRRELGPQSVVMDIGAATSMLS
+EVLEPLRYTNLDEHPAFAGRLSTTEAIAGHISDELRRHFDTTEFAGMEVLLREHPDAWAA
+HDVDFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002722.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e756d4bff0f1596b8794bd122de563b2fb60ccb6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002722.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_00843
+MRSLYSGVSRGTEMLVYRGEVPPEVAGRMRAPFQEGEFPFPVKYGYLSVGVVEQGPDDLL
+GRRTFCLYPHQDRYVVPVDALTVIPDDVPSRRAVLAGPVETALNALWDAPPCIGDRIAVI
+GGGMIGASLAVLLSRFPLGRLQLVDTDPVKRDMARAMGIEAVEPEALQAECDIIYHASTT
+EAGLAQGLERLGDEGELVELSWFGSHVPAVPLGTSFHARRLRITASQVSTIGRARRYRRT
+HAARMDLVMHMLQDPVFDALISGESGFADLPGAIAGLAQGELPTLCRAIRYPDPGPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002723.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc27e5254f225f76262b5a842ee6b84cba20a5c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002723.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_00844
+MRHPTTPFRRQAMVDVLCTVVGSVGLGVTLVHFGKTSAWGSVAAIASGLTLVSVAVVTMV
+RRNPLFSTLADRVTLSRAVLGGGCATIVMLAALDTAPHRSWWLVLLAAPAVLLDAVDGRV
+ARHTGTASAQGSRLDMETDAALLLVLTVPLAFTIGPWVLAIGLMRYAFVVLSWFRPAWRE
+PLDFSQFRRVVAAIQAVVLVVALVPVVPLTGACIILALSLALLLTSFLRDIITLERGTSS
+RGDREPTRVGRTCSSHADLSDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002724.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f430e22de24726f8e1d38fbcd3727cfc050cac6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002724.fa
@@ -0,0 +1,8 @@
+>MOLHKGIG_00898
+MLREQLGGRAGLDAAQRLRTRVGEALGHAALEQRPLPQHDALPRRGRVGSPVAGRLGLGE
+RLTAGLPEGGEHVLAWPRPVQDGRLRDLVRHPEGLGHHARHHGVGLVLLTEGDGPCVDVA
+TLQQGEQGAGVLPAGEPQLHRAAGEHVLDPIHGRGEGGGRRLGPLLRRVVLRQRRAQARG
+DLPERGGAPHDLQRPVDRQSRDALERGDVLEAVPRVQVVGQVALVPAHARPVSGGQGERH
+QERPVGDVHVLRVLRPVETVESGHGGPRGHPVHVAFHHHGRVLTPYRAVVPETGADPADI
+PDQLIPHGMAAGDGPPVPLGSGKRGATSALEHEGDGRDGGLHDHRLLVVGRAHERCVTVS
+DRAQAAPGEVEGETPAGPTRDGEEELGHAGSPPSKAGSRSPTPSSSAIAETVRSAARPSP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002729.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cd3b0c64c499c22182f5ad9bea6be6e88198419
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002729.fa
@@ -0,0 +1,19 @@
+>MOLHKGIG_01491
+MTAPAVHEASQKRLLGTQHAAKTPSQTPLAAAAYGGTPVAAAADGWTIEYVTDSATSQKY
+PARFAVLTKTVGRAGCTGSTTSFGAYPSVAAMGTGRDAIVVGFDTEFVSAEEVDEQRGWV
+GEDVHVVRRIVSYQFAAIDPTDPSRLRLAVVLPQEYHGPRGPRTARLSFEKALEIAVTAL
+GLHEHPLASGWSSQGVPRAEVVDKKGETRPGWWFNGRAGVSRALPIALVAHWQQADLTTF
+VDRRKAHNTWNAAYPERARKVSTRAGLDSRRGRWLDSSTSDILRAVISASAGMVSPTPVR
+MVLAGANKRWARPVEVSIRDTMAQSGAQPLRALGEAVGVAKLDVPGDWIARMDDYLLKDP
+VAFMDYAANDAIIALEYVSQVYGDHQEVPLTLPTAAARAVKGLMSGEIEARPDTFDDFNA
+VFGGLVKVAKNVEATTGVENQLDFYKKRELQPIDGAAATWIHASAMAFRGGYNMSAELGL
+FEQVTHDLDLQSCYPTSSATIWDVDYLHPDGVILRTVNNVELGLDDFAEGGPLTPFVGFV
+SFEFPESVAFPCLPVPAEGSMIYPRTSGGARGVWAVGPEVWLALTLGAKVTCQIGHFGRT
+LRTSDGEPSRLLRGAYKTLLDDRARAKREFGKSSFQQGVLKLMANSPYGKLAQGVMGQRG
+WDAWAQERDAVGGSAITSPWHASMTTGLVRAVLLAVLNQLHDRGYATPSCTTDGFITDAE
+LSVVDGLDLFGLGQLWRDSREALTGSREMWERKHFQTDLLNVTTRANFSRQPGGVLAHGG
+YKLPEGIVPDSQEDRDHMYDLMVSRDGALPVTMKVFPSMEELTRIENRLDFAPKVVHKQQ
+TIEFDRKRRPVPEGMTAHMVMVGEQVFEVAHVRTVPWESPEDALRGRSVDQGLKRWDEEL
+GEPVWTRSPVRRTRAQWQDYFKRLERLLDEDGRVAEAERLDRIAKGIVIAHRQEVVHIPW
+LGSDRPLAERLDAFEDFGLPRPRERFWSHARSKTERQIEIDLEAIAPYVAEMKAVDPFES
+ETFLQEVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002732.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02f04d7ee6bf1a97c8571e05ca937cd1d4ccab76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002732.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_01499
+MSPFPSPGRISFTKFTSPEGITDVLAGVVPGVTTAAEVLQDLAAAKLADPLWDDLLSYDP
+PFEPGKSRAAGSQVAVDNELLRACREGREDRFLLLWAQLILADPRLDAIVREVFTDSTGK
+LVPEMVNASKLGAALTARHAADPDEPHDTKAVSNLLSLLERCRLVEPVKHGKTIVGVERV
+LPTAHAVPAVVRLIGERLAERGFGAQPGRELDLALALGANAWLNLTASEFRDAFDGKTPP
+AAQPQSVPGALPEDLKVIATLLRRKGQVLLQGPPGAGKTYVARRYVDWVSAGRRADSRLQ
+SIVEALPDDRRTVPAIADEIVSRGLSAVWDIVQFHPGYEYTDFVRALVAQPHGQGVTFVA
+QHRIFSLVCAVGAELARRGYELEMVLILDELNRGDIPSIFGELLYALEYREEPVASPYTV
+DGTPSLTVPHNVRVIGTMNTADRSIAVIDYALRRRFTPIDLEASDSPIRGYTGFDDETAR
+EAALYLYERTRDALSEASQGLQVGPSYFLAEPDGEDGSIAVLATRFVYEVLPLLDEYTLE
+GEVDASRVESLRQELGLGQRAKQWDQGAALAAHLVAGQPWKPAAADPEVGEPEEALSVDL
+GGPLADGGDAPASGEDTRDQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002735.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17d15f502add5f635201c765eec6cd3d7ff0ad72
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002735.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_01508
+MSTIYRTQEWSGHGKQNYFWNEYRLEGDTVVKYRCNRFKFFDGDENVWEHTEDAQESWAK
+GDPNMPDWLLQYL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002737.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36b1ec92e71756faf55e7d0eb5f79154a41d912f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002737.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_01609
+MTFACGVAIAGLHVVNRRFITPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAALAVLAWL
+ILAVRTVRARRAGHKSAGQRPAGAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002740.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4076bfe825da7a6cea4bca17bfb388e7f480aba0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002740.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_01954
+MIDAATLTKDLRALVLEVEEDLRGVLQSRPEEDAAWKSKHGILVKEEQTALSWTEFRDGR
+ITQVAVAWVLATVFVRFVEDNSLVAPVWLAGPTEGRRQEAQDAQLAYFRQHPEHTGREWI
+RQAIRHLETLPATRALVQDSAHLHLPISGRMADRIIAFWREDDPAGGLVRDFTDDRLDTR
+FLGDLYQDLSEYAQKTFALKQTPVFVEEFILDRTLEPALAERPLEGFRVIDPTCGSGHFL
+LGAFDRVADRWAAAGATADEAVDRALESVVGVDINPFATAIARFRLAVAALQRAGETSLE
+TATPRHVRVLTGDSLLHGRQRPGTGESFDAVDLQLGGFFASPEEIDELREALRSGSYDAV
+VGNPPYITVKDKALNQLYRRLYPATTKGSYALSAPFLERFFDLARPESATTPAGWTGQIT
+ANSFMKREFGTPVVEKFLPTKDLELVIDTSGAYIPGHGTPTVILVGRNAAPEGETVRAVL
+GIQGEPGRPTEASEGKVWRAIAGHVDEPGYEDPWVSVIDVPRASLATHPWSLQGGSAPQA
+MATLDEKAHATLGSLNPDIGLSVKSGMDGAYFAGIDVFRRRGFETEQVAVVIGEDVRDFS
+LINNLRTFFPYSADGTRRDPSEAARRYLWPNRAHLTNQRDFGKVKSERGLEWFEPSMFFA
+RRYTAPLSIAFAFVATHNHFVLDRGGKVFNRSAPVIKLPAGATEDDHFALLGVLNSSVAC
+FWLKQNSYPKGGDPVGDSGARVSQLPWADRYEFTSTTLKDFPLPAQMPADRARRLDALAG
+ERAALTPAALAERAVPTADALATAEAEYDRVTRQMIAEQEELDWKNYAAYGFTSEPLTFT
+GELPQVRLGERAFEIALARRVAAGEATSEWFTRHGSTPITEVPEHWPADYRALVQQRLEL
+IEADRSLNLLERPEYKRRWAAEPWDKQVDAALRTWLLDRLDVPELWRDRAGRPTPRSIAQ
+LADPLGRDADFMAVLRLWSGAEDISTVKELTRLLTDEAVPYLAALRFTESGLRKFRAWQH
+TWDLQRRQDAGEDVGHIPAPPTYSQADTRKATWWKHRGKLDVPKERFILYPDAGREGDPT
+LLLGWAGWDHAQQALALNRIVDERLAEDASAERLVPLVAGLAELQPWVEQWHAEEDPAFG
+LPLAEFTRGTLEEYRRELGVTAAQLEAWRPAPTGRGGRRKRT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002742.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d46cedc2536a87a5ffc2953a84b42aebdf4916f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002742.fa
@@ -0,0 +1,17 @@
+>MOLHKGIG_01956
+MTRSTRRGTAGRITGAAVRSVIADAQRQGYAPSEDTPAVVGIYADPAGVAELGDVVVDGA
+AVTVLPAASTLAALDQVHHAPRGSWSALVTNRPEEDLGVGVLSALVGGVLRTPDLWETVR
+TDFAATGLEPALYGVPESMSVALGILQVTPDGGWPVVPGGALTRDHALGAVARAHLGLPQ
+RSLDLAGLLSWSVRPGLTTSIARLRETGTQALADVVLTWISDQAGDPRLAQLVRRLLLDG
+TPDLLVPLGLVLDVLVPRADRAGTTSAGDVDRLNAVLAVRGVPSRSLTRWADAALDEIER
+LLGSEDASTASEALLAAEALLDRIGATDAALQSAVLPTGLRHRQRLVAEAVAAATTVPAG
+YDGTPAELHAAASAGLDAVERAWSWLGSHRLVGVASAHVPAVRHLPVLESAVRLTRWLAA
+ERPEPTGLAALALRQAGESAWVDAAVARAHRGVTDTALSHALDSVLAAVRTVRDAEDRAF
+ALAWAAQTPHDLATDTGYGTAPDAVGLIEHTVRDHVVPLARHAPVLVLLVDGMSTGVATV
+LIDALLAEAGASWDEALLPGLTRRHAAVAALPTLTEVSRTAFFTGTVQRGGQAQEKAGFA
+ALMDAAGLGATELFHKAELQSAPDARTFSDEVAFALQDVDGHRVVAAVLNSIDDALDKSD
+PGGTDWTPDAVRHLRDLLDAARMAGRAVLLTSDHGHVVERRAGTLRSTPDATSARSRGPV
+PPPHEDEVLVTGPRVAGGSAVLPSSERLRYTALKAGYHGGATPAEAVVPVAVLVPDSAKH
+LLTAGSDSGLRVAPPQHPAWWAGSTHVPVPPPEAVTGPVPPAVHEPTPAAPPATAGAVSP
+EAGTTPVSAPASAAVEDAGLGAAVVASPVFQDQRETAGAVLLADAAVAAAVSALDAAPGQ
+RLPLAELGAVMGVPRSMAGGAFAQLTMLLNVEGYPVVSTVPGAVRLDRALLREQFELD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002747.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce2b1ba9870201e40963fb6506c8d1fd492c8853
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002747.fa
@@ -0,0 +1,7 @@
+>MOLHKGIG_02038
+MSTGLRGTQVITLGTAGGPRWWRHGGGTPRAGISTAVVVGGAVYLIDCGYGAGRQLVRAG
+YGLDDVEAVFLTHLHSDHIVDLTAIALFSTFEITQDDRDAIRLIGPGDRGALYPTSPHTT
+AAPTPLTPHDPTPGTAETLRRIVAAHATDLNERILDSLRPSPLDRIHAHDIVLPSNIAFD
+PDAEQPPAMDPFVVFEDSRVRVSAILVEHPPVAPAYGYRFDTDEGSVVVSGDTAATDNMR
+RLADRASLLLHEAIDLDWLVAKFPDPESPQAHAIRSHHERAHTSVADALRIADDAAVGSL
+ALHHLVPGTSGASLGRQLEGHHPFSSTVPSDLQVIPLASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002754.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0771a5e734bbf6ccd6e0d20e9a1dbe5bcaeab765
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002754.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00054
+MLIVLRGNAASGKSTVALLLQDRLDRPAAILSQDHFRRSIYAECEQDSLAHADLLEAAAL
+HCLGRGHHVILDGIFHAGRYGPMLERVAAASDDARFYAFDLTFAETVRRHAMRPRAAEFS
+ADEMASWYHGWQALPFVDEHRITATEAPEQIVTRILHGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002757.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..354c97802dd2cc8837594032bdd0d2880f3725fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002757.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00078
+MKRLNVTARLAAAVLLAAGLSATPASAASPLPVSDGVVAEAGLAPVRDGGVDSGVRDGFC
+TVFPFMCDER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002758.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36a0cde36ab4354f7a850e7c5a5709f2adce234a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002758.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00084
+MVNRTAKRAGWDYDALAFLMGFLGAAAGGFAVAFLQLLGAEGLDAFLGLTVLFGIGPVHA
+LVAALVSPPLLAGLRRVHPRWLHVLIAGGVQAGIAAGVASLWLQNADARHLPGYVLTSGV
+LLAVAWAWALRRSAWRPAGGPADGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002761.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b65f2feed591236b2d1a255ffa9a170bbed08abb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002761.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00167
+MDIPTRRSAVALAAAGAALLAGCAAPTPEITVVDDAGTRLFLAASPWEQREGESRGLLTG
+TLEVSEGGCLVVDDGAVGVPDHTSLPLAFPSGSTLVRESDRVTGVRAPDGATVLLGDSRG
+WTGGRVLVDDLERDARDALTQCTTEQAVFVPLAEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002767.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42ba8f2d6384cd08a48cf194b8e8cd5f4222933c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002767.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00209
+MTRTHPAENQHASGRYLDTTARDAEDLAAVADAAAKDADAMARIAADIVAQHAEDLAGIT
+ATTADDSQAHT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002773.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31f9b73e12df6d8611b5fe01013f48c5a46b1f07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002773.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00215
+MSHFPTDQEIGRRVRDAREDAGIKQQGDLVPLLRAAGLPWSQGTLSRVELGQRSVKVTEA
+AVLAEVLGVTVPALIGAPESTTREVLWEAYLGAENVAKVLRTVEDVYWETVRGVRDKARQ
+DDELRSRVQERRDKYLAIRSEDLRRQAIRDGDDVSTPEAWAAYTKLWGLDAIPAIRAATD
+VLEGLESADDTVGGEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002779.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ece59cab1426554403b19fac9e7f8336da89988
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002779.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00287
+MPDVLYAWPSAARVGRRVPKESLYGAGHVSPAVRELFVSSVDRITWDYKLAGGTIGISGT
+PEVPEIQVFRVRAKGDDVPDQVLAAIDRAVQQPVFFEVTRGLDDAEVRLGATYKIAGSAP
+AAEYARTAWLPACAPRRPIPTGVDMAQVYAQVLRPLLGVRMEPGERPQAIAARLVALREL
+ERRHAAVASRHRRERQFNRKVELRKELKGIEQEMEQWR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002781.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6239852a508da83629b630d7c6cc661072dff16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002781.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_00291
+MPLTLTPNESAQRALHLMAARLEPIIARTLAPHLGGLEWTAFLDVMDDVKGKPSYPYNRM
+DPQPQLRILTERLGNLGYPFGAGRSRMVSALGSQLRIARNMVAHNAEIEPLDAWRVADAA
+SLLLGELGDAEGAQELAAWRDQILRLDAPADDEPDHESGEDLHDGEGGAQEAAKEVTAPD
+AEVFRIQTNEPSPTVGAGLRHERQPYDPWIPGAAGEKSVLDGVRSQHNKDLLRSVLEEIV
+EHEGPIHIDRLATLAGRSFGFGRLETKRKDLLKRHVRKCPGLQVRGEWVWGDSVDPDQWT
+EFRPNDSTSERKFVEIAPQELRNASAFLRTLHPKDDQATHERRVLQTFGRRNKSKAIREH
+LARALD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002787.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d30c8028c99947c91bc188423711ac533279e560
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002787.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_00322
+MSRHHGTLTTGALLALALTACGTTTPAPALSSTGTSSTAAPTSAATTSDSPSSSASEPAV
+GGPKTARAFGPATWAIKPEIDTIALAKAHVYGNRVLLHTATETVAYDPQGQEVWRLTRDS
+QTPPAIVPMSPTVIGLVTTGSSDNSGLAQSKPQTQVQVVDLADGSTVAEHTLDAVTNTAN
+PTAPGLSLASPDGGSEVITPDGAIRTLEDVDMAGAVGDTVITSKDEVIGTDTWSSEAFWD
+EPQYTNAAVAAANTTDLLLIEGQFGVEKTNVLVDAATGTEYARPKCGAGAFYKPMVSSPN
+GDWNVSYGAVISPDHKVTCIGGGEDEKAVDLIAVTDQGRAFGTTTEGPTLLVDARPGAEP
+TTEELAPGTVLPSGVVGGNLAVHWDPSTGVLSANPIQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002791.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..515f918e6d01181b7be0225c655fa1fc5d32dba7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002791.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00338
+MGFSLEMTDINVFQKANTESAVSGEELMQEIENLRTGVEALKETFKGQGATSYNNFMVAV
+NDAQNQLAEALGKINVGQADVFQAYVTQEDEQVSTNEPAVSEAQSFSFPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002792.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4753677503dca56226c76d5be6ff7c80e9dfa0a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002792.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00339
+MDHDAQLIEAVTVRRHRLLTALTHGTNPTEQRWHGRGRLYVAGAVLAAVICALCVLVSLV
+ISILTAWLDNREQVEQQRQQQQIEQQQRQEERERAQQELDDERQVTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002795.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c9e8317fadb41f47e73b949fe16e43feffb2686
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002795.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00348
+MAEKFGWRPNDYLENPRAFGKEDTSPAWRETWFDGTVIQDDPRHHDRQIAAKIQHLVAIE
+VTRAARLRDETLADVSKHTRMGADQFRRLMRGEGPMQVVDFATFRRVYHVDFGINPDPGL
+ANIRETKF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002799.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25fb3cfbca7a5dbf65c1f2437371ad14b7a2119b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002799.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00365
+MEGIRNTTHTPALGRDDARTDGGGPLSWVEGRPASERPPGGWGPSRAPADGDVPAGDRTL
+WEDGRAPGQRGRWWVWLLRHLAAAVACGAALVITAGAVMAELFAVADAAAPYGSLPLLAA
+AAAAVGWALMLVVLLALLIVGVFGGWGLGGTLFRASGPGVWSVWDGEALTEAMGAMAAAS
+TGLGRSSSESAAQATRSPRWRRFLRWTGHAVRWVLVALLVLAAGAAAVLGAMGPSPTTLV
+VWGSAAGLVVAAVLVGCGVIGLEPGPDRSPHTRW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002802.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaddaff2366eaa3d2dae0d497620d8572d4ef478
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002802.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00411
+MTVDAGVLVGENGRVRGIRASSWTPERQRRVERLLRVVEAAALLLFGVCAAVLLLTEPRL
+SGTIRSVSVEGVGARLSRYGLLFAAAVITYVPRRWKWALPGYAVSALFVVGMVKMLEGAP
+SEGFPGLQVFRTDLPWLIGLLLVPQVAGVARRAGLSVRRRYASALAWTAFVEGAGAGRND
+CGCVKNRVVQNGAQETRVLLQRFDGTRRSGQVWGVVEPSECIEVDAARAVVARTDWRNAL
+SWAALDRWGRRLPGREEAQRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002803.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd1d11b3ddb722bd78972bb1b8901cd457c15a96
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002803.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00414
+MSQRPACPYLPLPRATTLRDALVYTRASMSRLPDVVHGSLPLRRLMEAARPVLTAATSLL
+PLQDVLAAAAGAVLALSALLWAVLFLHRLLLCRGWHGHLVYTTDGRTAFLTIRSTSQGWE
+LSDHVATRSAKGDGRGLREALAPALRNAADAAGAPILVTAANRTLADLYRQEEPELREVG
+TTLLGRVRLVRPPRRAILPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002814.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d4055f5bcc6f5f01ad6d8a0381d2ca24214e179
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002814.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00513
+MDPRTRTRRPLLPLTTAALALALGLTGCTGGPQEAASSAAASETTSAAGDVVRGGAEIDA
+PESAEPLSNARAAAEGDDRAASARASHEAAASSEATAVPRHAVVTLPAALFETGGGGTTF
+DAWARTTDAWQADGSDPRMPDLGGWDPKTEPVVAEAVLPADQDSLRNPGVLTVPVSGPGV
+THRLVLLCEYTSPRRDEETAGVDVVAGETHAAIASSLGCTPIDVRHTVRPEHIVDGAVRY
+EFQVAPLEAGRLAVLQGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002818.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9454899550011a67137312fd07478d2182795ec6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002818.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00530
+MSSSSPALPVTALRFPEHSAPRPGVPGADAPAGPRTRGAVSWGVYLAVCAVAGLRLPAIL
+EATRDRIAAEAGADAGGGFVDLALGVTGVLAVVAFVIVFALYVSTARLLERHTLAPAPGS
+VVGAHTLALGCTLLSVHGAALLTGTLAPVPVRLGIAVAASAAAVALLRGQLPTGSAPRRV
+AAAATVLLLSALSVAF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002819.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5edcb0bac2ea4a1e950f3baf7af8f4301e3b224
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002819.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00531
+MRLTTTHLRIALGAVGLLGLGVLATLLWGGVLPAALSSTQRGIVLTAAAVAAVAPLLGAV
+LPVTRIERPSSAVLPSLGLFGFGVLFTDALDVFPVRIIVILGGLLALAAVVAALFGGPER
+AEAAEVPERTAHRFH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002821.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74d00fe285328100c879c9ef5de9f823d569ea56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002821.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00548
+MTPVRGDAGTQALAAVVAATRDHRMTFPIQARVSLTSPHQPEPEVYEVRARGDGGFAAWS
+ARHDLFYDPRTGQERLVVHASPGREGFTREWVWPWLSPSHRVLAMFAPAELGIWGGNHDQ
+HRVCAARWLGECAVRVDLVRREEPAGSEATGYAEVDLGNAVVTRMLLDGEAYVLEAARVV
+DDGDVTGPVVGPHLPGWPRSFVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002822.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac22aab4c0908d64708885e6a24ea6879c8b9f57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002822.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00562
+MITSAGGTWLALLLCGLQAVLTTGTVTLVTSGVQTFTASLVSAVPADQAQLAVLNIDDAG
+VSTRLAQEVRREIDAPEDFGYRQVEAPTSAQDGPVVVVETPRQAADVLGLRKLDPQAEEG
+LRQGGALRALQAPEGELSVVDPHAADPTRVSARLATFPVIVVEGAQGSLAQGGAVILAST
+AARLPAPVSREVAHVFPRLTPEQQALAARLPQELHVNPDWMDLPKPPDTMPIPPAVTCGA
+AVLSAVDSALGVLTVTALQGVPLDLHVPWTLVGIMAGGTVLAFVGALWLALRNLSVRERM
+E
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002824.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53551e758d7c29311497738c01b4a8eca4425ac9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002824.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00605
+MSCRCILLGSVGCAVAVGLHLLAYADLAHAGPWLLAGAALWGFMVLLGNITQAAVTARAC
+PEGTLGRVTAMRRTLTRGSVPLATLAGGALGAMLGVGWALAGWQVLAVVSLAAVVPASRW
+VDAGLDDVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002828.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0daf57beb8ec37edc8b766dfb7c071d828701b00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002828.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00624
+MNTDRDACAYLEEILREVTPDEEARKKAASHRASLEDWLKKDLDIIRMRETGSWHHGTAI
+SRHSDVDYFVTMRGSRPSASWSALEELRSSLALGVSSAIVRTDRPAVNLMYFDSGPSVEI
+TPAYFRDTDDYDIPDPGGTGWIQSNPAVHLDYVNDAQKKTSSRAKSLIRLVKTWKARNSV
+PLSSFYLEMRVAKYALSNPTIIYDWDLRSFFKSLEGDGLREMNDPTNYGRRISTGASSLV
+DTIAAKYDIEQAVRSSSLALKAAQDGNPSLGVAHWRRLFGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002830.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc395c25cc5f5d10f0d3a331af4f206b10ff2226
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002830.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00632
+MTHQPPAEPAIIPSDTTHDQTADRKRARQWLKTLNVSPNPELVEGLIPLVSLYPKKSVLG
+FYAGRLLKKGKLPTEEAVLKLLWGQLEQIIYSIKALESRTGRDPFITPEQETEILQWVDN
+FWAQHGEGPLWSELAENFHWSRTQQNRLIHYLAARGLVTFSFAPRSLKTVRGATTIPSLE
+GPGSGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002833.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..028001211fdf9200968a6317b75b854204fd9268
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002833.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00647
+MVTRTESLTDEQWALVESLMPRPDEAGRPFRDHRMVVEGIIYRYRTGIAWRDLPSCFGPW
+QTVWKRHRRFSGDGTWDAILTALLGRADHQGLIDWEVSIDSTINRAHQHATNLPRTTGGL
+GELHETAPGAC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002835.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f15e6411b87f7928201524bcf8fa127cf3634056
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002835.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00657
+MPLTPDMWWPPAVLALALFSDAAMSLRPPRFIRDCLNGVGFPREWWWTLIVIKTLAVIGL
+IAGIWIPGIALAANTGVIVYFLSAAAAHIRTRFTGQAFWLNCLGMLALSIAVLILSFAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002837.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dc8b69d629b9b0d696056a3e3192f9a43a617cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002837.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00660
+MSLQRVPLAAGRRHSLVVVDGGRVLAAGPPGAGECAVTGWSDVVAVAAGNVHAARNTGRS
+HSVGLRADGTVLAVGWNAHGQCDVTGWSQVVGFAAGWRRTLGVRADGTVLAAGRRDDGAC
+DVGGWSGIVAVSAGDWHSVGLRSDGTVVATGMDTRGQGDVAGWSDVVGIAAGYLHTLGVR
+EDGTVLACGDTAAGLAGARRWRGVAAVVAGSYHSLGLTQDGRVLAAGDDGHGQCSTQTWR
+DVVAIAAGSTHSLGLRSDGVILAAGNNADGQCHWALSAPGQYN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002845.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9288a2307b959121c8a598b77790867f4b0083d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002845.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_00701
+MKNFRPFPKYGGTKTAAITVVVGAFLLTGCTAANDSSSASRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002847.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9ad43020f70a91e0ff463a407720b7543a25590
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002847.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00707
+MPRFSRLTPETAVGASRDLLGDLVERHGQVGDMVSTMAHSPAVLGGYLDLSKAMRRAKLD
+RKVSELVSIAVQSKQGCGMCLASHISAARSLGVSDDEIALAQQGTAMTSPVAAMIALGLQ
+VYREPTSITDEQIDELRGYGYSDREISDVVGVVSLNILTGAFNLVAGLTPGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002852.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0101895a3932f92bc71042f298d53f655f3d147
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002852.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00719
+MKAGGRLALYGAGLVVAFGGAFGLAGAVIPDSFAAAWAEGSGVNAHGEGHGDAAQETAEP
+ALNGVSASADGFVLSPVQAPTAAGEDGDLSFQILDESGEPVTEYTTAHEKDLHLIAVRTD
+GAGFQHVHPELDTSTGTWSVPWTWDEAGTYRVYADFTPAGEEAEGITLTRAIEVAGDFTP
+VETEAQPTDEVDGYTVSLNGDLTAGTSSELTISVERDGQPVTTLEPYLGAFGHLVALREG
+DLAYLHVHAEGDQPQAGDTAGPDIGFAAEAPTADRYLLYLDFQVDGQVHTAEFVIDAEHG
+DGTKTDDSHSDGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002854.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84b0719269153f0738f1ea17637b6b0db56eb1be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002854.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00737
+MGQTRRMPDPHELIAAALREQAAAERRLHGAVQAARDAGWSWTQVAEVLGVTRQAAHRRF
+HVAPAVALDDGGARGDGVPADVAAENGPGGASDPWAEARAAAEATVEAWLRGDVAAVHAR
+MTSAARAGLPQSALRGVLLEIEDLSGGLRAVRVTGVHDLDGELLSGEPASGGPSPAGGAG
+RAGRRRAVVVRCVVAGEDADPVVHVLIGPGGRVSGLSVRISDELEQWPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002858.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79d3fbdd844ef6ec74831c7a3db249d58b6ab11c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002858.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00782
+MTGAERGGAVAAHPVPTHPEAVPGDRATLRWAVPAGLLGMVGPVGDGPAPLEALRADGTL
+RALVAEPAALRLTVGEGRTWRAEGARVRAALQEALALLAAGEATCAPEAPASVVGGPGGG
+GKARAVARAGASADSDAVLRAAVEQVLAGPAGEYLRSHGGTARILGVEDGEVELALGGTC
+HACPARGFTLQMRLEAEIRRLCPDVRAVRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002860.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a6a71e75c17cdf015fb6b84f5e00a3c1a60daac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002860.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00822
+MAPGGVGGGLTGRRGVRAVPHASDRVRAPQDLHEVDGQAYDVVFHPGGPGREGAVAAGGP
+PPVRPGLTVPPAILDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002861.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afa12c85946153a108ae23b03c7da6c5c21f5588
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002861.fa
@@ -0,0 +1,13 @@
+>NAFOICDF_00824
+MSTHPHPGDGAGIAASAAPQPAPGSPSSPAPTAPSSADRSGGHAAPGHRPATAERARTGM
+LMLAIGALGVVFGDIGTSPLYALQTLFSADHNAVTPSFAHVTGAISLVLWSLILIVTLTY
+VLNVLRADHHGEGGVLSLATLVRRHYDEATTPDSDTDVAQDAAAPGPERRRRGQWAFTAG
+LIGCSFFFGDSVITPAISVMSAVEGVAVAVPSLEHWIIPASLLILIVLYGLQRFGTGGVG
+MLFGPVMAAWFATLAVLGVGPLLDRPDILVALSPLPGLMFALQQPMVALVAMGAVVLAVT
+GAEALYADIGHFGRLPISRDWLFFVLPALALNYLGQGALILDDPGAVANPFFRLAPDWFA
+LPLTILAIAATVIASQAVITGAYSVTRQAMRLGYLPPLAVRHTSGKEAGQVYLPLVNWIL
+LAAVVLVVLMFRSSVALATAYGLAVTVTMIITTTLVLVHMATTWRRPLWQPVLLGTLVLP
+LELSFLAGNLVKVFEGGWLPLTIGGLVLGTMTVWHRGRVAVSHRWSRTEADLETFMAKAA
+HHVETGDLRRVPGHAVYLAPSARLAPAALRINLRANRGVHEKITLVHVVTEEQPYVAEAE
+RCTVREVGPLSGVHQAVIRVGFFDALDIPGTLRAHAAALGLTNRDLVQAVYVLSRSRYLT
+PRGHGPKTWGTRAFVSLSRLADQPVWQYGLPVDHTLEVGSRVRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002864.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33fea63a77d9e1990024de5442e4bc25cfb0c44d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002864.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00871
+MHRTTITAPTSSRRHRSAGVAVGLAVVGLVMTACSAGKAQEPRPTTSAHVQAQGEGASRR
+SRKWREPGRWSTT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002868.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2320f1eb9ebd2746ba151c92fc2b56b72f1086c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002868.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00917
+MGVGKTTAVTALSDVSVAGTDVRRSTLAFTEPAQDGKTTTTVGIDYGEWTDPEGRRIALL
+GTPGQVRFSSARDSVTARRARLVLWVFGQRPDAAFEIGRWLELLGDESVWGRTVASLALT
+PGRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002870.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e922fbe051b604a656799ab5a0fbae3e97542e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002870.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_00927
+MPSHPRLRLTAGLAALALALTACGGAEQQPAAGSPAPASSSSSAAASTSPSSTASASSDE
+ADEASSSAASASESSAAASSSLGASTSAGAPSPTDGSGSWSPSAAGTPSAAGSSSASAPR
+STWSPAAPTAKPSAAPVHAAAPVEADLGGPTTGVAPADTPVAVSSTAPVVEKADPVHVAP
+AHPAAPSASQAPSTTQAPSASSSAATRTPSASASASASSAPAATAPAHTAPVPHAGVDCR
+AVKCIALTFDDGPGRSTARLLDILSAERVPATFYLVGHSAEINPSLVKRMTAEGHQVGNH
+SYDHPNLTTLSPAQIASQITRSDAAIRAAGGRPSTVRAPYGALNESVLSTFGGLPAAGNV
+TWTVDTRDWEHRNPAKTLAAVQQGATPGGIVLMHDIHATSVDAVPAVIAYLRSQGYTFVT
+VDTITGGVTPGTTVRRGMHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002872.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35308a28ec89a7f3a0d415bd57ce14d27c4fe642
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002872.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00940
+MSVRQPRIYTIPCDRRGDFLDRWQSTAQPLMETLGFRFVRTWEGTPDPVHRPHCRGCWAP
+RSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002877.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cd569fb4d758378a0c4123559894e4e79bde53a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002877.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00978
+MWTHALTGLLAGLALIVAIGAQNAFVLRQGVRREHVGLVVLVCLLSDAVLIAAGTAGVGV
+LVTAVPWLLEALRWGPCCGSPLSATVLACWPRPSPARPPGGCSTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002881.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec358d4539c3a35cbc28dd16434772f40a527512
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002881.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_01030
+MTIERSSAPSGGPLPRGIQHIGVTVPDLDAATRFLADGLGAKVAYDGLRPEDEPRSGPEV
+ERQLGLPAGAEIRRQRMLVIGEGPGLEMFEVSGEQRPASGLSDLGLNHISLYCDDIDGSL
+ARLVAAGGEALSEVHGNSRHEDTPGNGSVYVRAPWGMLIELQTIPGGHTYPADAEAEVWM
+PRPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002885.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b41099cfbbfd3edbe9507c0ddc7d3bf452eeca24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002885.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01179
+MSTTTTAPGRLFGYARREFVRNVRMIEGSFFIVVLPVALYLMFGALSDWGDLPVGHGNAS
+AYTMTGMAVYGAVMATTSIAGSAAVERQSGWGRQLSLTALTPGAYLAGKCLVALAMAALP
+VLAVLAAGALTGAELDGPLRWLTTGALALVSSLPFALFGLAAALLFRSEAAVSAASGILV
+VFGFLGNLFVPLSGIMLDIGRFTPVYGAGALARWPQMEGERAPMGTEPAAADPLWLPIVN
+LLAWTAVFAVVCLLASRSRTARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002886.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2eba147309b89ee484d10000947c817da303873
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002886.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_01183
+MGFVSIQDGLISLSPAGQKFSRDPSRDRLADQFANRIRLFAEALAVLSEGPKTINEINEH
+LVQSYSLSTWKTVANTRTRMTWLEVLGYVEWLSGNKLQVTGEGIDALARWELVTPEAIQL
+REEEPAVANIPPAPASIEALLDKLTRDPRAHESRNTYNIWVPSPASSPNKIANMRICIEA
+TAEPIEKEDLLSFIADTFGLKRSSVESMMPFMRAAGLIQEIRRGVYSATPAARAWLETGS
+DLDYVRIIHAHMRYVGEILRVAAPEALRSEVYAQGSQYGMNRDKVRWILNFLVEAGLIVD
+ISWSTIASTALGKAFAASLPLAPPNADEPLNPASQSSFAGLEDDSAEGITDSNSESLLIA
+QHLRRYAVDPFAEGVASGAAFENAIEAAFGALGFRSQRISGSGDTDVLVQWYDEDGQLCT
+AIIDAKSSASGSISHTNVSDVAIASHKEKHSADRVAIVAPGFSGETIRATGAKRGWALLT
+ADDLAGVLETAVDLGLTPVETSIMFDSSDGFSRLTELIDGRKRQLDLISLVVARLWSESE
+NDEPFSPRDISLVERKSDLEPTVDELVGVVSRLNALDSRVLRTVEASSDPKHETYRVGDV
+QAVARQLRAIARALEFGLDPKRQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002893.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c98c11f925c04caf3a2809137be116c0503b9e00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002893.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01224
+MDAAQLPAFLTSGTVEDLMADAAAPAWGTRAFVEQVMGGPVSVHVRAEDPRRADIAAAVR
+RVWDLLHRIDAVLSPWRTDSDLLRMRRGELDAAAAHPWLAEVRALTDESERVTGGLFTTD
+LPAPDGSRGWDPTGLVKGWAGDLAAQVLAGVPGISYAVNAAGDVRVGVTPGGPRDPWEVG
+VEDPARPGQMAVVVSLVEGALATSGTAARGAHVMDPRVVVDGHPAPATPQLTSVSVLGPT
+LTWADAWATASLLDPGALAAAGPAWAAYRVVSRTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002898.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9d9cab36b593d4bd2cb15f8210a20c151d8b186
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002898.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_01336
+MSSRRAATAPPGSAPGGAVPVWSASRARRVVLGAQGLAGPRPAASARRVAGVAARLGVVQ
+VDSVDVLARAHLMPFHSRLEDVDPAHVAALTEGRGRRFTEAWAHEASIVPATSRAALTLL
+QGRRWPLATALPEDRRTAAAADIRALLAAHGPLTAREVRDRRASPCGPGTSWGWNWSEDK
+RVLEHLFAEGSLASAGRTASFERRYALPELLWPQGESGRAPVPPEPAAGGDARLAAALQL
+TRIALRAQGVGVADEIADHHRAPVTLTRRALEVLADRGEALEVRLDLGGTRPVPAWADPT
+ARTPRRAGACTLLNPFDPAVFHRPRVERLFGVRYRLGIYTPVDRRVRGYYPLLLLQGERL
+TAQADLGAVRRGPDPRLELRGAWSEDPAAHPGPAGPAPTPDEVADALAEEALRAARWRGL
+PRVVVPEGAPGDLTPRVRRALLERDGGRVPPGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002904.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..510407d056b1e1b057a0802b34113ccb47201ea0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002904.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01593
+MRAGRRSRSLTSETEAKAGSCTTKDGKSYKAFGRFADEGAWWDAERGGFVFDASFDKAFH
+DGQIWFFDVKAGTITIDAYYPLTAPNFSEERRSAPAADRAAPGGPQLTNKLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002905.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8512ffffea2786472c0e2b96baa9f599c2c89d67
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002905.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01708
+MPRALIVVWALLIVPVLFCLVVVGGSAVAHASSSAGPATLRSALPLGAALLTAVAGTAAA
+RHARAPAARSVLTVAVALLLLAVAAPLVLSLFAAGTEEWCEGQPGGRGGAPITSEADVPL
+LCR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002911.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5004528e72bbeda55edd6b4b9d6569548d9b7e2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002911.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_01768
+MAVTQWPIEMAELSSLVLDPRNVRVRAGRGDGLAHADDEHAEQAIAKYMVEAEDLFDLMR
+DILRDGYLDNEIPVVVRDADKFIVAEGNRRTTALKIIANPKLLGNPMSLRVERMKARYPD
+HDSPTSIRVMIAPTWEAAQPLLARLHTGQPKKSWIREQQAIFYHAQLSDEVTVDDLRVRY
+PSEASTIPKKIRMGEMREVIRRLKYDDSSLRDFVMNSELKMTTFEYAYTPKKLHSALGLE
+FTKDGLLVSKDISDGQRRGLIYLLGRFKDKSLNTRSPELIAKNATEHEEFSKLLRGIVEG
+TPLEASTEDEGATKDHTNNQDGEPGEASGERNSAAPDDISRDEGRHRGTSETDEASTSGD
+ATASRGPNRGDTKSRLNMEGFEYQGTSPGMRRRFEELRRLDVRDFPNATHDLLRTVLECS
+IKDYFQSKGQPLPPGKTIGACIGELAREFQGNPKMTALINSINRKGRLTAEQYAGTTPSL
+NASNHELDHFAVGPDVHAAWDRIQPILKEIVGTKKQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002914.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3544fcfe0d5a6254331402cd6ca5fdec5575b711
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002914.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_01777
+MPMSSASQAPAATTEPPGTPSGWIALTAIAPVVWGTTYIVTTHLLPSGHPLFAAFMRTLP
+AGLIAVMIARKLPHGEWWWKSFVLGTLNMGVFFPLLFVAAQRLPGGVAATLGAAQPIVVA
+LLASAILHERLTSWRLSWAVVGLLGVGMVVLGPGASLDPIGLMAGLGGAVSMGSGVVLSK
+KWRQPQGVGAVAFAGWQLTGGGLFLALPTLVVDGIPNGIDSRAVAGYAWLGLIGALMAYT
+IWFAGIRRLSVTPTALLGLLSPLTAAALGSLVAGEALNIIQLCGFATALTALIAGQLSPR
+ARRRVLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002918.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978fb06acbf37860c181a87021f7abf7c1762eed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002918.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01782
+MTHTTTPTTGTAAETGRGSSATPSTPHPDRADFRTSEGLRALLEHLAEHGWRNNPQAKEL
+LEFAAERFAPLARKHGLDVWEAASAAFDVMRTPAARKAADPWAVVTHAVRITCIYEERAQ
+GLMCSVHQARRAHISAHHDPERFSDRETPLYEYHPAFHLTDLHHREDAEPSEDVGASVQA
+AVADATGLFALLGWPEASARAGVDHVTNALARIGSRRGTYEALRRDKHARALLDLPAPAW
+TCLLRVLLGHPEPAYATTTAGRGILLRLLLGETLADLLGDDALVASIVRATPGRGRVRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002921.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49b930a358aaea4c6e758c879f30afb3d682cebb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002921.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01789
+MSPADRLNEGPDRPRALALLNAVLEREGFHAFYAEDNHCYLRHMGTQSVTVLAANPHRPF
+SKAEQERRKLLAAYLDSCSEDDLIEKILLPMFRQLGYHRITAAGHKDKSLEYGKDVWMRY
+TLPTQHVLYFGLQAKKGKLDASGVTKAGNANMAEIHNQALMMLAHEIFDPEVNRRVLVDH
+AFIVAGGEITKSARNWLGNALDASKRSQIMFLDRDDILNLYVVSTLPLPDEAQPSSPPNP
+WLKTDEPPF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002922.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4983b5f91d536d3c2453b9d903790120276f09d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002922.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_01791
+MGVCDLPVISGVCETAGEAAASLVSAPFDWLAQAMGSAAGWLFEAVWNVFDATTLVDITS
+DGYLSVYNLLFGIAVFVMLLFFCLQLITGLIRRDPTALTRAALGLAKSVLGSFVVITLTG
+LLLEVVDQLCVGIVQAAGETTESMGEKITILAGGLTAINIAAPGVGAIITIFLAGLAITS
+AAIVWLSLLVRKALLLVAIVFAPLALSGSSWDATRGWISKWAMFVVALICSKLVLVVMFL
+VAITQVAAPIDGDLSSISDPLAGVVLMAMAAFAPYLTYRFISFVGFDMYHAIGAEQDAKN
+SLNRPIPLPDRQPGNPQQVLDGNNSGNGGGGGKQPPKPSSPNPSASQGGTEAGAGTGGAA
+GSGASGSGAASGGSAAAAGPAAAAVIGVQVAKDAATAGPKAGAELGQQAETAADAADHTP
+TPNGGAGNGGNTPPAPAPGGTPPQPGTPPASTQPTPPSTPSSQPPGSSSHGGGEQVSPSA
+PVPNPPPADNPPPPSSAWKEPQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002924.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce3ef10507057e02ed727a2316add4d4130a49f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002924.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01797
+MATFVDPVADAAEAYEGLRGLAHATRAFEDPADTYRVLGEVSGSVRLLRQVLDQLSRAHA
+EHRDIAFTDDRVPAEAVALAAADELHQAADGLDEVADRVMRAHEASGRIAWHTHTSLEPE
+RSQRWVNVVFLQGTEADEVLELIDVQGVQAGIAHLAQWDFGDETTGAAFVNGEVYHELPA
+GQWDCTFEADGYVLTYNPQMGYVGLVREHPDTAPDPSHDGDVVAARDAFSGVTSEPSRRA
+AAGTDWFAPKAGGAAASSSVGRSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002928.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb94c8a55ad82f4daf6415effc834f6129a47a7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002928.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01803
+MVRRYRRATARVEADRPLRVRYEPREEIDAAKVAEVLIRIALRTAGDQPGGQSGAHLRRL
+LVAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002931.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7716bd5a769b585b3f40dc6c547426a4e79da22
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002931.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_01811
+MTTPHESHRPDPDEELLRAVLAEEEAALTEEHGRRDPISPAARTRLRGGTAGAPVPQDRP
+SVEDVYGPVDRPSVGLPGDATADGSVTGAPGAASVPAAGDGSPEVFIGADAETPADVQAG
+RRGARPQRPGPGAAAHRAGHRGAAGRRGVVPVGPPPLARDHGDREHRPVGRPPVGRRGDA
+RRGRDLGGRGAIALTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002932.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f1755d87caad4b2e05183ee2a173528dab2c3dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002932.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01827
+MAGRTDGVEPDEIELGAVLSALADPHRRRVIHDLVNDADGSERSCTSFGLDLSKSTRSHH
+FKVLREAGLVHQVDRGNRSEVTLRRRDLDARFPGLLDLIGSDSGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002934.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be26926709d4a6390b2808750ea2fe1f13a6f8d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002934.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01833
+MTSNATDQPHVILVPGYWLGAWAWDDVVPALKEHGLDVEAVTPPGLDEQDLNRKNATLQE
+QVNALQALVEQAGGDVVLVGHSGANAAVSTVTDRIPQLLRRVIWVDSGPMTDGAAFAPEL
+PQDIEELPLPDFDTLGQQASLEGLSDGQLKTFRARAVPEPAGVARASVSLNNDRRYGVPT
+TLICCSLPSSQVLELAQARHPMFAAVNDLIDVQFIDLPTGHWPMWSRPEDLGKAIATAAL
+AS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002936.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9323d3271092ead4a724c27d24f233e6fb94472
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002936.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01855
+MNSLPLHPLMVHLPVILIPLTVLMALPAVLSRRWFQWSAPLTLAFSLAAAVGSVLTAATG
+EQLAASDGEASALLWQHAQLGEKTRNLAMLLFLLLLVWTALSWHRSPAALRRIGERIPAL
+HLVLAVLVLLVGVAEVVVAVQAGHAGAQLVWQGEGSGTQSGGGLGTGGGRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002939.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c16540460495d695b21703d5ffbd18aaf7ada36b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002939.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01905
+MRRIDRIAGGRQAHLRIAPAALHHPRTRRDFRWITWILTAELVIGAAAVGIAVWLTVQGH
+PVAMSAWMRAVVVLGMTATLFYFFYFALRAAAGWRWAYQRLRLFAQVFPVITLVLAAVPG
+LYPVWMVTEQIVFSLLMIGVGDILTSDHMREAYRHPDRPVPRFE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002942.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77ba927d97707b584b87ec709eeaa3645d0f11d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002942.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01943
+MKKITRSLASVAAALGLAGAGLVAAPAAQAADLTCSGIISGRTMTGDITVPGGATCTIRS
+STVTADYVYVAPNATLITENSSVSGFISVERGATLRATEGSLGDVLADSQKLIRIHGTSV
+GSLNVSQGGTVTTTRMRVRDDAYFHGMGGTVSHSWGRFSNYVSQYGSARNRFMIRSSVVG
+ADVSVQQSGHVLVGRNTVYGNIFVHDNRGTIYIEGNRADLYLSCDGNRYQPTGGNNTAWD
+KWGQCAAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002947.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f642d6aa9682e311d2da0be9b624fe89950a588e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002947.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_02014
+MRGGVFAEIAPREVTDEVCPPVNCLSAWETEVGRFVGFRHEGDAEYWHVVLGDEARRNDR
+VLVDFSGGKYDRDQVRHAVDVLFHDRDWT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002951.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..010a4d5cdc740bff59be77a8b74307f71126f124
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002951.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_02079
+MEAALFRETLIGDAGLIGGLLLVAVVLRAKVRVLQWLLLPAPVIAGLLGFLLGPQVAGAW
+GLRVGAWEFTGLPFSPYVGSYTTLLIAVVFACLALSQSFSFRKATGPLAGFTGYGVLMSA
+GQVVAGMLLVLLVLGPVMGSSDAIGMVLFASWSGGFGTSAALGDVFADAGRPEITSIAFT
+SATVGMLSGIVGGVILAKIGSSRGHTRAFSTQAAFTPSLRTGVLEHDDRPVAARHTMSGS
+SIETLTLHMALVGAVVALGWLFMTTTGEVLDDFALPLFASAFLAGLLARWVVVRSGASRV
+MEPQTLKALSGAASDVLIVCGIVSIEPAFVADHLAELAVVFALGLAFCLFLGLVVAPRYL
+GESWFEKQIFTWGWATGSVATGIALLRIVDPDLESGTVEDFGYAYLPLIPVEGAAVAIAP
+LLIVAGAPWSVVAIWGVIAVVGAVVMVRQGGPDPRRTTTAARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002952.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f0a931e0659bf4f7f2a7b26a5caeeaaf19421f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002952.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_02172
+MDPATISGRALGAVLAVVANAPAMLPRRQPLHPRGRTRRATWRVHAAWPESGIAAFAAAG
+DTPVLARTSRAVGLPEPLPDFTGLALRFADGGALLFASTGTGPFTRRLLAPRVPGAVDPL
+TTLLPLHCRLGAVDVGAQVRGDEVGILTSLDGGPWVDRARVVLGGPADVVVRFDPLRPPV
+GLWWSDFWAAARSPAYALARRLTPGAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002956.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e179267ac3b120bfe4125984211510cf533ae451
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002956.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_02210
+MRLPRPSDYIAMMIPYITLHKPAEVAALAAKDLCLVDVGNHTASEVEESVIFHPGARISV
+AIKQSFHMSMLQEH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002962.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..241d7da22d26352e461fb83a77c377daadc30c5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002962.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02233
+MTLTLIPPTTPDEATQQLAQLQGTTVALAVLRRVQLVKAAEVGVTQQQLAGALGRAQSSI
+SEYLTRARTSLADRPATHPLWPAEVIDLYAAGLLPRDEVLAYLASYPYIDPAPTDDPAYT
+VTQPGEFGEVAAAHWNDKLSDTDYANLYDLLHADD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002963.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89a8b8a343c3609016e4b4fc3f375eb4fb76e4fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002963.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_02238
+MDVSGIPTHDGLDDAFASVGMTIPRDTPSGESITKPRRMRTAFETADSNGLKATRRLISA
+LVDELRHRDVFQHPAPEIVAAVQAVRQLITEGGATLTTDGFITTAVAFPTVDAGQRETVD
+RLIARLRRNDQDPASILGTAKDLLEATSKHVLHERAPQQRQKDMPNIVYEAMEALDLSTK
+PSSINGPSAGAIAQLHQLIARTAQAVTASRNDGGDGHGHLNPTGVSPELAEYVRVVTLAA
+TKFLLDNAT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002966.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea41546b6592887256b19c33d7539089949bb220
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002966.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_02255
+MFDPEAIESARERLDAKQIAPEERAGQTPDVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002967.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40fc3476bb56125a83c00ea18f51999759cbd48b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002967.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_02257
+MERRVMAPRPGWERTIASQGLVFDETVHPDGTVTHYWNESACYALTMAEVEHLEQASERL
+HAMSLEAARFLADEQSVPGSPWRALGIPREAAQLAVDSLNAGEPSLYGRFDLVYSGPDAP
+TKLLEYNADTPTGLVEAAVCQWFWKEDVFGDAVDQWNGIFEALTDRWRRIAPPEADGTPA
+RVHFAHTELDETGEDAMTVAVLRDAAEQAGVRGESLLMSQIGFDTERLRFVGADLRYLRR
+IFKLYPWEDMVTERFGPRLKLDDEVRWIEPPWKMLLSTKALTAALWHLYPGHELLLPTFL
+NDRGGLREWVRKPLHGREGAGIEIRSRAGDVSSAAGRWGAEGHVYQQFHGLPDFPAPDGA
+PNRPVLGTWMVGDECFGVGIRESDGPVTDALCRFVPNIIDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002972.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c84d37f48b3d4251c42a2613f5d8594cd463cb2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002972.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_02306
+MDRPRRPGLTPTPSPDGAAAEEHGVTGLASHVPSQMTPAILGAADLILAATG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002973.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e621d9d2662516ec26cd4b6dec1b05eb46f1f2c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002973.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_02319
+MESTPPVPPLPDGRVGIVIPVYNTGSLALGAAHSARVALGSTENVVVVDDGSKHPDTLAV
+LDSLRVEGFHVIRQPNGGVSSARNTGIQQVTTPYVIALDSDDEIMPEAPHAMAEILDRHS
+DVTIVTGGAFEVVDGAEHLSSPPDGPVTRSAMRAATVLAMASMFRRSDWEAVGGFPEGLS
+VGEDWVFWMRLLRTGGKVEILDIPIARRHLGEHQVTRGYIDPRQSTQAAALVRSENSDLY
+AGQEVELIERLNAAELQLAAYRHAYRHVDRFKAGIRSLLGRARAKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002975.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37dee6766133a50d590e1b63c5165c8c921b9342
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002975.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02421
+MSDCEPCDLQSVPAMTDTAPALDVDALAADPVEQFHRWIRQVVGSGVPEATTVTFATVDA
+REQPDARTVLRAVRVRGGVRDAPLPEGARMRTVRPERVEFWQGSPEDHRHVRIVYTADDV
+GGFRGEVTRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002976.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9899dda9cce4d6212cd623f4cae16ea9ffb95211
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002976.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02423
+MTQPAPGPPAPWPASGGPGLAPAPWPGPDWQRAHDQAIVFGILAVTTGMLGLVFGPLALN
+QANRARAIGPDVGVARVLAWIGIGLAALSLLFLLGYFLFFGVMMAEMLRQLSQLSSGGTF
+AALGAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002977.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d798178155620e8f575c683fd2df5ba041982eec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002977.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_02428
+MTAPYRPQPQHQPQTVVVQQSRNTLIAYLLWFFLGNLGVHRMYTKRWVSGVVQLLLAWGG
+AATAWLLIGWIPLAIWAVWWIVDLFLVPGMVRDANAREAVDSWRTVGVRRF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002979.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae56d0771bfc7d3ffcd24e04682271f346682b21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002979.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_02489
+MTVNLVKLHVSQLNGCAPCLRLHPREAAAGGWESGCVSAEAGAALALAEDVTHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002985.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..054e60da2ec42302cfb6e53714d045b8786c6c0d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002985.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00090
+MAGGPLGVFLAAHLRRAKRRFGLRWILTLALWCLFWVLGLLMGEARPWAGAVTAVGIMTV
+TVGGAVWELRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002986.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea8a99513cdde57bce41e9b3898abcf3029616e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002986.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00097
+MSSSPQTMLSGSFFPISRFRLISATVLLIMSIVALTPWSFETRIGGMALINILLTAVMLY
+GLVVLIIDLMVTRETAAARTVSTEERHD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002988.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0e35cce3d7a3ca8a41b26d03a6453d44c2484e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002988.fa
@@ -0,0 +1,2 @@
+>MHAAABBN_00209
+MLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002989.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92259b19e3f922e1f6a43f4f683f1efe2381958e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002989.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_00234
+MDILHSARRLKHRLWLAQKHGAHVVTEGRDLIYRMSSAVSPARYDAARYELDFTALTGRN
+TSWKPDRPIPRVVWCVWSGTNAMSANRAACLQSIREVQHDLDVRLVTPDTLHEVVVNGHP
+LHPSYEHLSDVHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002993.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af01b30886b84e7c39d7b61cce2d9bac9eb9faa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002993.fa
@@ -0,0 +1,5 @@
+>MHAAABBN_00362
+MVLELRGEPDRTGLRFFRLKSHTACMETKPNATRTVLPPADLEEMLDLSRFLGALTQPAA
+LLGPDGQTVPLPLEAFNVLREVVEAMQVGKAITVAPVDQMLTTQEAANFLGISRPTLVKL
+LEGGELAHELTSGGRHRRVRLQDVVQYQEAKRRDRRAALEDLTGSASEAGLYDEDADRYR
+QALRQARRDLGRQAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002994.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51f42f1ef72223b3c2abd2b9fa6b3abca54a3254
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002994.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00363
+MARFSAVLDACVLVPIAQADTLLYMAEAGLYRPLWSERILEETIRALETIHPDMRETGAA
+RRRAAVMNQAFDDACV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002997.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d89575a4e9f8a72b9c2043dec90d7bb8fe2f40
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002997.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00375
+MVARCLVDADQGSQFRSGLLQDALTRHGLIGTMGQVGPAGDNAAMESFFALLQKSVIDRG
+RWATRDESIMDPTPAHAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003000.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e91a21784791d8ce11ad390e78053ab777f65de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003000.fa
@@ -0,0 +1,7 @@
+>MHAAABBN_01106
+MLHLLVDTSTWLDLSKRRDGQRWIVALRVLVHQGEVELIVPPLVIDEYERNRERVEASMT
+ASVAQRFKLIRQDLDDYGGTDTEQALSTIEDLARHAPLIGAMTTRNFDEVLELLRGGRTV
+EPTESERHAVVERGLVKQAPFHRSRNSIADALLIELYASAVAGVDLAREPHAFVTSNSED
+FSLPHGDKRQPHPDIAATFALGGSTYALGVDGLNEVLLAHFGPEIEALFADTDFVEEPRR
+LDEIVEAETRLFDRVWYHRSLQHEYRLQDANNHVEIEQLRAIAGPGRKRVEETCNLPGEL
+GPYTDFELGMLNGKLSALRWVLGSEWDFLDT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003001.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d3cae8792efadf98fc1afc9ac4acc2b222f27cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003001.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_01108
+MTTPTQFLRSKYRAIEGGCVTCAGDLAVVESLPGVKEVDALASGLVLVTHDGTVSDDAVV
+AAAKKSGLPLVAAGPARPVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003003.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..073b9f5a0dd6f8895ff507de4c6d446cd9a90696
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003003.fa
@@ -0,0 +1,8 @@
+>MHAAABBN_01301
+MTAQQHPAVFIGLDVGKAEHHAVALTAAGKKVYDKALPNDETRLRGILDELARAHGPALL
+VVDQPATIGALPVAVAQACDGVEVAYLPGLAMRRIADLHPGSAKTDAKDAAIIAEAARTM
+PHTLRSIRVDEEQIAELAMLAGFDDDLAAQITATSNRLRGLLTQIHPALERVLGPRITHP
+AVADLLGRYPTPAQLRTAGPGHVRARLRKHAPRLAASLTEQIFQALDEQSVVVAGTQAAA
+TVVPILAEQLAGLTRQRAGLASQVEAAVEAHPLHPVLISMPGVGIRTAARILTEVVGKDF
+VDAGHLASYAGIAPVTRRSGTSIRGEHVARGGNKRLKRALFLSAFASLSHPPSRAYYDRK
+RAQGKRHNQALIALARRRTDVLYAMLRDGTLYQDPTAPPAPSSVALAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003004.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..125fc088a9cd75f517451947c7162777694aa3ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003004.fa
@@ -0,0 +1,10 @@
+>MHAAABBN_01329
+MGQKQKTKSFQLGEIPSSSDAWWNLFNFAAEAQWEIPGVSLESFANPESIFLRSAAEISL
+NQPTRLRLEHGGFHFAVRLADNSSVPIDIDADIIPNEYILSSYEYEYSTKNFTYRGYKAQ
+RTSPADLTVILGHELTIDLKEVGSDNGKCDIKYPLSRYLAHRVRDLELYIDILEYGFLTI
+GSYGIQVDTTAVSDVHIQEDKEYLETLRNLLQNIEYFGGNAEKVLVDSINDDQVRAIQAA
+VESSRSHQRPPGYRGSTGRVRFGVGDKSLELFVYARDDEGQIDVTNLFGDDNGFWLASTE
+TVDGGESSRLVTPYEFIDDEDLVGLININLSSISRHYERIKGYDGVEQIADSMIIRLWRV
+AVKQEDRREEFRSAALSLALWVSCAYVNSTQRLRYLTNIHLLRFWANGFAWSDDSQRLAC
+RRLQQDVMRANLSDISLYHVCLTFLLGSEVDLGDTIQGLNENEMKQLQSWPVWDLIGEAY
+PKLTAT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003005.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41616f1dda39aa4282e128e83e675e2499d2734b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003005.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_01395
+MAENTSPTPDPRTRGEHGTEHAAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAICQG
+PLSSAHRRPVFLPAGGHQNCPLVASWFARLGGGAGHRDGISSVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003011.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82598544d5d80215c3601aadbd520a6e7634903f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003011.fa
@@ -0,0 +1,2 @@
+>MHAAABBN_01934
+MTLAELEEGQVLVTSTVMSVGPCMGGHMNDVASDVAPFEVDAPSTAAGSAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003012.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f5a6da9cb93af8df1c389a9fa3b4d46ae663774
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003012.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_01935
+MKYSFQANEANGAPQQAVLNGWHTNDLLGIQAKIAGDQRDQSHRLTALVFFLGLGLLGDL
+VLRNAEAFRESKGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003013.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ba701ca96054624e50431b9ef2a25980251f4e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003013.fa
@@ -0,0 +1,2 @@
+>MHAAABBN_01936
+MKDRKNPTSIAKAHQKRATGQFTRNFPPRDFFTFPFFDADPGAPPGWKPCPH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003015.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..546b7e88feda33554769d82d0ce07c42aee3c81c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003015.fa
@@ -0,0 +1,11 @@
+>MHAAABBN_01972
+MSKFHVDQIATRIRELYSTDYWDANLSDVNNLSRLLARYAVDLTIPESSDSGNQRIVEVI
+DGGEDRGIDAIGIDFVSQLVVLVQSKWRQDGSGTMDLAGLLKFRRGVETLLGIRTDNVPV
+SASPEMRMAVSDILKKPGTRMRFIAVTTAQEELPTQQQESMNELLSSVNEGGASEPIASF
+VHLGQGALFDSIVEREPMDLDLNMQIFNWGKIDEPRRMVYGRVDAAQIAQWYRDHEHKLF
+AENIRLVIPRSDINDGIRKTLTSEPENFAYFNNGITMVVRDMQVAPAGSATREAGYFTAK
+GVSIVNGAQTVSTIGRISKSEGSLDFLEAASVMIRCIVVSDEEAEFGRLVTRYANTQNDV
+STQDFAFLDAEQHRLKSEIKVMGFEYLLRSGEDVLTESSDKRIDVRSAAIALACAHRDVE
+LSVLVKREISQLFSDRYRTIFNPSTDPRLLVSSVLVNQVVENKLGELEPLTEGVKNGVII
+HGKRVISHLILRGIGTTNLSSSEFAIENYDSWIEDECERIVAALVENFPDNSYPGNVFKN
+TIRVRALLNESSLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003017.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3ff03953478826fbb45680c900da67ed6a5bd1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003017.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_02027
+MKDRGRLLGIAAISVTSLLWGTTGTAATFAPDAGPLAIGAAALGIGGLLQAAIAIPALRR
+A
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003020.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c40743d4ff1b72b475f1b382d341c6a0734326db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003020.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_02185
+MFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGTVGVLASVILVIARLLQGLAHGGE
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSHEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003021.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1fb11987d809251e683e55607b20b0ff9864b81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003021.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_02214
+MPPDGCRRRGGFICGERRHSDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDL
+TGVDDLSDGCGGYAAVRIEEPTGRAEYARRQREFAARGQALRVRLLAVLDEAVGAAPGTG
+PDAEWTSSARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003028.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c1bc17d5b56a02ead40603a2b351e01e8c7c11e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003028.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_02222
+MTGPSTDGVRGGRQTWAQWYYSGAPTAQDMADRRHADTARAERARLDAEALNARHAEPRP
+DPAARLRIALTNLGPSMVPPGAGPTLADVNAAIRREAGPDRALHQQMLDLHFTQQARRRA
+AGNH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003035.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..161baefbf84e44a93fc31dac566919b26ca88e59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003035.fa
@@ -0,0 +1,4 @@
+>LFPAFLNI_00112
+MDFWSTIWDAIWWFFTIFVFVAYLIALFSIISDLFRDRELSGVYKAIWLLFLIFLPFLTA
+LVYLIFRGRGMGDRAERQTREAKATADDYIRTVAGGPASEIAQAKQLLDSGTISEAEFQS
+LKQSALDGSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003038.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a732767e9ad1ec16f32fbf39f29ebb3fee725265
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003038.fa
@@ -0,0 +1,7 @@
+>LFPAFLNI_00118
+MMSAEGPKRRELFRWWEWALIALAVISIPAGPGALIFLMPVLPRIVLLIRKHRYFNSEEF
+QEKKAEIRAFVAEHNELKEYIDEIRARGSFSLGESSTGQHAHLAYSENTSRHNYIRDRNV
+ATLGAPNVHNCSLQVVRKAQMDPIRYLMKYFHINAEEDRLAEVEEMGSSLAQLEEALSNL
+QNREASITEAIQPPSFIQKHFLDEFMEQVGVEISPITIPYEIYTFEYVSAGGNSSERTNV
+VLNSQALDALIDTMSARIKFRKSAAGQRALMTSKLRHHIKDRDNFTCQNCGVSTYAEPHL
+LLEVDHIIPVSRGGLTTEENLQALCWKCNRSKSNKI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003042.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..445b72b04d9f818ce17e87cf395eb677189767a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003042.fa
@@ -0,0 +1,3 @@
+>LFPAFLNI_00165
+MIFIVVKFTVKPDWSDRWLDLTSSFTRDTRHEPGNLWFEWSRSVENPNEFILVEAFEDDA
+AEAHVNSEHFQNAMQQMRQALVETPRIISRQIEGNTWDRMGELAID
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003043.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d210791940ce428131c9542561d9457ad1b1a317
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003043.fa
@@ -0,0 +1,3 @@
+>LFPAFLNI_00170
+MLLYRWSRAEPVIRAELSLPSRMDRGDVVAWKERILLPEISLDQFDLSDFDVIAEDDVYF
+GISQTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003047.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0690e62b4aed0225cbbabc66d77bf283bbef83a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003047.fa
@@ -0,0 +1,5 @@
+>LFPAFLNI_00892
+MKSVLHTRTAIAAALLLGLTACGDTASPAEEDAPAAAGSSTASAPAGAEEETEADEPEQQ
+AGGTAGTREDPLPLGTPIEGEDWVVTVNEVTPDATDAVMAANQFNDAPAEGTQYLLADVT
+VEYTGDESEMIMLGTGFAFVTATGETIDAGDAFAVGPEELDTAQELYNGGTAQGNVVLQV
+PEGADGLLRVTTGMFGGEKTFVALD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003048.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f024fc0d5db55e0372e811c93085f0984ea1cc2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003048.fa
@@ -0,0 +1,3 @@
+>LFPAFLNI_01015
+MALDIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPIGLDAAAYKGRNVIERQYAHLK
+QWRGLATRYDKYAIIYRAAVVLNAVIAWSKRLSDMP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003053.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..428783d4cd7f78acd3bea871810dc43c979a9629
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003053.fa
@@ -0,0 +1,9 @@
+>LFPAFLNI_01545
+MSEGLALKCLAALLGSDAAHANLKYFRANPGIAVSELGPDAKDINSIAEQTEADGLFIIE
+DVAICVEVKAKSISSHARRGHVQRLSADLRETVGSATEQALRLENHIRTNHGLWLENREW
+LDLSEIREIRSVTVYLDDFGPLSTALDELVRAKVVGSDRFPWLVTLHDLIVIAEVIDRPA
+EFLLYLRRRTESEVSLKFSAVDELDLFMLFLSGGLWVEPDPDRVSEEFLGVAPPTVKERR
+RYQESAVPTRVMTQTDELDAWVYFNEGASDVEAEKPSFGVLPGIARIVDFLQDGRKPGWF
+RFSADLLNLDEESQESLGDMVEHLVSITRQDGLHHNSIMAFAGSWGYPTLFMGSKPRKMS
+IQEASTRLAAYGCAKKHQIRSDRALMVVFDEEQRIRSIRYDNSPPVENRELDGFVAEMGL
+IPPSVMGRPIPPSARRTTVRLNPSRKRKKRGKRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003056.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28f7b9dc3c9dde5abdd50df48e6ad77dcf7dd57d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003056.fa
@@ -0,0 +1,10 @@
+>LFPAFLNI_01797
+MLILSSRMRPKEQFEGYAFVGTDYVHGPAGMTAYRARTGRTVGPGEDGCYVVARRAGRLF
+GRRFEVGTDASGLGRLFLYRSGDDWALGSSYSGLVEHLRTEGMTLTPRLGRLRPFALRQT
+LTMQLSIFQTPFDEIRLLPVGTVVVIRGSVLSLERAPELQPLEYEAALQEYLDVWRGRTR
+ALLADPRVTFTADLSGGVDSRTVFAFLLESGLFRTDSDRFWLHSGVNQKEDLAVAKGIAE
+AHGLTVNGPKPPTRTLVSGSRAYRHWRENSLGVYTPVYMSSTFQNPFEVHAHGGGGGTIK
+QYYRHAEPLRLLEPFKEKMPAADFALWQEEMATTQEQLKQTAPGVVPSIQHYLEFRNRFH
+FGHIPKARPLFMPLNSKYAIRALTSLPQDVRRRFYFDVMESLAPGLKDVDYDNARKAPTA
+QELESLLVLPASDRLAAGTAYGDDTVETADPDDPLSAGFQRWLQDIDRAAARPEVRRFIM
+GRAMARTDRTVEALRALGKPFHSHSGHSVALSHLLMVDFTLGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003063.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1f9cf2ce5db0be3bcc23603c7399b66de06ddb2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003063.fa
@@ -0,0 +1,3 @@
+>LFPAFLNI_02182
+MAKHLLETDGQVCPFPLVEANQAMQQIPSGDELVIDFDCTQATDSLPRWAAENGHEVTDF
+VKRGAAEWTITVKKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003065.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca98cf07e4b5f6e2b03af9e2b50954b0882a697e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003065.fa
@@ -0,0 +1,6 @@
+>LFPAFLNI_02209
+MTTPSGAPDVSADPEVRLLTARLNRARTHYLDFAELWAAYLEGRPHSIAREILTDGTVTI
+RLDRVAPIPAELSILLGEFLYEMRAALDNCLYAAAVIASGQNPPPGAERLEWPIRTDQTQ
+WKSQANRYKHLPAELTEALEAIQPYNAELPAWNCLAILHGLARFDRHRRPWPLALFLVKT
+QLQVRPDVVEPLDVACNRVIHPGEKLATLRLSPGHVLSPTNFDFHVEFDVDLADIEPSEG
+PEGLHVRPWGSLAHRLQSVHRAVTEYCDDLLLLAASCRKH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003067.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9f3902676a2c6e76635df8b38a820281063e686
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003067.fa
@@ -0,0 +1,5 @@
+>LFPAFLNI_02211
+MRDLVYYIATSLDGYIAAPDGDFSAFPQDPVTLKTLFDRYPETCPAHARAALGVDGPARR
+FDTVIMGYRTYEPALTVGLPGGAYPHLNQIVVTHRPLPKAPNLTAISGDVSEHIAHLKTL
+PGRDIWLCGGADVAAQLIEHIDELQLKVNPIALGTGIPVLPFDGKPHSFHLAECEQQPGE
+VLLLTYRAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003068.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5199511037dcf1dd3833bfa9c01e86a7b5bc093c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003068.fa
@@ -0,0 +1,8 @@
+>LFPAFLNI_02212
+MNPLRPLTIPTYRWLFAAMVLTIFAQGAWALYLAMQTLDLGATPATLSGVVVWSGIGLLA
+GSLPAGVLADRMPNKSVIVGVLSLNLAIATATSTVAVFGMVAFWMLAASAFFIGVSTAFF
+FPAYTALVPVLVESDDLMAVNGLEGATRPLVGQALAPAAVGAVIGVSMPAAGGYLIAAAL
+AVALLAALQLPAPTPAESEADASAASPIGDLLDGFGYAARTRWVRTSVLFAAVMGLVVTG
+PLEVLLPALMRSSHENGPALYGAVLAALGVGGLVGSLLAGSWCTPERFLPAMIGAWALGC
+LPLTIPALTSNPWAIGVGLAIYGALIGIGMVIWGTVLQEHVPLEMLGRVASLDFFISIAF
+MPLSIALTGLLSRHIDTHTLFISAGLVPLVTAVLLATLGQLRMPRTTVGVAGGA