diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000001.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b62ec3c6d35b04c35f9001cd9b147e20d41c9cb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000001.fa
@@ -0,0 +1,235 @@
+>GCF_002008305.4_00174
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_00589
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_00602
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>GCF_002008305.4_00603
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGRV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSGKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>GCF_002008305.4_00623
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVTDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSNQDPDTPSTTGASAEVMPTLA
+>GCF_002008305.4_00713
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_01070
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>GCF_002008305.4_01202
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>GCF_002008305.4_01394
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+EVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>GCF_002008305.4_01399
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_01504
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVAGAWPGSGWSPLMPTPGSR
+TPSPRTCPVRCGNAAAPTTRRT
+>GCF_002008305.4_01505
+MGITPKSMWPAVKAMLHSGYDQPDAASVNAQFDRLLDYVSEKLPVVAEHLDAARADILAF
+TTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNRAAIVRLVGAVLAEQTDEGPRAVA
+TRALGATRACC
+>GCF_002008305.4_02030
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>GCF_002008305.4_02064
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFSATGLWARPARSCSSPPTP
+>GCF_002008305.4_02065
+MFLAADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVA
+RGLAGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSV
+YDQPDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAER
+LNREIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQE
+TVMSTEVMPTLQT
+>GCF_002008305.4_02226
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTETGAAWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVQAQFERLLD
+YVQDRLPAVAGHLDAAREDILAFTSFPRDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_02229
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGQASQSRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_02231
+MVADCYLAGVSTRRMDKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFL
+AADALTMKVREGGRVVNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGL
+AGVALVTSDSHRGLVEAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQ
+PDGPAVHAQFERLLDYVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNR
+EIRRRTDAVGIFPNRDAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVM
+STEVMPTLQT
+>GCF_002008305.4_02232
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPNGCSSAANGPSPH
+>GCF_002008305.4_02266
+MTAPHIVDPERLLREALGEASPDLLRHLLQTVINALLSADADAVCGAEYGKPSEHRTAQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMAQELDEHIEAFRHRPLGEAGPFVFLAADALTMKVREGGRV
+VNAVAMVATGVNADGRREVLGLRVATTESGAGWNEFFADLVARGLAGVALVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFERLLD
+YVQDRLPAVAAHLDAARQDILAFTSFPRDVWCQIWSNNPAERLNREIRRRTDAVGIFPNR
+DAVVRLVGAVLAEQTDEWAEGRRYLGLELLARCREPLTTEQETVMSTEVMPTLQT
+>GCF_002008305.4_02271
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>GCF_003691675.1_01126
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTRHHGPVEIAGLRDE
+>GCF_003691675.1_01127
+MSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVVKVAAMVATGINNDGYREIL
+GLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVEAAGAVFGTAQWQRCRTHYA
+ANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDSLATHLPAAAEHLEGARDEV
+LTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRVAVIRLLGAVLAEQHDEWTE
+SRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDPGHAALAA
+>GCF_005280335.1_00691
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLPAVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLHRCRLTPVSNTGDEVDTDTALELSA
+>GCF_005280335.1_00721
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>GCF_005280335.1_00896
+MTAPHILDPAGLLREALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPGRATQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMATELDEHVESFRHRPLGEALPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHTGLR
+EAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLD
+YVSEKLLYGGRAPGRCPGGHPGLHDLPEGRVDAGLVEQSGRAAQPRDPPPHRRGGHLPQP
+GSHRQAGRCGAGRADR
+>GCF_005280335.1_02500
+MTAPHIVDPAGLLGEALSEASPDMMRHLLQTMINTLLCADADAVVGAEWGKPSRDRTAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEQVEAFRHRPLGEAGPFTFVAADALTMKVREGGRV
+VNAVVLIATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHPGLK
+DAIAANLPGAVWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDAASVNAQFDRLLD
+YVSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGNEVNPDTAPALEFSA
+>GCF_005280335.1_02671
+MTAPHILDPAGLLGEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPSSSRTAQR
+NGYRHRDLDTRVGTLDVAIPKLRSGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGVNALSKSQVSRMATELDEQVEAFRHRPLGVAGPFTFVAADALSMKVREGGPV
+VNAVVLLATGVNADGHREVLGLRVATSETGAAWNEFFADLVARGLAGLRLVTSDAHTGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKNMWPAVKAMLHSVYDQPDAASVHAQFDRLLD
+YVSEKLPTVAEHLDAARADILAFTTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVTNTGDEVDPDTELTLGLSA
+>GCF_023573625.1_01344
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAPVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>GCF_023573625.1_01996
+MTAPHDIDPQAFLSDLLTQASPDLMRQMLTTFINALLSAEADSVCGAAYGARSDERTNRR
+NGYRHRDLDTRAGTIDVAIPKLREGTYFPDWLLERRRRAEAALTTVVATCYLLGVSTRRM
+DKLVQTLGITGLSKSQVSEMSKDLDAQVEAFRTRPLDAGPYRFVAADALVLKVREHGRVV
+KVAAMVATGINNDGYREILGLQLGTAETREGWLGFFRDLAARGLSGVELITSDAHAGLVE
+AAGAVFGTAQWQRCRTHYAANLMAVCPKSQWPAVKALLHSVYTQPDVEAVIAQYEHMIDS
+LATHLPAAAEHLEGARDEVLTFTKFPKEVWKKIWSNNPNERLNKEIRRRTDVVGIFPSRV
+AVIRLLGAVLAEQHDEWTESRRYMSLELLTATDTMLAEAAAKAAAEQAALQVSDTMTDDP
+GHAALAA
+>GCF_023573625.1_02197
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
+>GCF_023573625.1_02214
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPFTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGAAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAVGIFPNR
+AAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVEDTGSEVGTDTDTALELSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000002.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9751b6488836838adde69fbdfd7574004cb16d46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000002.fa
@@ -0,0 +1,112 @@
+>GCF_002008305.4_01069
+MFRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRGLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_002008305.4_01387
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675.1_00320
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675.1_00332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_003691675.1_00787
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675.1_01117
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATSITRHTGGW
+IELQESA
+>GCF_003691675.1_01328
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_003691675.1_01659
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_003691675.1_02266
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335.1_00757
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335.1_01280
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335.1_01303
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335.1_01313
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335.1_01318
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>GCF_005280335.1_02332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335.1_02348
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_005280335.1_02630
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155.1_00316
+MSRFQTLSDAQWELIAPMLPARTGRQGRPFADARTMVEAIIYRYRCGIPWRDLPEVYGPW
+QTVWTWHRRMAEEGTWDTVLATLTAAADAEGLIDWSVAVDSTIARAHQHATNTTRLTGGW
+IELQESA
+>GCF_020097155.1_00621
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>GCF_020097155.1_00626
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>GCF_020097155.1_01795
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155.1_01837
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155.1_02208
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_020097155.1_02231
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_023573625.1_00113
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>GCF_023573625.1_01019
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>GCF_023573625.1_01540
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+VELQESA
+>GCF_023573625.1_01883
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000004.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7941651d0263410b57c2f164cc28506917be764a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000004.fa
@@ -0,0 +1,190 @@
+>GCF_002008305.4_00376
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305.4_01393
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305.4_02069
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPLTQTS
+>GCF_002008305.4_02112
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_002008305.4_02277
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_00355
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_01012
+MGRTQWPLTDVPRDRGGSFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIG
+TDLSHETISNITDAVSEEVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGV
+DLEGIKHVLGIWVQDTEGSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSM
+VQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAA
+ATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLA
+ICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_01015
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVCKRP
+>GCF_003691675.1_01125
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_01746
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_01819
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_003691675.1_02016
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335.1_00228
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335.1_00229
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYA
+>GCF_005280335.1_00643
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335.1_00895
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335.1_00899
+MTDTADAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRMTQAVLERALETEMSEH
+LGYEAGDPAGAGTGNSRNGKTTKSVQTLQGPGQITVPRDRNGSFEPVIVPKRSRRLGRVE
+DMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVADEVAQWQSRPLETVYPIVY
+IDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSEGAKFWANVLTEIRNRGTK
+DILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYASYADRKTMAKDMRPIYTAA
+TVEAAQLALEAFAEIWQTKAPGAVLAWRTAWEDFIPFLAFTPEIRKVIYTTNQIESINYQ
+LRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGELGTGTQGWHQALNAFAVQFPNRLPL
+>GCF_005280335.1_01506
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_005280335.1_02100
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYGKGSEDASKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_020097155.1_01829
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQLLAQAKEQGVRLVGPGGLLNQLTKNVLETAL
+EAELTEHLGHDHGQTPIAANMRNGTRSKTVLTEIGPVEIEVPRDRDGSFEPVIVPKRKRR
+LDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAGELAEWSSRPLDPL
+>GCF_023573625.1_00116
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625.1_01547
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625.1_01549
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625.1_01880
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>GCF_023573625.1_01974
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000005.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8560bf70c64ab2508d5130bb9ec8fd7cd5a6b0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000005.fa
@@ -0,0 +1,162 @@
+>GCF_003691675.1_01778
+MDGDQDEMAGPGVLAVPEREWEQARLRAGVIGRLAEHDPVGLAAVDEAAMELGISRRRVY
+VLLERYRRGSGLVTDLVPRRSDGGKGGGRLTEPVEQIIRELVCQRYLTRQKRSIASLHRE
+ITRACAVQGLPAPARNTVAARIARMNPVEVGRRREGAESVRPLQSAGDEVPVVESILDQV
+QIDHTVMDLIVVDDRDRQPIGRPYLTVAIDVCSRCLVGMVVTLEPPSAVSVGLCLAHAAG
+DKRPWLERLGIDAAWPMSGKPKALYVDNAREFKSEALTRGCDQHGISLDYRPLGRPHYGG
+IVERVIGTAMRQIHELPGTTFSNPVERGAYDAEKMAALTIAELERWLVLAVATYHDTVHS
+TLGQTPAGRWVESVAATSTPMTTANPTAFLVDFLPVFRRKLTRTGFVLDHVHYFANALKP
+WIARREALERFLIRRDPRDISRIWVLDPEGTAYIEVPYRALSNPAVSVWEHRQALARLRE
+RGATEVDESGLFRMIEQMRTISETAQKTTKRTRRERQRRTQTGTTTTRPTPPVPEPPVVP
+TDLDVVARFGEIEQW
+>GCF_005280335.1_01282
+MSHANAALTPRHRLIVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGEPMQDRSSR
+PHHSPNKTNQQTARRCVRLRLRLREGPVQLASRLGIAPSTVHRILTDVHLNRLSHVDRAT
+GEPVRRYEHDHPGSMLHVDVKKLGNIPDGGGWRYVGRRQGDKNRAATPDKPKNKHYDPLM
+GMAYVHTVIDDHSRVAYTEIHDDETARTATAVLIRAVEWFNARGVTVERVLSDNGGAYRS
+HLWRDTCAELGIRHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDDWLH
+YYNHHRPHTACGNLPPFSRLINVSGQYS
+>GCF_005280335.1_02274
+MSHANAALTPRTRLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTSPAVVKQIVAARWRQRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDAYTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYSSETERRAALP
+GWLHFYNHHRVHSAIGATPATRLNNLPGHHT
+>GCF_020097155.1_00226
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_00227
+MVVQLRTVEKWGPARIAGHLSTVGDGSINISPATVWRILNRNGISRLRDLDMPTGESKRE
+PRRYEHAAPGDMIHVDVKKVGRIPEGGGWAVHGRGTEEALASRRVASRRPGYVYIHAAVD
+DHSRLAYAEVHPDERAGTAAAFWLRAVLFYREHGITTFSRCLTDNGPAYRSKVFNDALAG
+TGTAHKYTRPHTPRTNGKVERFNRTMKEEWLYVRAYASDGERTAALAAFLNTYNHDRPHS
+SLGNKPPASRVPITSYRVQPQPKVLDVPQIEGLGHEPTLFDLL
+>GCF_020097155.1_00312
+MSHANAALTPRARLRLAKLIVEEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_00315
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>GCF_020097155.1_00448
+MVDRSSRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRL
+ARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGT
+RDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVL
+SDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETER
+RAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
+>GCF_020097155.1_00627
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_00631
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>GCF_020097155.1_00641
+MSHADAALTPRHRLKVARLVVDDGWPISEAAARFQVSWPTVKRWVDRYLSGEPMSDRSSR
+PKSSPNRTPRVVAKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARMNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGGRNRAATPDKPRNQYGGPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFADLGVTIERVLSDNGGAYRS
+HLWRDTCEALSITPKRTRPYRPQTNGKVERFHRTMADGWAYARCYTSEAERRGALSGWLH
+QYNQHRPHTACSNQPPFSRLINVPEQYT
+>GCF_020097155.1_00645
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>GCF_020097155.1_00652
+MSHPNAALTPRHGLLVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGQPMQDRSSR
+PHHSPNKTSAKTTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKPRNKYRDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAITATAVLVRAVEWFNARGVTVERVLSDNGGAYKS
+HLWRDTCVELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEDERPGELEGWLH
+YYNHHRPHTACGDQPPFSRLTNVPGQYT
+>GCF_020097155.1_00678
+MDASERWRILRLHVEDAIPLATLARSTGVTERTLQRWLARYRTGGYAALADDARADHGVR
+RTAPELVRLVEGLALTKPRPSIATIHRQVGVHCAERGLPSPSYSAVRSIVNGLDPGMVTL
+ALEGPASYRDKHELLLRRRADRPNAIWQADHTMLDLLIVGPNGKPARPWLTVILDDYSRA
+ICGYMVFLGAPSAANTALALRQAIWHKPEPDWPVCGIPDVLYTDHGSDFTSHRLGDTAAV
+LHLRIIHSQVARPQGRGKIERFFGTINTELLPTLPGHFAAGSSAPTPALDLGGVDSAIST
+FIRSYNARTHRELRTSPLHAWIADGWLPRLPESLEQLDGFLLTVPTTRVVQRDGIHFEGL
+RYTAATLAPFVGSTVSVRYDPRDVTEIRVFHRDVFLCTAISTEHQTETISLKQIQAARNA
+HRRALRGQIHERIAIVNPKLDDTTTPAAVETDRPRLKTYEEDRS
+>GCF_020097155.1_00751
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_01361
+MTHLNAALTPRHRLKVARLVVEDGHPISEVAARFQVSWPTVKRWVDRYLAGESMNDRSSR
+PKSSPKKTNKAVTKRCVSLRMRLREGPIQLAARLGIAPSTVHRILTAARLNRLSYVDRAT
+GEPVRRYEHPHPGSLVHVDVKKIGNIPDGGGWRYVGRRQGQKNRAATPDKPKNKWHSPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFAERGVTIERVLSDNGGAYRS
+YLWRDTCEALSIRPKFTRPYRPQTNGKVERFHRTMGDGWAYARCYTSEQERRDALPDWLH
+HYNQHRPHSACGNQPPFSRLINVPGQYN
+>GCF_020097155.1_01794
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_01820
+MSHANAALTPRHRLKVAQLVVDDGWPISEVAARFQVSWPTVKRWADRHRAGESMQDRSSR
+PHHSPNKTSPTVTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKLRSKYSDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAVTASAVLVRAVEWFNRRGVTVERVLSDNGGAYRS
+HLWRDTCHELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDGWLH
+YYNQHRPHTACGNQPPFSRLTNVPDQYI
+>GCF_020097155.1_01832
+MSHKNAALTPRHRLKVARLVVEDGWPISEIAARFQVSWPTVKRWVDRYLAGESMEDRSSR
+PRVSPNKTPKTVTKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARLNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGERNRAATPGKPKNKWHNPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFANRGVTIERVLSDNGGAYRS
+HLWRDTCD
+>GCF_020097155.1_01835
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>GCF_020097155.1_01890
+MSHANAALTPRARLRLAKLIVDEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWLHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>GCF_020097155.1_02162
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>GCF_020097155.1_02206
+MPASTVHAVLVRCRINRLARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFV
+GRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVL
+RRAVAHFAQLGVEVERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHR
+TLADGWAYAKFYGSETERRAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000006.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be13106dd050607e68f866817fc76f778063ce07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000006.fa
@@ -0,0 +1,100 @@
+>GCF_002008305.4_00157
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305.4_01034
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305.4_01292
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_002008305.4_01384
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE
+>GCF_002008305.4_02077
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675.1_01011
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675.1_01104
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675.1_01112
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675.1_01114
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_003691675.1_02023
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE
+>GCF_005280335.1_01214
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625.1_00588
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625.1_00590
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS
+>GCF_023573625.1_01250
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>GCF_023573625.1_01339
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH
+>GCF_023573625.1_01885
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV
+>GCF_023573625.1_02205
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000010.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00564800a99dbb2821ce0b799fee5af9d8557eff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000010.fa
@@ -0,0 +1,79 @@
+>GCF_002008305.4_00454
+MLHPTFATPDLTTFCRLDELGLVAVGQLIEPDRATIECRVVEDDPWCRKCGVEGVPRDTV
+TRRLAHEPFGHRPTTLLVRVRRYRCGHCRRTWRQDMTRAAAPRAKISRGGLEWALRGIVI
+DHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHVWRHTRLGDKY
+VTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADWAKRIEVVAMDGFAGFKTA
+AAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGLKGDPLYKARRTLHTGASL
+LTDRQRARLDAVFASEEHIEVEATWGIYQRIVAAYREPDKKKAKAMMQEVIATISSGVPA
+ALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTHYIARS
+LLEAGGFRPALHPRS
+>GCF_002008305.4_00845
+MRRYRCSGCGYVWRQDTTASAEPRAKLSRRALRWALEGIVVQHLTVARVAEGLGVAWDTA
+NDAVLAEGKRVLIDEEHRFEGVKVVGVDEHVWRHTRRGDRYVTVIIDLTPVRDGTGPARL
+LNMVEGRSKQAFKTWLADRPQDWRDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTR
+LAGEALDECRRRVQQAICGHRGRKGDPLYAARRTLSTGVDLLNDKQKDRLDTLFADDAHV
+EVEVTWSVYQRMIAAYRHENRRHGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADV
+LAYFDRPSTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG
+>GCF_002008305.4_01392
+MSLLTDRQEEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
+>GCF_003691675.1_01124
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQTR
+>GCF_005280335.1_00108
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPRELTGMVDLS
+RDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQRLDDA
+TAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTDKQLAR
+LAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEVARLGR
+TLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>GCF_005280335.1_00508
+MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQ
+RLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTD
+KQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEV
+ARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAG
+GLTP
+>GCF_005280335.1_00509
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>GCF_005280335.1_01091
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>GCF_005280335.1_01092
+MTRSGVACRSRRWTRSCGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLG
+HRGRKGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRS
+GNLADGRAIAERLADSLHTSPIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGII
+ELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>GCF_020097155.1_00630
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>GCF_020097155.1_00638
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>GCF_020097155.1_00839
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>GCF_023573625.1_01343
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000014.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a1a02795aa03dc2eb81bb93c164469b1969781a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000014.fa
@@ -0,0 +1,97 @@
+>GCF_002008305.4_00160
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_002008305.4_01074
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_002008305.4_02060
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGKRALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMELDEV
+PESLLVIGGGYVALEQAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLVATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>GCF_003691675.1_00298
+MPTKYDLAIIGSGGGAFAAAIRATTLGKSVVMIERGTLGGTCVNTGCVPSKALIAAADAR
+HSAADAADRFPGIATTAGPVDMPALIAGKQALVESLRGEKYADVADSYGWAVRRGDAAFA
+GTPDAPVLQVAGDDGSTETIEAGHFLVATGSRPWAPPIDGLDETGYLTSTTAMELTELPE
+SLLVLGGGYVALEQAQLFARLGSQVTVLVRSRLASKEEPEVSRTLEEVFADEGIRVVRRA
+LPTRVSRDAATGQAVVTADVAGGREEFRADQVLVALGRRPVTDGLGLDRVGVETGDLGEV
+VVSDRMQSSHPRIWAAGDVTGHPEFVYVAAHHGTLVAENAFADADRAVDYARLPRVTFTG
+PAIGAVGMTEKDVVAAGIRCDCRVLPLHHVPRALVNRDTRGFVKIVVDADTGKILGITAV
+AKDAGELAAAGVHVLGKTVAEVADAWAPYLTMAEGIRIAAKAFTTDPSLLSCCA
+>GCF_003691675.1_00337
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_003691675.1_00346
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPFPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_003691675.1_00793
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTCGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_005280335.1_00723
+MTATANSRSYDLAMIGSGGAAFAAAIRATSLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDSHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
+>GCF_020097155.1_02220
+MNEAVPHFDLAIIGSGGGAFAAAIRATNLDKRVVMIERGTVGGTCVNTGCIPSKALLAAA
+EARHTAQDAGRFPGLTATAGPVDMEALIAGERALVENVRSDKYVDLVADYGWELRHGNAV
+FTGTAADPALEVTAQDGTRETITAAHYLVATGSTPWAAPINGLDTVDYLTSTTAMDLDEV
+PESLLVIGGGYVALEHAQLFARLGSKVTMLVRSRLASGEEPEASRALMSVFANEGIRVIR
+RSTVSSITQDTDGGIAAQADIAGGRETLRASKVLIATGRRPVTDGLNLAGVSVKTGDKGE
+VVVEDTLVSSNPRVWAAGDVTGHPEYVYVAASHGTLMVDNAFSDAGRAVDYSHLPRVTFT
+SPNLAVVGMTDKQARDAGIRCECRVVPLEYIPRAVVNRDTRGFIKMVADADTGRIVGITA
+VAKEAGDLAATGVYILQAGMTVDQVANLWSPYLTMAEGIKIVAQSFKTDVSKLSCCAA
+>GCF_023573625.1_01023
+MTATANSRSYDLAMIGSGGAAFAAAIRATNLGRRVVMIERGTVGGTCVNTGCVPSKALLA
+TAEARHVTLDASRFPGLPLPEVRPVDMPALIAGKDRLVGSLRGEKYLDLATEYGWDLHPG
+DATFVGTPSEPALRVTGPDGTVETVRAAHYLIATGSRPWAPPVPGLQEAGYLTSTTAMEL
+DHVPESLLVIGGGYVAMEQAQLFARLGVRVTMLVRSRLASQEEPEASTALDEIFTDEGIQ
+IIRGAVPSAVRRDPATGEVTVTATTTDGSQELRAAEVLVATGRRPVTATLGLDTVDVRTG
+DHGEVVVDGHLRSTNPRVWAAGDVTAHRQFVYVAAAHGALVADNALTGAGLEVDYRHLPR
+VVFTSPALAAVGMTERQASAAGIRYDSRVLSLAHVPRAIVNRDTRGFIKMVTDADTGRII
+GITALAQDAGDLAAAGVYMLEAGMTTSQVANLWSPYLTMAEGLKLTAQAFTTDIAKLSCC
+AA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000015.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45007bac598d71b25afdb67d6f4a0673d050d616
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000015.fa
@@ -0,0 +1,105 @@
+>GCF_002008305.4_00355
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGSARKVVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>GCF_002008305.4_01656
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>GCF_003691675.1_00071
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>GCF_003691675.1_01361
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>GCF_005280335.1_01238
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LDDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQA
+SRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDEHQH
+>GCF_005280335.1_02606
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>GCF_020097155.1_01149
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIE
+TAVAAVEKRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSP
+DLGMKLEQADLDVLGSARRVTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDEHQH
+>GCF_020097155.1_02465
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIE
+KAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENASLDLLGTARKVVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLNAAT
+GEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>GCF_023573625.1_00362
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>GCF_023573625.1_01586
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEAGHQH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000016.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33cb0bde2c5044dbf0cbe11f796334d6e4a46e4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000016.fa
@@ -0,0 +1,90 @@
+>GCF_002008305.4_00992
+MTPTPSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAP
+DHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVP
+GVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPT
+EIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEAS
+EKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGLRM
+RRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADG
+APVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWRAQEPSEESVIELLESRG
+VPYTTWAGWHALDEHEKSLGVQATEAGPVARERVKVVDREEMTRISREGVLLGAGG
+>GCF_002008305.4_01771
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>GCF_003691675.1_00706
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDA
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAGG
+>GCF_003691675.1_01478
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>GCF_005280335.1_01106
+MTERPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGAGGVRPTDETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDADGVPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDVDGLWTAQDPAEESVIDLLEAREVPY
+TTWEGWQALDAHEKSLGAQATEAGPVERERVKVVDREEMTRISREGAWAPTA
+>GCF_005280335.1_01897
+MTLTPSSPKPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSYGGADFASWYDGHPDVPRHWPLDATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDREQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVRYTTWAGWLALDDHEKALGVQATEAGPVERERVKVVDREEMTRISRESVLLGAGG
+>GCF_020097155.1_01032
+MTERPDRPLRIAVVGAGPAGVYTADILTKEERDFQVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFIGNVDVGTTVSLEDLRRLYDVVVFTTGAVRDAALDVPGVE
+LEGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLVTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRTEQASRRLHLHFLQAPEEFLDADGDGRVDGLRMRRM
+ELDGQGGITPTDETVDYDVQAVYRAVGYFGSPVPGVEFDDVRGVIPNAEGRVLDAAGHPV
+PGLYTSGWIKRGPVGLIGSTKGDSLETIKHLIEDEPGLYTAEDPSEQAVLDLLAERGVDY
+TTWEGWHALDAHEKALGAEATQAGPVERERVKVVDRAEMTRISRAGTGLA
+>GCF_020097155.1_01844
+MTPTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEQAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETITHLIEDEPGLWRAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRKSILLGAGG
+>GCF_023573625.1_00935
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAEG
+>GCF_023573625.1_01700
+MTARPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVPGVE
+LAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAQGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000022.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f9fa834ff5f114dd84d2c3a1966b6a64271837d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000022.fa
@@ -0,0 +1,109 @@
+>GCF_002008305.4_00633
+MSTPHHHDHPTDQTAEHPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>GCF_002008305.4_01289
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>GCF_003691675.1_01008
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>GCF_005280335.1_00405
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVLREGSVIGAVALE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>GCF_020097155.1_00711
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQHTGHQGHAMDHGQHSGHT
+GLDEHGGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGY
+EVPGWAGWVAAALGTVMYVWGGRPFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATL
+GLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAALLPDEAERVEGENVVKV
+APADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATD
+SGLRVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWT
+LIGMPDEAVVRTITVLVIACPHALGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDA
+VLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEHPLAKAIVTAAKDKGFAL
+QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEAWRSEGAIILHVLRGGQ
+VVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPED
+KSAKVSQLQEEGKRVAMVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSV
+LSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGILAPVGLVLPMSIGAILMSASTVVVA
+LNAQLLRRIDLTPEASTRSVLERQK
+>GCF_020097155.1_02196
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>GCF_023573625.1_00598
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>GCF_023573625.1_01247
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000023.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..439411437fce3da9b8059c6a5d5019a59c343eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000023.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_02238
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>GCF_003691675.1_01940
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNILAQFRLV
+KAALPHLKPGSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>GCF_005280335.1_00513
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVAQAVEAMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNILAQFRLV
+RAALPHLKPGASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSYVVGATIAVT
+GGMPTP
+>GCF_020097155.1_00440
+MTDVSTSTDTAVGDSDTRPAAARTDAPAATVLLAGRAALVTGGTLGIGSGIAASLRDAGA
+RVAVTGLTEQECAAAREAGFPAYVLDVRDRAACAEVVGAVVEEFGGLDVLASNAGIYPQA
+RIADMTDEDIDLIFDVNVKGTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYG
+ATKAAQLGFVRSAAIELARQGVTVNAVLPGNIITPGLEEMGQEYLDSMARSVPAGHLGEP
+ADIGATVAFLASDGARYITGQGIVVDGGQILPETPEALEGL
+>GCF_020097155.1_00454
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVERAVQELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINILAQFRLV
+RAALPHLKPGSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>GCF_020097155.1_00650
+MGIHYARDSTAAEAVVERVNEAGASGVLIRADLAEGAAGAAHLATRWRDEVRRHDARGTD
+VLVSNAGINGAQSLSELDEGTVARVVNVNLVAPLMLVHHLSDHINDHGRVIGISSGFARI
+AAPTHVAYTASKAGLEAAFRAIAAELAERDITVNTVRPGVIDTDINADWINEPGARDAVA
+AAAALRRVGQPDDVADIVAFLASHSSRWMTGQSLDATGGTQL
+>GCF_020097155.1_01865
+MSTHDLPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLKGRRALVTGGD
+SGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVDLRDEAATRAL
+VRDAVKFLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVFALIWIVQEALPHLPAG
+AAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTPRGIRVNAVVPGAIWTPIQV
+SLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASYVSGEVLGATGGTLY
+>GCF_023573625.1_02170
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000024.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d56c384ea46586746399baad6dfdabbbcc6cc82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000024.fa
@@ -0,0 +1,101 @@
+>GCF_002008305.4_02297
+MSSDQRTASAPRHALPPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTG
+GAGPIGQLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAEAAQQAARE
+SRAAEQSKRAEASASASPGSAAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGTDVTLIGDSVSLSAAPTLMEELPGMLLEAEVGYQIWDAADELEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMAAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>GCF_003691675.1_01990
+MSSDQRTAPVPRHALSPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFTGAFGRWGAAARRAFTG
+GAGPIGRLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARE
+SRAAEQTKRAEASASGAPGSAAPGDAEGSAGATPSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGPDVTLIGDSVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>GCF_005280335.1_00439
+MVRRDVWPTIAGVPSLTPSSPVRSAEERTDRGGGSRTRPLVHADRPGIRVSPGPGRIPAL
+DGLRGVAVLAVLVFHAWPALLPGGFVGVDMFFVLSGFLITTGLVRGVDGGRGLRLGPFWM
+RRVRRLVPSMVVALVCCTALAWLAVAEFPAGLGRQWLGALTYTSNWVMILSGSDYFAAAT
+PPLFEHLWSLAIEEQFYVLWPLVVAGLLTLFWPREPTLRGAFRADRARVLTVLALAAASA
+VWMAVGLRGGAPHTRLYFGTDTHAFGLLLGAAVALMLAHTRRPEHGGAVMRNPPVRSAIA
+WGLFAALLAAFVLVDGREDVTYLGVLAGLSLVVTLLLFHVVQGNRQDSFSRAMSGDVLRW
+WGRRSYAAYLWHWPLLVILRTALPVDAPAWVDPVAAGGVLVLTAGIADLSTRWMEEPIVQ
+RGFRGAFAHWRAGLRTATRGIGGKAAAGAAGLALVAVPVAAVAAVVHSPAETALQRQIAE
+AEAALEQARQAQAAARAEASARAEAERAGAAEEAVAKDSQEDAPGAGAGGDAGSAAPTAS
+STPSDTAAPSAGEDPAVEVAADPTASAEPEPTAEPEPEPPLTGDPSVTRPAFTGAELTEP
+MPPSSVGPDVTLLGDSVALSAAPELLAALPGIAVEAEVGFQVRDAAARLAELDAAGMLTD
+VVVVSLGANGNAELGDWDRILAAAGPERLLVLVVPHGPMDWIGPAQQEMAEQAALHPDRV
+VLADWDAASAHVDEWSADGVHPKGNGQGIYARLVRLTVEARLGLR
+>GCF_005280335.1_01839
+MAVLSVLVFHAGVTALPGGFVGVDVFFVISGFLITGLLLKEVDRTGRVGLAEFYARRARR
+ILPAALAVIVLTVAAGLLVYPVSEWTRLGSVAVASALSVVNWLFARESTDYFAQEEAASP
+FQHYWSLAVEEQFYLVWPLLLILVTVGVAALRRRGAGDAAPDADAGARRRPSAPVAARRV
+LLASAVIGLASFVHSVSYSASDPGAAYFVTTTRVWELALGAGLAAALVVLPVIRPAVRTV
+LGWAGLGMIAVSLVLITGAMAYPGSVALLPVVGSALVILAGAHEDGSTPGHPARLLATRP
+MQWVGDLSYSLYLVHWPVLTLAAWRFPDGRLPLWLGLILAVVSVGLAWALRRWVEVPAMH
+GSLLAGRRRALTRGGLGMAAVAAAGALVLAAGAALAPARPGEESPVAGARAVMDGQDPMA
+ALAAGMRIVPDPAVAKEDRSPRSAAGASSRTPRPRAWSPRRACWRTASPTRSATSGTAPC
+PTSWTGSTRTSCWSRAPGGRPWRRTPRRRWPRRGGS
+>GCF_020097155.1_00392
+MTVSTSDHHAARPAPRHAQAALADGPAPRTGLRVSRGPGRITALDGLRGIAVLAVLVFHA
+WPEALPGGFVGVDMFFVLSGFLITTGLVRGVDAGKGLRLPSFWMRRIRRLVPAMVVALVA
+CTALAWLAVAEFPTGLGRQWLGALTYTSNWLMIFDGGDYFDRASPPLFEHLWSLAIEEQF
+YVLWPLIIGGLCLVVRPKRDTYASGRVADRRRILVVLVVALASAAGMVLGSLGGADQTRL
+YFGTDTHAFGLLLGACVSMGLAHVPRPEHGGPELRTGPARTAAAWLAVVVLFTGFALVDG
+TQDATYRGVLVGLAAVVAFIVWHVAQGDRRDSLSRALGNPFLRWWGRRSYAAYLWHWPLL
+VIMRIVVPVDAPSWAEPVAAGAVLLLTAGIADLSSRYFEEPILQKGFRGAFGGWGDAARR
+AFGGAFGPGGRLAAGATALALVAVPVAAVAAVAHSPAQTQLQEDIQAAEQSLQDAQAQQQ
+AQLEARRSAQAEKSKDAEAGGAEATGSAGASASPSGSTLGDPQVTRPEFTQEELTASLPP
+SDVGSRTTLIGDSVALSAAPALLEEMPGIVVDAKVGFQIWDAADKIRAMDREGTLGDVVV
+LSLGANGTAGRGDWDKIRQAVGPDRLLVVVVPHGPMSWIEDAQRKAVEQAEAHPDQVVLA
+DWEAASTYVPGWSADGVHPGHEGQGIYAQLIRLTVEERLGLR
+>GCF_020097155.1_02437
+MPRPVDTKASYFPGLDGLRALAVGLVVAYHLGVPGTDGGLLGVGVFFTLSGYLITSLLLR
+RHERHGDLDLKNFWIRRFRRLLPAVVLVLIAVLAATALVSPDLLGARLGQSVAALLYVAN
+WHTILSGRSYFDQAEGAGPLDHLWSLAVEEQFYLVWPLVLLGLLALTRRLGPDARRRVLA
+AATLVLGAVSFVLLAVFADPAGDSTRAYEGTDTRAGGLLWGAVLAFLWRPDRVARLTGRA
+SRVVVDLVGVLGLAGVLALSATTGQEDAALYTWGLAALTVATCAALLPLVHPGSWVARVL
+GIPPLQWIGARSYGIYLWHMPVVAFLPDRVLFGQPVLRGLLIVALTLVLAALSWRLVEDP
+IRRHGLVAALARARGVLGVGAVAVLASGALVLTAALPQTSAQEIAAQEPAAPAGDAVAHP
+ALDGRTSCTSVLHVGDSTSLASGNTDRTRIADPAQRITGRYEAVGVETVVEDIAGGRSTR
+EHIDGSADLNAPEAVAAGVSRLDAGGCVVVNVGLNDAATMTKDDAWDQAAARIDAVVDAA
+DGRPVLWVGPAIMPWSSRPYYEPAGAERFTRALVDATARHPDLRVHDWARESRSHPDWYL
+SDDANHNTEAGAVAKARSMAAALTAAFPAGRPASAEKVVLGE
+>GCF_023573625.1_00587
+MTNPPVYPRGYRPRHAADGPDSTPAAARRRADWRPEIQGLRAVAVLLVVVFHIFTDRVSG
+GVDIFLFISAFFLTGSFTRKMESGRPLAVGRYWLHVFTRLMPMAVLTILTTLVAVATVYP
+LADRASWRTEALASALYVENWALAFNAVDYYAADNTSLSPFQHFWSLSVQGQVFILWPLL
+FLVSALVARRTGARPRAVLTTAFASVFVVSLLWSVTQTSQNQAFTYFDTRARLWEFALGS
+LLALALPFLHLGRRTRVFLGWAGLASMIAVGVVVDVQGAFPGWIALWPLMSATAVIVAGT
+SGSHFGVDRILASRPLTRLGDSAYALYLVHWPLLITYSVLTGSQKPGAAAGVALVLVSLG
+TAILLSARVERPLRAWGWPQTAAWRSAVVLGACAALVVAPVTLWRGAEAAESARVLEAAD
+RNNPGAAVLRPDYEPAGDPGAPVLPVVEGRYPFPEYPEECDPALEAQLTEVGAESCHVLV
+PQADPAGVVLMAGNSHVMQWSPALRRLGEERRLEVVSYTRGSCLVAPMEEQVDDSPKCPD
+FLADLNLVVEHVRPDVVFMQGTRSTYEDEEMLTPGMTGRMEEIAGTGAHVLALRDNPRFA
+AGSPTTCGTMHGVDAVTCRWTHAVLDPNTSPLAGLADAHPRIAQVQLNDMICPDRQCQPT
+VGNVHVYWDDNHLTPTYVETLAPVFIERVLAALEHDGMRLGR
+>GCF_023573625.1_02238
+MPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTFLRGGFVGVDMFFVLSGFLIT
+TGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFPAGLGRQWFGAL
+TYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILWPLLLWGLLLLTWPPRSTVNS
+GRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGTDTHAFGLLFGACVAIGLAHV
+PRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHASTYRGVLAGLSAVVAFIVWHV
+VQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAIL
+LLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTGGAGPIGRLAAAATALGLVAV
+PAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARESRAAEQSKRAEASASASPGS
+AAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGD
+SVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTTHRG
+DWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKAHPDRIVLADWDAAAKQHVTD
+FSADGVHPRADGQAMYAQLVRLTIEDRLGTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000025.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f7be3f08997ef33bb85acb344bbd8d90d18ec88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000025.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00099
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>GCF_003691675.1_02112
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>GCF_005280335.1_00292
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK
+>GCF_020097155.1_00617
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+>GCF_020097155.1_00670
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
+>GCF_023573625.1_00094
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>GCF_023573625.1_02014
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000034.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb60a4316f89180c15bada6d7fd04648cf6326ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000034.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00617
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_002008305.4_02075
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_003691675.1_00340
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>GCF_003691675.1_01780
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_005280335.1_00718
+MNLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLRAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHILF
+PIVLIGLGIVILVSGGAFGL
+>GCF_020097155.1_02214
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>GCF_023573625.1_02003
+MTLSSALQAIGLFLVTNIDDLIVLSLFFGRGAGQRGTTVRILVGQYLGFAGILGAAVLVS
+LGAGVFLPPEVIPYFGLIPLGLGLWAAWQTWRGDDDDDDDEAKIEGKNVAAWTVAGVTFA
+NGGDNIGVYVPVFLSVGPGAVVAYCVVFLVLVAGLVGLAKFVATRRPIAEVLERWEHILF
+PIVLIGLGVFILISGGAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000040.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c5622d4172fd261b74a383cb697bdd819cb9bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000040.fa
@@ -0,0 +1,63 @@
+>GCF_002008305.4_01015
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+SAVVRDPNERTHS
+>GCF_003691675.1_00729
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTVV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>GCF_005280335.1_00822
+MSSVLDAAGTPATPHPSPAAPSARVPSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAG
+GITSNFAVTGLLGVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAGVG
+AALVALVSYACMQVGIAGMFGFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFS
+AKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQLFTSGVGAALVFSVAAFMGFE
+SGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSAWAMVMTEGPGGVVAAAQAVGPDVVF
+AFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGA
+PVGGSLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLMALTSVSVI
+GYLRRHRDEFGVFTRVVAPALAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTP
+GALGTAWALWLRARRPATYAGIARGGELS
+>GCF_005280335.1_01873
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTALDSTDPDYG
+SGSSVFGVGTVFVLGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>GCF_020097155.1_02256
+MLSTHQSVSVSTSSVAPVYSAVVTVPLVVGLVGSGAPLAYLLALLPILGVWAGMSANDER
+EPDKGSVYSWAVTGHPVLGWTAGWCLALTGIVATSGLAYVALDAWLPGLGAGVKVLIGAG
+IIAAATALASANVRITAAVQTAGVLVQVAATAYLAWVLARVGLTPLPPAGTVQDWVHAVL
+LAVFAFWGFDAVYALSEESHRGVPRRSAAVSLGLLAAIFLVFSALGASEDPAAVAALTHP
+VVMAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLAPLRAAEVVSALLAIAWLVVSL
+AVPGVFEDSIEMLSVFVGGYFTISSATAAAHASGGARMLHAATAVVMGLITAASLAWMFE
+PDYGATVVGGVGGVGLLAVGFAVLGLILAVGAGHRGRAVHPTSGV
+>GCF_023573625.1_00958
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALG
+>GCF_023573625.1_00959
+MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIA
+DLAGNLWVNIPLTLVYLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG
+AGFDPTPVQLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAA
+VTVFVIIAVYILSALAVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAIL
+VSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTR
+LLSENALWDTITALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLV
+MFCVTAMDSTDPDYGSGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQT
+DSTRPIPIIRPDDDGTAVVRDPNERTHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000042.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54e60f6605fb7109614db780c14f379297d44221
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000042.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01288
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>GCF_002008305.4_01627
+MTMRFWTRTVAVTAASLLALTGCATGGEEAATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLMADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+SAG
+>GCF_003691675.1_01007
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>GCF_005280335.1_00620
+MKTRRLTLAAVGILASAGLITGCSTADDAGPSASPSSGQSAATSSSQPASESGSASESAS
+GGGHMDHKMDGGPAPEGIAEAASPAHPVGSEITLTADHMPGMDGATARITGAFDTTAYSV
+DYTPTTGGEPVEDHKWVVHEELQDAGDAPLQVGDTAVMEAEHMAGMKGAEATVASVTDET
+VYMVDYTADGMTMTNHKWVVESEIQPKG
+>GCF_020097155.1_00712
+MQRRLRTGLAAGALGVALVLAGCASGADDNQQTDPSATEEHQGHGGNNAESGDEEMEHPM
+DGGPAPEGIAEASEPTYPVGTEVQLTADHMEGMEGATATISGAFDTYTYSVNYTPAGGGD
+PVTDHKWVVQEEIEDAGDARLADGTEVTLLAEHMEGMEGVKAIIASSTDETVYMVDYETD
+GMKMTNHKWVVESEIQPAS
+>GCF_023573625.1_01246
+MRKHLMTTVAAGVLGGALVFTGCSTGGGQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANATIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>GCF_023573625.1_01556
+MTMRFWTRTVAVTAAGLLALTGCATGGEEVATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLVADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+PAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000043.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d29211da5b9df14e5ffdfd88c43ea5b3129eed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000043.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01397
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_003691675.1_01130
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_005280335.1_00412
+MPKEQTAGKPTTRRYSPEEAAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVKQ
+ADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155.1_00325
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155.1_00648
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_020097155.1_02216
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>GCF_023573625.1_01347
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000045.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26068e61a31bffd25efdfa2a1afca2805cf8284c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000045.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_01590
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRELGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>GCF_003691675.1_01302
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>GCF_020097155.1_00643
+MLFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRIGDDYGR
+RRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAK
+AFGAYGAVQGLASVAGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDSRA
+AARSRLDGVGALLAAVGVLLVLLPLVQGRDWGWPTWGWALLAAGVLVLAGFLRYENALAR
+RGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTGRSAWDTGLVILPY
+AIGSMLTSGAGVALAARAGRALLLTGSLTLAASQALLWWLVRDGSTTPDYWPLAGAMFLG
+GLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGPA
+TAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD
+>GCF_020097155.1_00714
+MAGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTL
+LAALLYLGPLSDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPA
+LSAMMIDFESPSHRNIAALWNTIGPMIGLGAGALGAALLLDLTSEPTTAVFGSLVLAFLI
+VATVVWSTPELVPKTQIRRGDLRPRFTVPPHLRRMFTVGVPVIIAGWATNGLFLALGADL
+VGSELGGSTHTQAGIVLFALAISGVTASSVLQRRSARTISLYATSALAFGTAVSIGALAL
+GSYPAYVASVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAG
+LLVPVLTLSGTMTILGAIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPD
+REEQP
+>GCF_020097155.1_01240
+MNPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSIS
+GYTLAFGMVLVPAGRAGDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGA
+GLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVAAGPLLAGGLIAVLGGDLGWRATFL
+VNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFLDRGLGPWRFA
+LLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVA
+MFMQNGLGYGALQAALVGLPSAVCSSVMATVAGRLVLRAGRRLVVVGVSLVLAAVVGSIG
+VVAAHQAFGLSPWWLLATLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVG
+TSVGSAVIVGVYLGVAGTGGPDRGFMAALGLIAVSIAAALAVAVADQRRRARQGGR
+>GCF_020097155.1_01828
+MPRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIV
+WGACSDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILS
+HLFEGKARAQAFALFGTINGLGLAAGPALSGLLLSAWGWQGIFAAHTIVLIVAFIGAARL
+PQLGRGGTSLREILDFSALKAPKFLAMTLVPIAGAIGFVTFLTYLPSALGAIHGLTAGVT
+GALMLVMTIPVLIAPVAVHRLMERSHLTPTAIVAVSFACLIVGGIGVLLLLRPDLPVALG
+VTPMILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAV
+ITTTLPGTTGELIASGSPGEPWIYHSGLMAAAGTMIGLVAIAGVTFLALTRAANRSAVTA
+RQVEVAR
+>GCF_023573625.1_01517
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASSADWDGAFMAAFALVAGCMALALLVALADLRGPRTAAPR
+G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000051.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ace5cb5ec6e2d261e9a86b402418c9c61d32d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000051.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_02094
+MNMLQAIRRYYAGYVQFSGRASRADFWLAALYVWLLQAAVRFVSTALDVFVLGAPDPSLR
+DAAILLVGITHALPSLALLARRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGATAARR
+>GCF_003691675.1_01802
+MTMLQAIRRYYAGYAQFSGRASRADFWLAALYVWLLQAVVHFVSTVLDVFLLGSPDLSLR
+DAAVLLVGITHALPSLALLARRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGATAARR
+>GCF_005280335.1_00684
+MNMLQAIRRYYAGYAQFSGLASRADFWLAALYVWLLQTAVHFVSTALDVFILGSPDLSLR
+DAAVLLVGVTHALPSLALLARRLHDAGFSRAWLLLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGVTASATAARR
+>GCF_020097155.1_00599
+MSTALDVFILGSPDLSLRDVAVLLVGITHALPSLALLARRLHDAGFSHAWLFVGLVPLVG
+PLTLLVFALQPTAPRFGHPTDASDPVPAGPRPRGADPRRHVRPDQ
+>GCF_020097155.1_00600
+MTMRQAIRRYYAGYAQFSGRASRADFWLAALCV
+>GCF_020097155.1_02101
+MTQPHDPSQNPYGQQPAAGQPPYGQAPSGQSQYGQADYGQTQYGQTQYGAPSPGYGYGYQ
+PGVPFPEDPRVAPAPGVGPVEAVKRFYTRYALFYGRASRSEFWWVQLYLVLVSLVLTALM
+FAVLVPAGAFSNTTTELSEAGAVGVLAITGLFLVFVLAHLVPSIALQVRRLHDAGFSGFW
+FFIGLVPYVGELVLLVLSVLPSKPEGARFDR
+>GCF_023573625.1_02031
+MTFLRAVGRFYGRYAQFGGRGGRAEFWWVVLYLSLASLGITLLFGALGADTTTAAPSAVV
+FPGFAVSGLSVPAVDSMTEAYQAFSGVWGLLHLVPAWALTARRLHDAGLSRAWLLLALLP
+VLGAIALLVMVLQPSDPRVAAEHVVEVSVGHAPERESIGGLRDHPTILPTALNRLLVFDM
+CVKPPPPRSPRCRRRGLPRSPHEDAEGVAGRVREHVQGLVLVVGAVQDEAPAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000063.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b90e2fcfb63e029ed9978f664725cab231f9ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000063.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00105
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR
+>GCF_003691675.1_02118
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR
+>GCF_005280335.1_00038
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF
+>GCF_005280335.1_00285
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA
+>GCF_020097155.1_00231
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS
+>GCF_023573625.1_00100
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000067.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f848174799f817ad17ca35e89699c348dd8b04b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000067.fa
@@ -0,0 +1,53 @@
+>GCF_002008305.4_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>GCF_003691675.1_02200
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSTVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>GCF_005280335.1_00184
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARD
+YNTLGYWTHLAQTLEKGLFDGLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAM
+AAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQM
+EHDERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGHEGRYFKVPGAA
+VTEPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINSPTKELTAATVKKIRQALVDAGRDP
+YDVKIFAMQTIVTGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDV
+KSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDV
+DGYNLAYHITPGTFEDVVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASF
+ALRRRG
+>GCF_020097155.1_00130
+MSTAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGTWFKVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>GCF_020097155.1_00132
+MSTPTPTLGIALTTQTPADARGHWTRLSQALEETSLDWAVLTDPLGTAPQAGTHRIDAVL
+AACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGWLATVSAAPEVSALFG
+RRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWESWEPDAEIRDIATGRFIDRERVH
+HVDVEAERFSVRGPSITPRPPQGRLPVLVEAAGPAGLEAARRTADVVLLPAAEVGRTDAA
+RLPDRRRRGATPAVPVEPTRIVADVTLEGDGARVADAVRHALQAGADGARLVPNPTADPF
+DALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPEDPTARPTDEEATA
+>GCF_023573625.1_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000069.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98860b048cc772c9f9737dcb746b5c09afa24193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000069.fa
@@ -0,0 +1,108 @@
+>GCF_002008305.4_00221
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKAH
+GAKAEISFQRAVNAFVAELTAEEAQSIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPDTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAADKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATVVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGREVNVPSLAIPDVVG
+SATVTRTVTALENGRWQFSASVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSAAVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLVSSALAVSTVTVEEGTKSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>GCF_003691675.1_02234
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKTH
+GAKAEISFQRAVNAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPNTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAAGKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGRDVNVPSLAIPDVVG
+SATVTRTVTALENGRWRFSANVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLESSALAVSTVTVEEGTQSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIADPAPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>GCF_005280335.1_00086
+MTPPLSRRHRALGMTSALALVLTGASAAGATSGTGAPAAAEADAVTAVTGAAGTADQGPR
+TAPEVFEDGGYIVLMAEAPVASYDGGTPGYAPTKPGKGLGRDKGFNPKSANAKKYAAHLE
+RGQDRALERAGAEAAPHTRYTTSLNGFAGELTAQEAAALASDPAVLAVVPDEIRQPDTVS
+SPDFLGLTGKKGLWAQVVGKKAPATDAGRGVVVGVVDSGIRPEAASFQDRGHPAAPADWA
+GGCETGDEEAFPADSCNDKLIGAKYFVQGFGAGRLAPVETLSPLDAGGHGTHTASTAAGN
+AGVPAVVDGTPRGEISGMAPGAHVAAYKACWEGVPSGGCATSDTVAAINAAVEDGVDVLN
+YSISGTTSNVVDPVEVAFMHAAAAGVFVAASSGNSGPTVSTTAHPSPWITTVAASTQAVY
+EQTLVTGDGQRFIGSSITAPLEAETPMVHAADLAADGVDAARAALCLPGTLDATAAADML
+VVCDRGENARAEKSQVVADAGGAGMVLVNVADSGLNADLHALPAVHLPHTERDRLLAYVD
+TEEPTGRILPTTEGTTTRVPEVAGFSSRGPSLAAASDLLKPDVSAPGVDVLAAYSPDEAG
+EDFAYASGTSMSSPHVAGLAALVKQGRPDLGPMEIKSSLMTTAGDHASATSPFAEGAGFV
+DPMKILDPGLVFDTDQGDWYDYLAGQGIVFSGSGEPVSETPIDASDLNVPSIAVGELYGS
+QTVTRTLKNVGGNNGVWTARVEGMEGMDVSVSPQVIKPRRGQEQDVEITLTAAGAPAGQW
+ATGHVVWSGPAGKEVRIPVVARPGVADAPASVTVDRDADGLELPVLSGVDGTFTTRVNGL
+TAGTEHIGTTVRRMFFDSTDPALTGHDFAYPRGYPTVRIEAETSAEDVDLDVYVTGSWTS
+YPVARSVTRGTGMEVFQGPIYSSAPQHRIFVVAKTGADGVEHDEPIDYTLRVFFPQAGGG
+DNGVLSFDPASAAVKPGQTHVFHGTLNTDGTSVYTGTVDILHEGKVVDTTQIRVQ
+>GCF_005280335.1_00159
+MRKAEAMPHIPTPARRRRALAAAVVGASLVAAPALAASAIAVELPDGSVVTSPQGEAKVE
+QQFEDGRYFVVLKDAPSVTAQEAGAPAPGAAPKAKFDPDHPRVKNYEAKLQRQQEKVARD
+NGVEPKTTFQRAVNAFVAELTAEEAMRLSKDSAVLGVAPDEQVAPDYSSTEFLGLPGKKG
+TWNTTYGKPENAGKGVVVGVIDTGIHPDNPFIDAEPVKPLKGKAKVGEPYRTADGDIAVL
+KADGTTATAECETGPGFPADSCDTKLIGAYAFSDDFERFVPVENRHPAEQLSPLGVFSHG
+THVATTILGNTGVEQTIDGTSFGEGAGVAPAASLISYKICWEDNDPNTGGCYTSASVAAI
+EQAIENNVDVLNYSISGSNTTIVDPVAMAFKSAAEAGIFVAASGGNSGPTPNTVNHSSPW
+LTTVAAETFSNELTGTVEFSDGTKYRGASSAGSDAGPAEVIHASEVAAGDAEAARLCLPG
+SLTAEAADKIVLCERGQNARVEKSAVVAEAGGVGMILANTPTGSLDADIHSVPTVHINDT
+DGVIEKVKSSDLTATIVRGDTTGLPQDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNV
+IAGVSPLDPDYNGNEFGLMSGTSMASPNLAGMAALLIGKEAAWSPMAVKSALMTTAGDVF
+NADGSVNEDNFATGAGSADPKAAARPGLVYEADSTQWDALLLGEIAGREVNVPSVAIPDV
+VGSASVTRTLTATENGRWQFSGSVPGFEVTASPSMLDLKKGQSAEVELTFTRTDAEVNTW
+AHGSMSWSTAKGKAVPTVTSPVTLKALSATATSAVEGSGAEGSATVEIEPGMTGELTPQI
+LGLGKVEAAEVSAVANTSASGAALAGRVVNVEEGTKALVASINAGAEGVDWDLYVITPQG
+RQLNMATAAGDETLTIQNPVPGEYTVIGHLYSAPAGTDTASLETLKLREDVGNLTVDPNP
+VPVTTGEATTAELAWSGLTEGTWKGLVTWDAGVTTDVTVTVP
+>GCF_020097155.1_00117
+MNRHPQRLRLLGAAVTAVGLMAAPLAAPAFAAPQAEHAVGVQAATPLKAGRYFVILKDAP
+SAVAESQATAPGAAPSAKFDANHPRVKNYEAKLKRQQEKVAAQQGVTPKVTFQRALNGFV
+AELSAEQAQAYAEDPAVLAVTADEQVAPDYTSTDFLGLNGKKGAWNTTFGKAENAGRGVV
+VGVIDSGIYPDSPFLDGTPVGPRTNNGKLKAGDTFRTADGRIAVQKADGTLATAECQSGP
+DFPASTCDSKLIGAYAFSDDFVRGTPVEKRDPAERISPLGVKSHGTHVATTIVGAKDVEQ
+TIDGASFGLGSGVAPAAKLISYKVCWEDTDPDTGGCYSSASVAAVEKAIENNVDVLNYSI
+SGNNTSVVDPVALAFRSAAEAGIFVAASGGNSGPTPSTVNHSSPWVTTVAAETFSNELTG
+TLELSDGTKVRGASSARTGVGPAPVIHAADAAAAGVSADDARLCKPGALDPAKAAGKIVL
+CERGVNARVEKSAVVKDAGGVGMILVNVTPGSLDADIHAVPTVHTNDASLIAKAKAGGLQ
+ATIVPGDTTGQAPDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNVIAGVSEYDSDYHG
+NVFGLMSGTSMASPNLAGMATLLIGKHPEWSPMAVKSALMTTAGDVYNADGTVNQDNFAT
+GAGSADVAAANRPGLVYESDATQWNALILGDLAGREVNVPSVALPDVLGTASVKRTVTAL
+ENGRWTFSGSVPGYTVTASPSVLDLKAGQKAEVTLTFTRTDAALSQWTHGSFSWTTAKGK
+AVPSVTSPVTLKSVPATADASVTGTGASGSAAVAVQPGFTGQLTPSVLGLNKVESQAVTL
+QPGGSKVTPVTVAPGTKSVTFAVDSGVDTADWDMLVQTPSKKQFTSATESSDESVTIQDP
+EPGTYLVLTQLYANPAGADTAALETVQLRSDAGNMTVTPNPIPVTTGQETSATVNWTGLT
+SGTWRGQVTWAEGTATQVEVTVP
+>GCF_023573625.1_00222
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKAH
+GAKAEISFQRAVNAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDGDSFGEGAGVAPAANLISYKICWEDTDPDTGGCYTSASVAAVE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEAAAGDAEAARLCLPGG
+LTEEAADKIVLCERGVNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGRDVNVPSLAIPDVVG
+SATVTRTVTALENGRWRFSANVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLESSALAVSTVTVEEGTKSLVASINAGAAGADWDLYVITPEGKQ
+LSRATAAESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGEATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000074.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9b945a07f9242bb251ae3807342f26cd6c38700
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000074.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_00279
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>GCF_003691675.1_00203
+MPSLFDPLDVGALRLDNRIVMAPLTRQRAGEDGVPTELPAEHYAQRATAGLLVTEGAFPS
+FRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGRMCHPDLLRGAEPEAPS
+AIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFADAARRAVEAGLDGVEVHGANGYLL
+HEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAIGAERTALRISPEHNVQGTIEEDR
+ADVLATYDALLAGLADLDLAYLSVIHQDVAGDLAAHLRESFSGPLVLNSGFGAVTGLEEA
+RRIVEDGLADAVAVGRELIANPDLARRWREGLPLNEPDPTTFYTGGAHGYTDYPFVDGSP
+SS
+>GCF_003691675.1_02294
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>GCF_005280335.1_00074
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>GCF_020097155.1_02346
+MPDLFDPLPLGGLTLPNRVTMAPLTRQRAGEDGVPGDLHVEYYRQRASAGLIVSEGVFPT
+VDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGRMCHPDLLRGAEPVAPS
+AIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFASAARRAVDAGADGVEVHGANGYLL
+HEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEIGAERTALRLSPEHDVQGVLEQDR
+ADVLATYGAILDGVADLDLAYLSLLHRDVAGDLVAALRARFGGPVLLNSGFSEVTGAAEA
+RRIVEGGLADAAVVGRALIANPDLVRRWREDRETNAPDPSTFYVGGAHGYTDYPSLEG
+>GCF_023573625.1_00278
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000076.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e117940976cd46c867932b2046c43f1e05556689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000076.fa
@@ -0,0 +1,165 @@
+>GCF_002008305.4_00287
+MSGPAESAAGTATPAADVVLGRFTEPTRAWFTGAFETPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALTGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDAPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGTPGGAAAG
+DTAESAGTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLGAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEAAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GAASLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGTAGGTGGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSSEGGARGTAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEESGELRAAAEALVWALRTGHTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN
+>GCF_002008305.4_01958
+MTTSVEGFSALDPVIQHHIVNTLRWPDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAF
+FPVLTRAEREQWTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSASVRHGDTTQAERRRQ
+GTERPDVLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERL
+SAVVRRPIQRIGLSATVGNPEELLTWLQGGNAAAGLPASVIAPPVDRTGAAAPELRLDFV
+GSEDNAATVISRLHGGEKRLVFAESRRTVELLGNALHERDVTTFLSHSSLSLSERRRSEQ
+AFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQRLGRTGRRPGAQRNMLFL
+ELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILALTLQKGQLQRGAALAGLQA
+LGMSDSTTYRTIEDGLLEHGHLDSDGGLLFVGPETQRRYGGLYFRDLMAVFTVEAEFPVF
+HGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRWASPP
+RALSWALSDAMRRVLLGADPAGVVLTGRAQDALADHREAEGYTAAADHTVLASTADDLRW
+WTWGGAGANALLVAALEQVAPELLGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGD
+LAGVDPLVDDAAVRGLKFHEMLPLDLARATLAARLADHTGVARVLERPVQMLRTAEDGRM
+WG
+>GCF_003691675.1_02309
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLSALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAEVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAGGDAGGAGRAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLSLG
+KTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTSPEGGARGSAGLT
+AGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPGGF
+AGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDTAPLALAL
+AATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTLLA
+FTEDPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGIRF
+RN
+>GCF_005280335.1_00067
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+GLGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARSALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDSLLETPVQRIGLSATVEPASEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPSAAHDLGPGSSPGGPGAEGGPGGAVTGGSIWPHVEE
+RIVDLVAERRSTLVFANSRRLAERLTGRLNEIWEARLEAAAAVEDPDAVPGFRTPGAGAG
+AASSTPATPSSSYPAQVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGRIRCVV
+ATSSLELGIDMGAVDQVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTA
+VVAERMTAGRIEALRIPANPLDILAQQTVAAVAVADLDAQEWFDLVRRSAPFATLPLSAY
+ESVLDLLAGRYPSDEFAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLA
+SDGGPDGAPGGAAAGDTAESAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDI
+TADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPAAGRERLAAAGLDA
+WAQDNLLAYLKDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGA
+RLAQRYGLETGSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELEEIVTAEVGGSALF
+AARFRENAARSLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVY
+DLPALKDLAGRVASRAVRLVEVTTPAPSPFSQSILFGYVAQFIYEGDSPLAERRAAALSL
+DPTLLAELLGTEELRELLDAGIIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSAAEA
+ARRVRPEAGADDDGGAAAADVAAVGEMLAGLERAGRAFRLRQDGVERFAAVEDAARLRDT
+LGTPIPHGVPAAFLEPVDDPLGDLVSRYARTHGPFTAAEVGAALGLGGAVVLPVLQRLAT
+ERRVSTGAFRPDGAPGATGLDAEWCDAEVLRRIRLRSLAALRAEVEPVDQSAYARFLADW
+QHLRPRVGRDGAWRPPATLEGVDGVATVLDQLAGTPLPASAWESLVLPTRVRDYAPALLD
+ELLATGEYVWSGVAEAAGNDGWVALHPADAVDLTLRLPERPDGTGPDAAAPRDAALRADV
+REVLAGGGAWFFPQLVERVRAAQSARLGTGGPDGHGADLARGPAVLEALWGLVWAGEVGN
+DTFAPVRGLLSLGKTAHRTGRQTPRARTARTGGAGAGTAGRGLGGRLAGVRGRGRYAGLA
+SPDGGARGTAGPAAGMAGLSAAEQARAAGRWSLLPAAERDPTIRAHATAELLLDRYGVIT
+RGSVVAEEVPGGFAGQYRLLTRMEDAGQVRRGHFVAGLGGAQFSTGAVVDRLRGFQDDDG
+ADAPAAPRLDAFGLPLPAAPAEQRTPAALALAATDPANPYGAALDWPSVPAGPDGVVPTG
+HRPGRKAGAVVVLIRGELALYMERGGKTLLCFTQGAAELKAAAEALVWALRTGRTERLSL
+EKVNGGPVLGTPLAEAMLAAGFYSSPSGLRYRS
+>GCF_020097155.1_00046
+MREDGGEGPAPEEAAPSPAAVPDADAVLARFSEPTRRWFTGAFAAPTAAQLGAWDAISSG
+RHALVVAPTGSGKTLSSFLWALDSFVREPAEPDVSATRVLYVSPLKALGVDVERNLRAPL
+IGITQTARSLGAPVPEVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSKARSA
+LSGVRTVIVDEVHAVAGTKRGAHLAVSLERLDALLDSPVQRIGLSATVEPAAEVARFLGG
+VQPVTVVRPVSAKRWDLTVTVPLPDMTDLSTPPPSALDAGRDGAAAGVPGEATGGSIWPH
+IEERIVDLVAPRRSTIVFANSRRLAERLTGRLNEIWEARQEAAAAVHDPDLVPGFRTPST
+AGEVLTDWLGTATGQTPAGAPRPPGGSAATSFPAQVAGQTGTGSGTVSDFARAHHGSVSK
+EQRALVEEALKTGRIRCVVATSSLELGIDMGAVDQVIQVESPPSVASALQRVGRAGHQVG
+EVSRGVFFPKHRGDLVDTAVVAERMAAGRIEALRIPQNPLDILAQQTVAAVALEDVDAEE
+WFDLVRRSAPFSALPHSAYESVLDLLAGRYPSDEFAELRPRILWDRELGELSARPGAQRL
+AVTSGGTIPDRGLFGVFLATEASDGAPGGAALGDTAESASGASSGSKRSGGRRVGELDEE
+MVYESRVGDVILLGATSWRIVDITADRVLVLPAYGQPGKLPFWRGDAAGRPAELGDAVGR
+FRRELDADPDAARDRLAAAGLDEWARENLLTYLADQRESTGRLPTEQALVVERFTDELGD
+WRVVLHSPYGMAVHAPWALAVGARLAQRYGLETGSGAAMAADDGIVLRVPLMDAEPPGAE
+LFEFSAEELEEIVTAEVGGSALFAARFRENAARALLLPRRDPGRRTPLWQQRQRSAQLLD
+VARKYPSFPVILETVREVLQDVYDLPALKDLAGRIASRAVQMVEVTTPAPSPFAQSILFG
+YVAQFIYEGDSPLAERRAAALSLDPALLAELLGTEELRELLDPEVIARVEAELQRTAPDR
+RVRGAEALADLLRIVGPLSVAEAAARTLPVEDAAPAPADEAAAGAPSAAHLAAVTAHLEG
+LERTGRAYRVRLNGEERFAAVEDAARLRDALGAPIPLGVPVAFHEPVEDPVGDLVSRYAR
+THGPFTAAEAGAALGLGGAVVLPVLQALASQRRVSQGAYRPDGTPGATGLEAEWIAAEVL
+QKVRRRSLAALRAEVEPVDQAAYARFLADWQHLRPRPGRPSPATLEGVDGVATVLDQLAG
+VPLPASAWESLVLPSRVRDYTPGLLDELLATGEYVWSGTADAPGNDGWVALHPADAVDLT
+LRRPEPPAQDVAAERLTARDHLLTVLAGGGAWFFGPLVERVRADAARAAEAEAGGEDGPR
+DPHAAAATLPRGPVILEALWDLVWAGRVGNDTFAPIRGLLSLGKTAHRTGRQTPRARTAR
+TGGAALSAAGTGGRGLGGRLAGVRGRGRYAGLAAPGSGAGAGTLPGAGLVGLSAAEEARA
+AGRWSLLPDPEPDPTIRAHAAAEVLLDRYGVITRGSVVAEEVPGGFAGQYQLLTRMEDAG
+QVRRGHFVDRLGGAQFSTGAVVDRLRSFQRDEDGPSPAEEEPAPRLDAFGMPVDESPRTD
+WSGWVADGVGGWTPAPQGHGAGMGTVGGAAGAREEPLPPALALAATDPANPYGAALDWPD
+LPAGPDGVAPTGHRPGRKAGAVVVLVHGALALYMERGGRTLLAFTQDGPVLRAAAQALVW
+ALRAARTDKLSLEKVNGGPLLGTPLAEALLAAGFYSSPSGIRYRS
+>GCF_023573625.1_00293
+MSGPAETAAGAPTPAADVVLGRFTEPTRAWFTGAFEAPTPAQLGAWDAISSGRHALVIAP
+TGSGKTLSSFLWALDSFVREPAAEGTAATRVLYVSPLKALGVDVERNLRAPLVGITQTAA
+HQGRPVPRVRVGVRSGDTPAAERRRLQQDPPDILITTPESLYLMLTSQARAALAGVRTVI
+VDEVHAVAGTKRGAHLAVSLERLDALLDTPVQRIGLSATVEPAAEVARFLGGTQPVTVVR
+PASAKRWDLTVTVPVPDLTDLSSPAAAHDLGPGSSTGGLGDEGAVTGGSIWPHVEERIVD
+LVAERRSTLVFANSRRLAERLTGRLNEIWEARAEAAAAAEHPDAVPGFRTPDPTGFHGPA
+QVAGQTGTGSGTVSDFARAHHGSVSKEQRAIVEEALKTGQIRCVVATSSLELGIDMGAVD
+QVIQVESPPSVASGLQRVGRAGHQVGEVSRGVFFPKHRGDLVDTAVVAERMTAGRIESLR
+IPANPLDILAQHTVAAVAVADLDAQEWFDLVRRSAPFATLPFSAYESVLDLLAGRYPSDE
+FAELRPRILWDRENGTLAARPGAQRLAVTSGGTIPDRGLFGVFLASDGGADGAPGGAAAG
+DTAESASTASAGSARSGGRRVGELDEEMVYESRVGDVILLGATSWRIVDITADRVLVLPA
+YGQPGKLPFWRGDAAGRPAELGDAVGRFRRELDADPEAGRTRLAAAGLDPWAQDNLLAYL
+KDQREATGVLPTEQTLVVERFTDELGDWRVVLHSPYGMAVHAPWALAVGARLAQRYGLET
+GSGAAMAADDGIVLRIPLMDAEPPGAELFEFTAEELDEIVTAEVGGSALFAARFRENAAR
+SLLLPRRDPGRRTPLWQQRQRSAQLLDVARKHPRFPVILETVREVLQDVYDLPALKELAG
+RVSSRAVRLVEVTTTAPSPFSQSILFGYIAQFIYEGDSPLAERRAAALSLDPALLSELLG
+TEELRELLDAGVIAEVEAQLQRLAPDRRARGVEGVADLLRLLGPLSVAEAARRTRAEGEA
+EEAADEDAVAGMLAELERAGRAFRLRQDGVERFAAVEDAARLRDALGTPIPHGVPTAFLD
+PVDDPLGDLVGRYARTHGPFTAAEAGAALGLGGAVVLSVLQRLATERRVSTGAFRPEGTP
+GATGLDAEWCDAEVLRRIRMRSLAALRAEVEPVDQAAYARFLADWQHLRPRTGRDGAWRP
+PATLEGVDGVATVLDQLAGTPLPASAWESLVLPARVRDYAPALLDELLATGEYVWSGVGE
+ATGNDGWVALHPADAVDLTLRLPEPAEETPADAALRAAVLEVLAGGGAWFFPQLVERVRA
+VQAAAGDGGTGAAGGAVGPDPHRDPADLARGPAVLAALWGLVWDGRVGNDTFAPVRGLLS
+LGKTAHRTGRQTPRARTARTGGAAGAAAGRGLGGRLAGVRGRGRYAGLTAPEVGARGSAG
+LTAGTVGLSAAEQARSAGRWSLLPAAEQDPTIRAHATAELLLDRYGVITRGSVVAEEVPG
+GFAGQYRLLTRMEDAGQVRRGHFVDGLGGAQFSTGAVVDRLRGFQRDEEDAAVDAAPLAL
+ALAATDPANPYGAALDWPSVPAGPDGVVPTGHRPGRKAGAVVVLIAGRLALYMERGGRTL
+LAFTEEPGELRAAAEALVWALRTGRTERLSLEKVNGGPVLGTPLAEALLAAGFYSSPSGI
+RFRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000077.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17cab3036487ce2c0dfbd6595b174cf974a06f97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000077.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00297
+MLSEKSRPVIEATAAAVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPE
+VADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTFRFEPADDTP
+QSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDAS
+WEAVALREQVTESLAALAHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>GCF_003691675.1_00005
+MLSEKSRPVIEATAAAVAEHMPEITPKFYAHMFEAHPELLDGLFSRANQRNGEQAQALAG
+SIVRFAVHLLENPGTLPEAVLARIAHKHTALGITEDQYQIVYENLFWAIADVLGDAVTPE
+VAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTFRFEPADDTP
+QTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>GCF_005280335.1_00057
+MLSEKSRPVIEATAAVVAEHMPEITPKFYAHMFEAHPELLDGVFSRANQRSGEQAQALAG
+SIVTFAVHLLEHPDTLPEAVLARIAHKHTALGIVPEQYQIVYENLFWAIADVLGEAVTPE
+VAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTFRFAPADETP
+QTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEV
+GDVIELSNPYGDITLRDDAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASW
+DSVALREQVAESLQALENGTGRLWLGVPPQEAPAAFTTTEGLMEFDDVELPADASYLLCG
+PLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA
+>GCF_020097155.1_00035
+MLSEKSRPVIEATAAVVSANMPQITPAFYGHMFEAHPELLDGTFSRANQLNGEQAQALAG
+SIVHFAAHLLEHPDSLPEAVLARIAHKHTALGITEDQYQVVYENLFWAIAQVLGDAVTPE
+VAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTFRLEPADDTP
+QTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEV
+GDVVELSNPYGDITLQDSDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWD
+SVALRDQVLEDVASLPHAQADLWFGVAPETAPEGVSVHEGKVDTAAAALPEGADYILCGP
+LAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>GCF_020097155.1_01222
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPP
+PLTPAPGPAGIRDRPAGRIPAWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTS
+LGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHRRVGFTSFTLMFAHLALITAG
+YAWDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESWHLIHLYG
+YLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSARAGLRVQS
+VTAAGPHAVTVTVAGRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTA
+AVVGDGTGRLWDMRPGTRVLVEGPYGRMHDGVRTGRKALLMGAGIGITPMKALLESLPAD
+AGEITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRPGADSWLPASAGDVDDVTA
+LRRICPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF
+>GCF_023573625.1_00304
+MLSEKSRPVIEATAAVVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPA
+VADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTFRFEPADDTP
+QSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000081.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce0d8b24ec9eb9c8cccdd527d2a99f78a99faef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000081.fa
@@ -0,0 +1,72 @@
+>GCF_002008305.4_00366
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAADGRYAELYTTQFADAE
+>GCF_003691675.1_00082
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
+>GCF_005280335.1_00193
+MAPARLDPADRTQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVI
+DDALPNQDVPLLIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQP
+LAFFTRTRGGEVQSRLTHDIAGMQSVVTSTATGVASNLTAVVATAAAMVALSPRLSLISL
+VVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLGTTGHDAERF
+TGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTAL
+QGQVFRPVMGLLNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEG
+VDFAYDDGAPALSGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDV
+ARLDPADLAAIVGVVSQETYLIHASVRDNLRLADPEATDERLWAALETASLARTVAALPE
+GLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQAALDELAE
+HRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAP
+AEPALAR
+>GCF_005280335.1_02595
+MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASP
+VLAGDVVNAITGGDDGGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVF
+DHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVATSW
+QVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFGRP
+AAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGD
+VVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPLS
+VRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGSTVALVGSSGAGKS
+TIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLLARPD
+ATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVL
+DEATAALDSTNERAIQEALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAE
+LLAAGGRYAELYTTQFADAE
+>GCF_020097155.1_02454
+MSMESVARVSMMRLQRGGTAPQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVAS
+PVLAGDVVNAITGGTDRALVVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRV
+FDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANAVSLALTLAVMLATS
+WQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFGE
+PGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAG
+DVVTMALLLTRLYAPLTSLANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL
+AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVLHGVDVDVPAGRTVALVGSSGAGK
+STIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLLARP
+AATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVV
+LDEATAALDSTNERAIQEALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHA
+ALLAAGGRYAELYTTQFAEGA
+>GCF_023573625.1_00373
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000082.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3527e9bacca4c71a1704a7fd6f95d4302334b551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000082.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00386
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>GCF_003691675.1_00110
+MSDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHLLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>GCF_005280335.1_02569
+MTDEQTTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVE
+NNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPLVVVASQIPLSGLGAR
+RKGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLL
+GEVLVPPVQDALAVPYDHPPRAELVDESVRWLRDAQRVAIVAGGGVRRSGRAAMESLREV
+AELLQAPVVCSPGGNTAFPWQHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYF
+TLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAEDAPVWHGRTP
+AEVVAETMGRVAARLDAQDLGVERRLLADIRAAVPSAMQTYWDMTIAAYWAWNCWDAREG
+EFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSIAELAAARQHD
+AAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGAL
+ERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>GCF_020097155.1_01756
+MSARHDAAVPQEAADMAAAAGGAGGGTARRNGGDLAVETLHALGARTVFGIPGQHALGLF
+DALSRSSLRFVSSRVENNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVP
+MLVIASQIPLSGLGARRKGMLHQLDDQKASAKNVTKAQFTVHHASGIPSAIQDAWAEAVT
+VPQGPVWVEIPQDVLLGEVMVPPVQDALAVPYDHPPRAELVAESVRWLRGAERVAIVAGG
+GVRRSGRAAMASLREVAELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRHVTELLEDAEV
+LLVVGSSLGEVTSNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALAALADALRA
+DETARPAERPWHGRTPADVVAEVNAKVTARLDAQDLGRERRLLADIRAAVPSTMQTFWDM
+TIAAYWGWNCWDAQDGEFHSAQGAGGLGYGFPAAFGASVGLASAGRDARVLAVAGDGSAM
+YSIAELAAARQHDADVTWLIIDDGGYGILREYMEGAFGKATATELARPDFAALATSFGVP
+AETVGVEDVRGALERAFQEDGPNVVVVQTRLAMWAPSHLEAPVPADEAGPGLAETTRPEG
+RAA
+>GCF_020097155.1_02444
+MRALEDRRPRNSRSETLSGRGVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQ
+DVLLGEVMVPPVQDARAVPYDHPPRAELVAEVVRWLRGAGRVAIVAGGGVRRSGRAAMES
+LREVAELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALQALAAALRESGSVARDAAVWH
+GRTPAEVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWD
+AQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAA
+RQHDVDVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>GCF_023573625.1_00392
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTALAGLQEAYATGVPMLVIASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESVRWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIEGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000089.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31bc6b18271ae15c25c018865c0c2fc3c3145ddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000089.fa
@@ -0,0 +1,48 @@
+>GCF_002008305.4_00509
+MIPEAARTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGAGPLEGELRAQAEALGVAEAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVVRAAADGPGEVRVGDVETMARATA
+EATLEVLGRRVGKVGTR
+>GCF_003691675.1_00229
+MIPEDATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRV
+TLAGSGPLEGQLRAQAEDLGVADAVHLPGFVEPWGTMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPEAIADAVVRAAAEGPGEVRVGDVETMARATA
+EATLEVLGRRVGKGGHR
+>GCF_005280335.1_01218
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIGR
+FLRDNITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAHGIDLFEERQSTDYLP
+GRAINLGALDELHSVSRAGAEYLRARHPEFVEKIKVSYLGTEDHGVRPPRSSSQVLRLVS
+CSEVAPVKRLELLVEALREVSDSIQVEWSHYGEGPDMDRVRAMASTLPGHVSATFHGWTR
+NDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSCGLPTIATDVGGTGEIVSDGVNGRLI
+SANPMPREIAAAVEEFARMAPEAFARRSAAARETWSTHFDSDRNYRQFVAKMLS
+>GCF_005280335.1_02441
+MTPEAATTTPAPLTLWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAP
+ALVSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPI
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGVGPLEGQLRAQAEALGVADAVDLPGFVEPWGAMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVMRATVEGPGEVRVGDVETMARATA
+EATLEVLGRRAGKTSG
+>GCF_020097155.1_02325
+MIPEAATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRL
+TLAGSGPLEGQLRAQAEDLGVADAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVTRAAAEGPGEVRVDDVEGMAEATA
+RAERDVVETQDARRRKTR
+>GCF_023573625.1_00508
+MIPEAARTALAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGSGPLEGQLRAQAEALGVAEAVDLPGFVEPWETMAEHDVLAQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPAAIADAVVRAAADGPGEVLVGDVETMARATA
+EATLEVLGRRVGKAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000091.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..805b5ca413fcf946a0656593f75572f6dbcb3afe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000091.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_00547
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQAAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKRVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>GCF_003691675.1_00272
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVPTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTATDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGHHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRMRHVTPDRGTIETEVSAGDVAHLRGDVHRGA
+>GCF_005280335.1_02399
+MGVNLDHRGAAPVATATDLAEQIGAEAVPAPRGLAAALRDAVVGAADRFAAAVAGEAEAV
+DGRHPAVAAVTQRLSTLGREVRAELPGGDVLEGTAVALGPGGALRVSHVTADRGRIETEV
+SAGDVAHLRGDVHRGA
+>GCF_005280335.1_02400
+MHAPHDPAAPGLVWLDSAGSTQDEVLARVGREGPRHGLAVATADQRAGRGRHSRVWSAAP
+GAALALSVHLRPAAGGTPLAPVHLSWLSLVASAAVVEHLAGLGAAAHLKWPNDVLAPDGR
+KLCGVLATVAPAADGGGPGWSWAWG
+>GCF_020097155.1_02283
+MGYTWGMGTLLWLDAADSTQDELLRRLAAADGAARPGHGDGVGTADQRAGRGRHGRAWQA
+PPGAALALSVHLRPTGPSGPLAPAHLSWLSLVASAAVARRLVGLGVPAHLKWPNDVLDAE
+GRKLCGVLATLAPAPVFPGADAGETPGVVVGMGVNVDLSSGRPVPTAAALTDHLPGAEVP
+APRDLAQALLRDVAAAADRLARDLDGVVEPVDGTHPALAEVAAVLSTPGRRIRAELPGGE
+VLEGVATGLGAGGVLAVRVVTGERETITREISAGDVVHLRGDVRRGG
+>GCF_023573625.1_00550
+MHPDDAPTPDLTWLDSAGSTQDELLARLDREGHRHGAAVATADQRAGRGRHSRVWSAAPG
+AALALSVYLRPESGGVPVSPAHLSWLSLVASATVAERLAARGVLTHVKWPNDVLATDGRK
+LCGVLATVALSSDGKGPGVVVGMGVNLDHRGAAPVDTASDLAEWIGADAVPAPRDLAVEL
+RDAVVAAVDRFAAGVAGQTAAVDGRHPAVAAVADRLSTLGRAVRAELPGGGVLEGTAVGL
+GPGGTLRVKHVTPDRGTIETEVSAGDVAHLRGDVHRGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000093.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d42d3b1e524c0867617960ba1422bc5bbfd9882f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000093.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_00604
+MPKMSGIETAFCRSALWGRFARDIIVPWSLGGQDLGGDVLELGAGSGQMAAALLQRSPGM
+RLTLTDIDERMVATARRRFPTSPRLTVQQADSTALPFAESSFDVVLSFLMLHHVVNWKAA
+VAEAARVLKPGGMLIGYDLTAWSSPS
+>GCF_002008305.4_02174
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>GCF_003691675.1_01888
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>GCF_005280335.1_00578
+MFDAVAERYDLMNTVMTWGQEPRLVRHTVARANVPAHGRVLDLATGTGDLAFEVLRQHPD
+ATVVGADISAEMMEVGRRREGGDRVEWVVADAQDLPFEDASFDSVTHGYLLRNVADIPAA
+LAEQFRVLRPGGWMAALETSPPPANIIRPFSTFYMHQVMPRLARVITDKPEAYEYLSSST
+KAFHAPEEIADMLAHAGFVNIGHETHMFGTLATHWAMKPVA
+>GCF_020097155.1_00505
+MSETSPSPLPRPASLAHDADHGARVSGMFDAIAGRYDLMNTVMTWGQEPRLVRRTVERAN
+VPAAARVLDLATGTGDLALEILKQHPDAHVVAADFAPEMMEVGRTRPNGDRIEWVEADAL
+ALPFADGEFDSLTHGYLLRNVANIPAALAEQFRVLRPGGWVAALETSPAPDNLIKPFSSF
+YMHRIMPRLARLITDRAEAYEYLSSSTRAFHTPEEIAGMLADAGFVNIGHELHMFGTLAT
+HWAMKPLD
+>GCF_023573625.1_02119
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000095.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35bff63bf51c96819bab045df3f63033622df941
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000095.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_00611
+MTSTDPTPAKAASAPNRQRRAKIIVWVVLAALVLAGVVAFFAARAPSTPEAAPAQAGQAA
+SSGTGQTAASEAAPVVRPDSRVLSQAPNEKAVLVEFLDFECEGCKAAHPVVEELRAEYAD
+TVTFVHRYFPLPGHPNSMTAAVAVEAAAQQGAYEAMYQKMFDTQEQWSHTGQDRSPVFRG
+YAEDLGLDMTAYDKAVADPATRARIEADVADGVALGVQGTPTFFLDGQVLTLNTLEQFRA
+EVDAAASN
+>GCF_003691675.1_00327
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
+>GCF_003691675.1_01771
+MTSPDPTASTPSSPTPSRQRRAKIVVWVLLGLVVAAALIGYLVARGTATAQQQDPNQSTA
+QSTGQSTGSAGQLVRENSRVLSQAPNEKAVLVEFLDFECEACAAAYPFVEDLRAEYADTV
+TFVHRYFPLPGHPNSVTAAIAVEAAAQQGAYESMYQKMFETQTEWSHTTEDRSPVFRAYA
+EELGLDMAAYDAAVADPATRDRVELDVADGTALGVAGTPTFYLDGEPLTVNSLEEFTAAV
+EAATQD
+>GCF_005280335.1_02344
+MSTPTRNPTPANSSTSGTTSRKAKTIVWVVLAAVVVAGVIAGVVAVGAARNATPDAAATQ
+AGQSAAQGSGPTTAEEAGELVVRPNSRVLSKAPNEQAVLVEFLDFECEGCGAAYPVVEEL
+RAEYADTVTFVTRYFPLPGHRNAMPAAVAVEAAAQQGEYEAMYQRMFETQAQWGEATEDK
+SPVFRGYAEELGLDMAAYDKAVADPATRARVEADVADGIALGVQGTPTFFLDGEMLTLTS
+LEQFRAEVDAAASN
+>GCF_020097155.1_01190
+MSWRTIRTEAGSAVLLVVVTAVALLWANSPLSEAYFGLWDVEIGFDVGGFGLHMNLHHWI
+NDGLMMTFFLVVGLEVRQEFAHGTLRDASRARLALIAGVVGVALPAVFYILIVAAAGGEG
+LGGWGAVVGTDTAFLLGALALVGPKLSGQLRVFLLTLTVVDDFLAVSIIGIVYSDEIRLV
+PLLIAGACLVGLWLLGRSRQWSATPYVLIVIVLWFATVESGVHASLAGMVAGLLIPAYPT
+RRQQVVEARQLFRDFWQSPSAASARAVDRGLAQGISVNERMHEVLRMPTALVIVPIFALA
+NAGVDLRGGVLVDSFQSSVTWGVIVGLVLGKLLGIGLATFVAVKLGAGRLPEGVGMGSVF
+GGAALSGIGFTVSLLVIGLAFGSTSDLGRQATVGVLVAMVLATALGWLIFRVAAKRWGEE
+TADLPMVLTPPVDPEVDHIRGPEDAQLTLVEYIDFECAYCAHATGSWDDLRSRFGDDLRY
+VVRQLPHHPHGPLAARASEAASNQGMFWPWLDFVFTRQDALEREDLIRYAEELGLDVAQF
+TADLDSAAVGARVERDLESADASGAHATPTFFVDGRRLLGSYDARTLTSALEASRRGTRT
+QEVRS
+>GCF_023573625.1_02008
+MSTPTRNPTPSDPSTPGTTSRKAKTIVWVVLAAVVLAGLIVGVVAASGPRDAAPQGSGQT
+ASSGTGQSAPSEATPVMRPDSRVLSKAPNEQAVLVEFLDFECEGCKAAYPVVEELRAEYA
+DTVTFVHRYFPLPGHPNSMTAAVAVEAAGQQGQYEAMYQQMFDTQEQWSHTTEDRSPVFR
+GYAEDLGLDMAAYDAAVADPATRDRIEADVADGTALGVQGTPTFFLDGQMLTLNTLEQFR
+AEVDAAATTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000099.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3e4dad3dc33bc64c93895e28fbddae0f810dbfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000099.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00630
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>GCF_005280335.1_00402
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDTDPARYIDTVRGVGYRMAE
+Q
+>GCF_020097155.1_00452
+MTGPDLLLIEDDDRLGPLLRDLLSLDWEVTWSPTLAAARAELDRRLFAVLVVDRGLPDGD
+GVDLVRELRARGVAVPALLLTAYGELEDRVHGLDAGANDYLVKPFEVAELQARLRALTRD
+YSGRGAGVEIGSWMFYPDNRTVESPYTGRILLTEKESALLAVLASAPDTAFTRAHLLSAV
+FEHGEQEGTVDTYVHYLRRKTDRSLVETVRGVGYRLGTPT
+>GCF_020097155.1_01060
+MARLLMLTRAASAVEVLPALDLLTHDVERADPRAALAAGREDVDGVLLDATSGLAEARTL
+ARDLASLAPEVPVVAVMAEGALTAVGPEWSLADIVLTGAGPAEVDARVRLLRPADAPVAG
+GAAERLAVGGVEIDPVGYRARLDGRALNLTFREFELLKHLAQSPGRAFSREQLLREVWGD
+DYFGGTRTVDVHVRRLRAKLGPDREQMIGTVRNVGYRFTPRPDGDA
+>GCF_020097155.1_02199
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCWRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>GCF_023573625.1_00601
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLATHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000101.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8befceb42c2fff53133c56ff58f94964a151fd42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000101.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_00650
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLIEAVARRTDAPGPEGADVEVEVAMLI
+SDERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILT
+LHDLIYYEHRTPPRNLPEPIRWLWRAYHLTKTPQRLLLDRADAVATVSRTTAELIDRHRL
+TRRPVHVIANAAQTVPEPRDPDETPDRTLLYMGSFMDYKDVESLVAAAPLLPGYALHLLS
+RISPERRGQLEARLAARRAAAGAAGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGL
+PVAEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAEFAAA
+SRASVAQAARFSWDESARRLLDLTAALGAARRAARARTDRSSR
+>GCF_002008305.4_00841
+MRGQRMMSTSHEPLATTFIIPTGLPGPSGGSRYNKALIRALEAAGCSVSVCGVPGPWPRP
+EARDLERLRAALAGREQVVVDGLIASSAPDEIQAAAASGTRVHVLFHLSLLVDGAVPPDG
+SGRAAALERRALQSAHTVICTSNWAARDVVNRYGPLPTRVVSPGTDQAPLAVGSAPPQLL
+LLASVTPRKNQLAILRALAALTELDWQALLVGPDAADPDYAQRVRLFAEAAFPPGRVQVL
+GSRTGPGLERIWSASDLLLLVSRAETFGMVVTEAVARGIPAIVGAGTGAEEALALGPHAP
+PGIAVAPDDTAALEEVLRGWLSDPAQRAAWRRSAEGARGMLPTWDDSADLMLRILTP
+>GCF_003691675.1_00387
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLLEAVARRAAAPGPAGVDVEVAMLISD
+ERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILTLH
+DLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLLLDRADAVATVSRTTAELIARHRLTR
+RPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMDYKDVESLVAAAPLLPGYTLHLLSRI
+SPERRGQLEDRLAERRAVAGADGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPV
+AEAMAHGTPVVCSDLPIFREIAGAGTASFRGVPLEGDRVAALAARVRELEDPAEFAAASR
+ASVAQAARFSWDESARRLLDLTAALGVARRAARARTGRSSR
+>GCF_005280335.1_02313
+MSPSRPLRLLMDARYTRTDFHDGISRYGASLTEAVAHRAAAERGEGADVEVVMLISDERQ
+LALLPKGVPWHRVSGPTSPREPFVARQMARLRPDVVFSPMQTMGSWGRRHALILTLHDLI
+YYEHRTPPQNLPEPIRWLWRAYHLTMTPQRLLLDRADAVATVSRTTADLIAAHRLTRRPV
+RVIANAAQPVPRPRDPEEAPERTLLYMGSFMDYKDVESLVDAAPLLPGYALHLLSRIDPA
+RRAQLQERLEARRAAVGEDGAEVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPVAEA
+MAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAVFAAASRAGV
+AQAARYSWDESARRLLELTRELGQARRAEAPRAARGRRDRSSR
+>GCF_020097155.1_02170
+MTGSQLLLMDARYTRVDFHDGISRYGASLTEAVHRLADPAGLRVEMLISDERQLALLPDG
+VPWHRITGPTSAGEPFVARQVRALRPDVVFSPMQTMGSLGRDYALILTLHDLIYYEYPTP
+PRNLPEPIRWLWRLYHLGYAPQRFLLDRADAVATVSQTTADLIAAHRLTRRPVHVVPNAP
+QPAGVPRDPEAAPTRELLYMGSFMDYKDVESILDAVPLLSGYTVRLLSRLTAERRRELAE
+HLRRARAAAGARGAEVVFHDGTDEAEYTALLRRATASVTLSRAEGFGLPVAEAQAQGTPV
+ICSDLPIFREVAGHGTAAWNGVPLEGDRGAALAARVRGLEDPAAFAAASRASAEHAAGYT
+WDRSARRLLDLVEGLLADRGR
+>GCF_023573625.1_00620
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLLEAVARRAAAPGPAGADVEVAMLISD
+ERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILTLH
+DLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLLLDRADAVATVSRTTAELIARHRLTR
+RPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMDYKDVESLVAAAPLLPGYTLHLLSRI
+SPERRGQLEDRLAERRAVAGADGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPV
+AEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAEFAVASR
+ASVAQAARFSWDESARRLLDLTAALGVARRAARARTGRSTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000107.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4846e6fcd43892ddbbf0219763ce002a342e206
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000107.fa
@@ -0,0 +1,51 @@
+>GCF_002008305.4_00769
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKPG
+DPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVITD
+VDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG
+>GCF_003691675.1_00499
+MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGSDPYIVLSAPDARAAARDALATRMGNW
+GQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPGDPTSRDADVYGPLSSESAADGLTEQI
+AAAKEAGATVHVGGERVSGPEGEGFYVSPAVITDVDQENPAYTQELFGMAAVVYKVSSAE
+EAVALANDSQYGLGGAVFSTDLDEAKRVADQLEVGMANVNLASAAGANLPFGGVKRSGFG
+RELGPMAVDEFANKRLYAVQGPLEG
+>GCF_005280335.1_00806
+MARYITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLARAADLYE
+ERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGGGTAYVRR
+DPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLLDAGLPEG
+AFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGGSDPFIVA
+GDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPHGDPTDES
+TVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGPGAYYPPTVLTDVDESARAFRE
+EIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLETGMVWVNSTSK
+SSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA
+>GCF_005280335.1_02161
+MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVKR
+ISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSGQ
+EAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFRE
+AGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKAA
+DPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVITD
+VDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLEV
+GMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG
+>GCF_020097155.1_02057
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATVVGGERLSGPSGEGFYVSPAVITD
+VDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLEV
+GMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG
+>GCF_023573625.1_00733
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPG
+DPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVITD
+VDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000110.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d89b2224e2ca2cb7e2378afac65e0a8b3e0db482
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000110.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00965
+MTEHSAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVLQ
+PAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPGR
+EHVTWTALTPPRGGWTPVAEVADEELTEVATRGADAVWDALPENPGEALVRKIRAQMWGP
+LLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>GCF_003691675.1_00678
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKVRAQMWG
+PLLGGEALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>GCF_005280335.1_01922
+MTEPSAAPVLRFADERAVRDLEQFATRARRVSDTGMRLHVVPAAGPSRTPMLAQWVSVLQ
+PAGLGDEVPVVLGLRTVPLATAEMAADLDAVVALGAVTERTARMRSRQPVDLDFSVPPGR
+EQVTWTALTPPRSGWTPAAEVADEELADVAERGVAAVRETLPENPGEAMVRKVRAQMWGP
+LLGGDALGFPAGMAFGAHALGFLQPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>GCF_020097155.1_00709
+MPARLILADAPPARDALTFAQRAAQAGAHGVRLQAAAALTPRGPLDRTPTILVLRTLRSD
+PELQCDVTVDTLTATADPLTLALPETALAPAWTSVEPPQHGWRLIADVTSLTLMRSARAG
+IEAVAQALPDKPGDDVVRKIRGTVWGTPDTALASLPQGVAFAAYVFGFLSRGNGATISTA
+GRWTRLTLPTGHVLLRGPVASGLTPIRRTRPRVSKSVTSIE
+>GCF_020097155.1_01871
+MPDQPSSRRDARDAARAAVPVLRLTDERAVRDLDQFATRARRVADTGMRLHVVPEAGPRR
+TPMLAQWVSVLQPHGLGDGVPVVLGLRTVGLTSADAVEDLDAVVPLGAVTERTARMLGGT
+PVALDLPVPPGRERVTWTALTPPRAGWTVRAEVPDDELAEVAVKGAEAIRDALPQDPGEA
+MVRQVRAQMWGPRLGGEIGFPAGMAFGAHALGFLRPGGRARLSTAGPWVRLDTPGGFVLG
+RSAVGV
+>GCF_023573625.1_00911
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKIRAQMWG
+PLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDAPGGFVLGRPAMAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000111.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffd519829e2a9b2d03416d5ed553703c0f60b96c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000111.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00993
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETTRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESATGGSL
+PAPRSFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>GCF_003691675.1_00707
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSAGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>GCF_005280335.1_01817
+MAAMADFPVTADRQGPDYAAASRAALVEALTAAGPGMPTLCAGWRTEHLAAHLALRDSSP
+TAPGLFLPPLAAVLERRTRALGDAHAGDRGYAELVARIGRGPLPAPADDGVRGRLRGLAA
+RARGSRPGRAVAGRVQLLEFFVHTEDVRRAQDRWAPRILADDYADALFTRLHARAALLYR
+GEETGVVLVRRARAGSRTDNAPLTARRPGPDGVGVRVTGPAGELAMHAFGRRGAALVTQD
+RFDADPAEDGPGAA
+>GCF_005280335.1_01896
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSCH
+LDRLTAETTRRDYVEVVREWALGPSALNPMRAADKHVNAAEHFIHLEDVRRGESAAGGSL
+PAPRSFSPDEEDALYRSLRRMAPLVLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>GCF_020097155.1_01843
+MTTFAAAERARLADLLLEKGPHAPTLCEGWSTRDLAAHLWLRENRPDAMASMFVKPLAGH
+LDRLTAHTKRREYVDVVGEWSQGPASLNPMRVADRHVNAAEHFIHLEDVRRGEAVAGGVT
+PAPRDFTPSEEDALYRSLRRMAPLLLRKSAAPVVLQAPGRAPITVAREAVAVKAPVTVSG
+PVGELLFWASGRDAVHVDLDGDHAAVVRGGI
+>GCF_023573625.1_00936
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSRH
+LDRLTADTKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSTGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVEIDGDASAAVRTAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000113.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79459dfc764c31455a47184a5ab3ecf497347832
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000113.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01028
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>GCF_003691675.1_00743
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>GCF_005280335.1_00185
+MTSRSPLSSRSPLSPRPSRRALLAGLAGVGSAALLTGCGLRTGTAAGGGGASRTITLCAT
+EDAPYQEPVRIAERLLAERGWELKTTFVTDIIQPNIAVDRGEFDANFFQHIAYLKQFNAD
+NGTSVVPAFNVYTSPAGLFSTRYSSLEELPDGARISVPVDPSNNGRALRLLAQAGRITVR
+EGVSVIRLSQHDITANPHGYEFVEVDQQSLALTIEDADAGFLFARQSAKIGLPISESLLF
+ETAEDAVPFRVVVATREGFRDTEAGRALREAFQSEEVRRWYADYLDGALGTEAWGDDPQE
+AIAALEI
+>GCF_005280335.1_01852
+MALSPLSRRTALGAGTAALALVLSACGAGGSDTAASSAPTPDPANPVVVKVGANPVPHAQ
+ILEYVDENLAKEAGIDLEIQEFDDYQMPNTALDEGKIDANYYMHEPFFNKQVEERGLKME
+HGKGVHIEPYAAFSKKFDSVDQVPEGATVAITNDPGNQPRALKMLEQAGLLKDVKDDSAA
+LTLTPEQNPKGLTFEENQPEILVQILDDPAVDLAIINGNYFIQAGMTLEDAVVVEEISGE
+NPYANFVAWREGEKTPGVEKLDELLHSPKVKQYIEQTWPGGDVTPAF
+>GCF_020097155.1_01744
+MPTRAGDVAPSSKENPMTTPSNISRRSFAGLSLAAVGALALTACNSQAEKKGDDGAQTVR
+IGVVSENETHRALVKLAKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYN
+QASGKDLTLIGTTEIIPLPLYSKKYKDVSEFQKGDTVAIPNDTVNQARAINVLVAAGLLK
+LSNETIRPEPKDIDEAASTVKVQTVAAQQTVNALESVQGSVINNTFSADAGIDTNTALFK
+DDPKADSAKPFVNGFAVRRADRENETYKKIAALYHEQAVLDESAKLSSGTSVPVQLDAAQ
+IDETLKQYQDAIAKQGA
+>GCF_023573625.1_00972
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000114.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cde2eae27b3c98bf678a66745156581705b2b0e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000114.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_01029
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>GCF_003691675.1_00744
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>GCF_005280335.1_00187
+MISIQNVSTAFGEHRAVDDVSLEIPTGSIQGIIGFSGAGKSTLLRNVNLLLRPSAGRVVV
+DGTDLTALSPSGLREARRGIGMVFQHFNLVHNLTAAQNVALALKFAGVDRRARQARAHEA
+LEIVGLADHAGRYPAELSGGQAQRVAIARALSTRPSVLLCDEPTSAVDPRTTATVLQHLV
+DINRDLGITTVIVTHEMNVIRAVADDVAVMEDGRAVERFALADLERADFAPRTGIGRYLL
+EDEIALERPPLRGAAGAPDGDRAGSGTTPGTSPGTTSIPGDVREAVVAGV
+>GCF_005280335.1_01854
+MSSSPTVSTSAHPVGTPMIEVRGLEKTFRQGAKEIRALRGVDLAVAPGRIHGIIGQSGAG
+KSTLVRCLTLLEPPTSGTVSVAGKDLTRESRSGLLDSRRRIGMVFQHANLFSSRTARDNV
+AYPLEVAGGSDAAARRARADELLALVGLKGFEGSYPAQLSGGQKQRVGIARALASDPDVL
+LCDEPTSALDPASTEGVLTLIQDLSQRLGLTVLVITHEMHVVKRLCHEVSLLQDGRIVQS
+GDLGDVAADLDSPLSSALLPLPAPHAAPDQRLIEVLGRGAAASLPITQLVRDAGAGEVEV
+LAGTVEDLAGERFSHQLLGLAGTWAAGDAAVARLQEAGLTARTLSARQASQDQHTADEIG
+GAR
+>GCF_020097155.1_01743
+MAGSHSSDRDAVTPGRHSEGAPGEPVIVFDHVSRVYAAKKGRGVTAVDDVSLSVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSTRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DTGRVVETGKVYDLFSRPAHSADAASFVATALKDRPNADEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>GCF_023573625.1_00973
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000118.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..772f4e8e8b9f222440f01e40d2dbdc836e547463
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000118.fa
@@ -0,0 +1,90 @@
+>GCF_002008305.4_01106
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>GCF_003691675.1_00825
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>GCF_005280335.1_01787
+MTSPLTRLHDALGLRTTPAIFFGSAAVVVLFTLAMGLFPGPVQAGFGVVSSWLRYDAGWI
+YTLSLTVLVAFLLLLAVTRYGRVKLGDDDAVPEYSGLAWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPLAGTEPFSDQAASQAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDIVSVVSTVFGLGVSVGLGALQINAGMNYVFGTPVAGWVQA
+LILAVITAVGTASVLAGMDKGVKRLSYANILMAIALLVYVLMWAVSSMDVIRGTVQAVGE
+YLTMLPMLSTFNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFAKISRGRTIRSFIAAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAAAPGTGGDLTETIVTEGNVQAALFQHLQGTPLYT
+VAAVLALVVITLFFITSIDSGALVMDAMANGHEDPAPRRQSVIWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAGLLLQALREDAGTARPLRTRQWKPVLPAEEYHRR
+AHEEGVDVSDYVIRPEFEVGTEPEHDTHTPNTWHQQRTVAAKALVTVGLTGGIAAGRTVV
+GEELERLGAVVVEFDDLMGEILVPGSPVLEELREVFGDDVVRADGTLDARTLNRLTAEST
+TARTRMYEIVSPAVRDEANRRARAIGEDSVLVVDLALLAETGSAGDFDQVLAVSAPAEQR
+VARLMDSHDLPREQAWAFIDEEALDAERAEIADTVIENDGTLEDLHEAVRAYWEAKIQPQ
+IEAARGVSP
+>GCF_005280335.1_01788
+MNSLLTRLHDRLGLRTSPAVFFSAAAVIILFTVAMGVLPGPVQAVFGAAAHWLRYDVGWF
+YTLAATLLLAVCLILAVSRYGRVKLGDDDASPEYSGLAWFGMMFASGIGAVLMFWGIAEP
+MTHYALPPLEGTEPYSDQAAVQALNIANLHFGLHMWAILVVPGLCFGYFTYKRNLPPRVS
+SAFQLLLGDRIHGPIGKTIDVIAIVSTVFGMGVSTGMGALQINAGVNYVVGVPVAGWVQA
+LILAVALMLWVLMWAASSMDVVRGVIESFGRTLGALPLLTTFNDTLGGGTWSGDWTLFYW
+AWTVSWAPSVGMFVARISRGRTIREFVFASLGLPTAFVIVWMGVYGYSAIFADRAAAPEA
+GTGGPLAQTIAVEGNVQVALFQSLQEMPLYLPIAVLALIVIVIFFVTSIDSGALVMDAMA
+NGHEDLAPRRQRVFWGVSVGAVCTAIIVTAGDDGLNALREVIIVIGFPVMVLTVLQALLL
+LQALREDAGAARPLRTRQWKRVLPPEEYHRRAREDATVREEYAIRPEFEVGTEPEYETHT
+PNTWHAQQPAARRATVSVGLTGGVASGKSAVAAEFERLGAVVVDYDDLMREILVPGHPAV
+DELRDVFTAEVVADDGTVDWLALDALTAESPSARTRLHEVVAPVVRAETDRRATDAGESS
+VLVVDLALLVDAADVRDFDQVLEVLAPAEVRVARLMDERGLDREQAWAEVDADEQRRPAL
+GGTHTVLANEGDRAELERSVRDWWDEVVEPARERGRRPGPRLRRLTRTVPPPPPAAGGGG
+RGWRPGAGSPYRRDRVPDGTRPSARPLDRPPRSVGDPVPGDS
+>GCF_020097155.1_01679
+MNSLHTRVHDALGLRTSPAIFFTSAAVIVLFTAAMGLFPGPVQEVFGVVAGWLRYDIGWF
+YTLSATLLALFAVLLACSRYGRIKLGDDDATPEYTGVAWFGMMFAAGVGAVIMFWGIAEP
+MNHYANPPMPGTEPFSDQAALQAMDIANFHFTIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDVISVVSTVFGLAVSTGLGALQINAGMNYVLGTPVAGWVQA
+LILAVITAAGVCSVLAGMDSGVKRLSYINIVVAVALMLFVLMFSISTNDVLRGTVQSVGS
+FVGHLPVLSTFNDVFGSGRWSGDWTVFYWAWTVTWAPFVGMFVAKISRGRTIREFVTAGL
+GLPSIFTMIWMGIYGYSAFQADRATAAGPGQGGDLTRTIVEEGNVQAALFQHLQGMPLYL
+PVAIVALVVITLFFVTSIDSGALVMDAMANGHEDPAPRRQGAFWAISIGAVCAAIILTAG
+ENGLDALQEVIIVIGFPVMLLTLVQAAMLLQALREDAGAARPIRTRQWKQVLPAEEYHRR
+AQEDGVDIQEYVIRPEFEPGTEPEFDTHTPNTWHQQRTVAQRALLTLGLTGGMASGRTAV
+GEELERLGAVVVEFDDLLDELLVPGAPVLDEVREVFGDDVVRADGTLDARAMNALIDASE
+AARSRFYEIVSPLVRAEADARAKAIGDDAVLVVDLALLAETGSARDFDQVLAVSAPAEVR
+VQRLVDERHVTRERAWALLDEGAQDDERAAIADTVIENGGTREELRAAVEAYWAEKVAPA
+VEAARIAGGVG
+>GCF_023573625.1_01055
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000122.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8708cd8420ef5191229a52df12f2cee19b16310
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000122.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01152
+MGEVGTREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSARIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>GCF_003691675.1_00871
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>GCF_005280335.1_01740
+MAEPAATAEPDGREVRLARAEDLADPRLVPYTTLTDAALRRRVDAEHGVFLAESSQVVRR
+ALAAGHTPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRP
+APRPLADVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVS
+MGTVFRLPWARLEGPVAEAVPALREAGFAVAALEVTERAVGLDSPELEPLRSADRLALVL
+GQEGPGVRTETLEHTDADVVIPMPDGVDSLNVAAAAAVALWELRAR
+>GCF_020097155.1_00545
+MSSESPAQPASADQPAEAPAGVIVDPKDARLRKVRELLKGKNKASRAIIVDDEENLLAAL
+AAGVELFTVFHGEDAELPAALAAVLPADQDVQVVSTHAAKELFGVERRSRVFALARRPKP
+LTVAEVLEHPGDVLVLDGVKLMGNIGAITRSARALGAAGLVLVDADLASVTDRRLIRASR
+GMVFSLPVALASADDVAAQLAEAGVPLVSLDLGSEKALDSVAEIPGRVALLLGSEKHGPS
+ARLAETAEHTVSITIHPEVESLNVSVSAALALYERRASNPLPQA
+>GCF_020097155.1_01634
+MPDDGAPAPFPGEVRLQSAADLADPRLAPYTTLTDAALRRDVDAAHGVFLAESSPVVRRA
+LDAGHAPRSFLLGDRYRETFADVIAAHPGVPVFTGPDEVLTALTGFHLHRGALAAMDRPA
+PRSVAEALDGAHRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPRAADPLYRRAIRVSM
+GTVFRLPWARADGPLEEALPALRAAGFATAALEVTDRAVGLDSPELEPVRTAERLALVLG
+QEGPGVRPETLAAVDAHVVIPMPAGVDSLNVAAAAAVALWELRPRDTPAA
+>GCF_023573625.1_01102
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000125.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09ca82097998bc017e75084f929fd698f5fde0a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000125.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_01334
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_003691675.1_01055
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFTAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_005280335.1_01557
+MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAEHHNMPAIA
+SSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGRTRIPGIEAYPGKGTDVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTREEADR
+EWEAARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTMLECTAVGTGEETATWLRDFA
+AKVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_020097155.1_00131
+MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGEHHLNPGVLGSNPALT
+LALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDLGLGRAAAPGGPPPGT
+RAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAAPDLSAALGSPLRAAS
+RALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARPAVDVEPWVLGSGPGVSA
+EVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVVSVSAEVLIADTAAEARR
+RASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRLQTRFVGTAEQVAERLDA
+LARLTGADELLISASAHRVEHRVETLTRLAEIWRTA
+>GCF_020097155.1_01453
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRAPGTDQRTLQALRRSPEAADRFPQDVLELQGYLRGESRMPGIDAYPGRGTDVPLWI
+LGSSAFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHFIAAANVVVA
+DTDEEAQRLWEATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGMLRHTAVGTPDVV
+RAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR
+>GCF_023573625.1_01290
+MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAEHHNMPSIA
+SSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDLGLGRAPGT
+DQRTLQALRRDPSAAERFPQDVLELQGYLTGQSLIPGIDAYPGKGTNVPLYILGSSAFGA
+QLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHFIAAANVIAADTEEVAER
+EWQAAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGMLECTAVGTGPTTAAWLHDFA
+ARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000131.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cddf20809ddb7e1d87bea0e52bacd0979fe80ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000131.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01549
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>GCF_003691675.1_01259
+MSALQPQPTVKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>GCF_005280335.1_01376
+MSALQPQPTVKHASWAWTESRGVEDEVVLRARERSAELDVRPVSEGTAALLTVLAATRAP
+SAVVEVGTGAGVSGLAMMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTGRTRMITGR
+SRLVLPRLTSGAYEMVVVDGDPASRQFDVEQAARMLAPGGVLVLVDALDADRVPRPAVRG
+ESTVSARAVDRLIREDEGWVSAVVPSGTGVLIAVRR
+>GCF_020097155.1_01267
+MSALHPQPTDKHASWAWAEARTAESEVLLRARERSAELGVRAVGEGTSALLTVLAATRAP
+SAVVEIGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEAHLPTSRTRMISGR
+SRLVLPRLTTGAYEMVVVDGEPASRAFDVEQAARMLAPGGLLVVVDALDSDRVPRAAVRE
+DSTVSARDVDRLVREDEAWVSAVVPTGTGVLLAVRR
+>GCF_020097155.1_01296
+MDPRRRALLDRLWQEGRDFDAAQPDRLDRRRNLEPESAELLNILVRTLAPAEVLELGTST
+GFSALWIADALEPHGGRLTTVDPDAPRLAEARTNLEAAGVADVVTVRQADAADVLADAED
+GCLPLVFLDAERPAYPDYWPDLARILAPGGLLVVDNCLSHADDVRPFRALVDASPGFRST
+LVPVGAGLLLVSKDRPGHGSGVG
+>GCF_023573625.1_01476
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELDVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000132.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d80417fd0a558805c8942d3273245ad1b115d3bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000132.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01563
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRADRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGVSWTAGLWAAAPGAVVASVAWNVGQPALGLVL
+LAVGRRLDRRPAGAADGATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
+>GCF_003691675.1_01273
+MPERPRRRARPADVVGGALLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQR
+WWMVRRAGRGGRALPAGAAVVAGAFTVVLALQRLPVDDALGLSWTAGLWAAAPGAVVASV
+AWNVGQPALGMVLLAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRA
+QREVDGQP
+>GCF_005280335.1_01363
+MVGGALLGVVAGALGTAVHLTLSPLPGGWTLPWGAVLALVLAGSVQRWWMRRTAERGGAP
+LPAGAAVVAGAFTAVLALHRLPVHDALGVSWTAGLWAAAPGAVVASVAWNVGQPVLGLVL
+LAAGRRLDRRPAEAADGATRPRRTSVTARETRPGERVPWTAAPQPRAQREVDGQP
+>GCF_005280335.1_02268
+MSRRVLLLLTAAVLVYALQFLPPLIFHDLVIAPSLGEHFGWALPYLAPVMVVPPLAWAAV
+AAAPVLRGGSTRRASGLSMTLLFFAPFAYAFATPVTWVAVRGVDAIGGLEDDPLLLGMVL
+PFLSGMILSPVLVGVVLQWWLRRTARRAAAGGAQAEAAPERPAPEAPTHDASGLPLP
+>GCF_020097155.1_01254
+MLPGLALGVGTGALGTATHLSLLPVGSWLLPWGLVLALVLVGSTQRWWMRRAAAAGGRPV
+RAGAAVVLAAFTMASALRWLPATDRLDLPWTAGVAQAMPVAFAASVGWTLGLPVLGVVLL
+WLGARAGEGRAAGESTLERTPNPVPARKVDGQP
+>GCF_023573625.1_01490
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRAGRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGLSWTAGLWAAAPGAVVASVAWNVGQPVLGMVL
+LAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000133.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea837ac94332d5d0830e3501157463d634ee7e57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000133.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01569
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
+>GCF_003691675.1_01279
+MTDTAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
+>GCF_005280335.1_01355
+MGGGETGIGSGARPRPHRTHQHRRVHDRLAHPVAGPAAGPRFALPRGVEPGRAVVVGAGP
+NGLTAAALLAREGWEVDVYERAPVPGGASASAPVLGEGTVVDLGAAGHPFGAASPVFRDL
+DLAAHGLQWLHPAVPMGHPLPDGPAAILHRDLDATAEGLGPDGRAWRAVHGALVEHIEEL
+VADVLGPLVRPWPHPVAMARFGLRAPWPAAHFGRAVFRTEQARALYTGSAVHAIMPPGRP
+LTSAFGALFGALGMSSGWPVARGGSGVITDALVSVLRAHGGRLHLDQEVTDLRALPDVDA
+VVLDMTPRQVARLRGTDLSPSYAAALQRWCPGPAVSKVDFLLDGPVPWRDGRLAGAGTVH
+LGGTAADIQRAEADVAAGRMPARPFVMLCQQQSADPSRAAGPAAGRTVLWSYAHVPHGHP
+GDVRPLIEAEVERHAPGFRDRILGAVDMRPADLEAWNPNLVGGDIAGGSMAGLRLLLRPT
+ASPRPHRAGRPGLYLASASTPPGAGVHGMAGAWAVRTLLADRARATSR
+>GCF_005280335.1_02577
+MNAAPTQDTAEDHARFPLPRDAEPGRAVVVGAGPNGLTAAALLARAGWEVDVHERHPSPG
+GACASAPLLGEGTVVDLGAAGHPFGVASPVFADLDLIGHGLRWAHPEVVMAHPLPDGEPG
+LLYRDLERTAAGLDADAARWWAVHAPLVEGAEQLVDNVLGPIVRPWPHPLTMTRFGLRAP
+WPASWLTGGLFRTEQARALFVGSAVHAVMAPSRPFTAAFGALFAALGMSSGWPVAEGGSQ
+AIVDALVRVLRTHGGRLHLGSPVEDLRAFADVDAVLLDLTPTQVARLRGTDLPKHSLSRM
+RRWRHGSAAFKVDMLLDGPIPWADPRVGQAGTVHLGGTAAQVQRAEADVAAGRMPDEPFV
+MLCQQQSADPSRAVGPAAGRHVVWSYAHVPHRHSGDATHAVLARIERFAPGLRDRIVRIV
+ATSPAELEAWNPNLVGGDIAGGAMDGLQLLARPRISAAPHRLRAAAPSAWRTSSGRTAPG
+LYLASASTSPGAGVHGMAGAWAVRTLLSDRRCAR
+>GCF_020097155.1_01248
+MPRDAAPIDAPAARDRGFALPQGAEPGRAVVVGAGPNGLTAAALLAREGWEVDVYERHHA
+PGGASASAPLLGRGTVVDLGAAGHPFGVVSPVFRELDLTGHGLRWVHPEFPMGHPLPDGP
+AAVLHRDLDATAEGLGVDGRAWRALHAPLVRDADRLAADVLGPLLRPWPHPVSMARLGLR
+APWPAGWVNRAVFRTEQARALYTGAAAHAILPPGRPLTSAFGALFGALGMSSGWPVAAGG
+SQSIVDALLAVLRAHGGRLHLDHEVTDLRELPAADAVVLDLTPRQVAALAGTDLPPAYAR
+SLRRWRHGSAVSKVDFLLDGPVPWTDVRLAGAGTVHLGGNAAQLQHAEAEAVAGRMPEHP
+FVMLCQQQAADPSRAVGPSAGRTVVWSYAHVPFGWDGDVRPLVEEQVERFAPGFRDRIVH
+AVATRPADLEAWNPNLVGGDIAGGSMGGLQLLLRPTASPRPHRAGRPGLYLASAATPPGG
+GVHGMAGAWAVRTLLRDRARAAF
+>GCF_023573625.1_01496
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAVPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRALGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPARPFVMLCQQQ
+AADPSRATGPAQGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIEAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASIRPHRAGRAGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000136.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed2f92715486ef1cfc04c27465480cbee0bcbaa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000136.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01584
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>GCF_002008305.4_02249
+MISSLFSWFADPAHWAGPNGVPARVLEHLGYSVLALVIAAAIAFPVGVWIGHTGRGRRVV
+VALSSALRALPTLGLLTFLAIVLDIRLRQALIPTVMVLVILAIPPLLAGTYAGLQAVPRE
+VVHAARANGHSTGQLIGQVELPIALPMAVGGLRSATLQVIATTSVASYLGLGGLGRYLFD
+ALAVQDYVTMLAGAVLIAVLALLCDGLLLLVQRILTPAGLRARG
+>GCF_003691675.1_01295
+MIARLRAASAEDRLLLIGLPLLVATLLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>GCF_005280335.1_01338
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>GCF_020097155.1_00458
+MIADLFAWFADPAHWTGPGGVPARVAEHLGYSLLALAIAAVIALPAGVAIGHTGKGRRVV
+VAVSSALRALPTLGLLTFLAIVLQVGLRQALIPAVIVLVVLAVPPLLAGAYAGVHAVPRD
+VVVAARANGHSTRQLVSQVEVPLALPMIVGGLRSASLQVLATTSVAAYLGLGGLGRYLFD
+ALAVQDYTTMLAGAVLIALLALVSDAVLLLFQRLVTPA
+>GCF_023573625.1_01511
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000137.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b96995ba5b9f6b279855164d46ce22d6f3bddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000137.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01585
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGEPVLDAATPISEALAALVMA
+PTEEIAVVRDGTVIGLLDYPTLRAHARASDEQARP
+>GCF_002008305.4_02251
+MIRFEHVEKTFPDGTRAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTGGRVL
+IEGRDVASLDPVKLRRGIGYVMQNAGLLPHRTVLDNVLTVPRLTGRISRQDRDHAHELLE
+LVGLPAAVASRYPSQLSGGQRQRVGAARALAPDPDVLLMDEPFSAVDPVVRADLQAEMLR
+IQRELSKTVLFVTHDVDEAVLLGDEVLVLREGARVAQHGTGEDILLRPADDFVRSFVGGA
+RRELHVEDRTGTPIVVDASGRVAGTLVQP
+>GCF_003691675.1_01296
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDTL
+TRQRLQKEMLDIQARVGKTIVMVIHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAALVMA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>GCF_005280335.1_01337
+MSTDRDAGAEIRLESLTKRYPGQDRPAVDALDLLIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAVYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQQEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAHHPTGTLPDGPVLDAATPISEALAALVTA
+PTEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>GCF_020097155.1_00456
+MIRFEHVGKVFDDGTAAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTSGRVW
+IDDADVASVDPVRLRRRIGYVMQQAGLLPHRTVLDNVLTVPRLTGRVSAADRSRAHELLE
+LVGLPADAARRRPDQLSGGQRQRVGVARALASDPDILLMDEPFSAVDPVVRAELQAELLR
+IQRELAKTVLFVTHDVDEAVLLGDEVLVLRTGAQVAQRGRGEEILLHPADGFVDRFVGGD
+RRRLHVEERAGTATVVDAAGRVAGLLETP
+>GCF_023573625.1_01512
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELFGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAVLVTA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000138.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..579ce20b9187127684bdf64fc39623d699f86ca1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000138.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01601
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTRSAPVTVPTTYVWGTRDAALGPRAAELTAGQVAGEY
+RFVKLDADHWLPEREADAVARAILDRVR
+>GCF_003691675.1_01313
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
+>GCF_020097155.1_00271
+MLHRREYGDPDGVPVLHFHGTPGSGREAAALDAAARAAGVRLIAPDRPGMGRTPHLPGRR
+LAHWPAEVTRLLDELGIDRAAILAWSGGGPYAVACLARIPERLTAVALLAPAGLLRGIPW
+ANRLFPRLYLPAAGAIARARDWAPAAALGVFRWRRMRSRLADGPPAASPEREPLAPSSAA
+VLAASWREAFRQGHAGPVQDEQVINEDWSPLLTSARRAPVPVRIWHGRRDRVVPHRHSRR
+LAAALGAFLVDAHDGDHPGALLTAGPEALGWLAASAE
+>GCF_020097155.1_01201
+MTGGDALWGRVDAFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDSTSWRHVEPLLHAAGLR
+TLAPDQRGYSPGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATA
+HPERVASLTVLSTPHPAALARALRGSDQLRRSWYIAAFQAPALPERILSRRLGSLLQRGQ
+VPGAEHYARRFSTPQSLRGPVNWYRANPDLVTTTRSAPVSVPTTYVWGTRDAALGPRAAE
+LTAGQVAGEYRFVALDADHWLPEREADAVARAILDRVR
+>GCF_020097155.1_01824
+MTIPGFALEHIPLPSGVTLRVATGGEGPAVVLLHGHPRTHATWHRVAPALADAGLRVVCP
+DLRGYGQSSAPEPSDDLHTHSDRTMAGDIALLMTHLGHDHFSVVGHDRGSYVAYRTALDF
+PERVDRMAVLDCVPILEALERADARFAEKWWHWFFFASPHAERVICADPLAWYQPDAQKM
+GQENYQDMVAAISDPQTVRSMIADYRASLHVDRDADARDRARGHQIQCPTLVAWSKHDDM
+EDLYGNPAEVWESWCAHRPESAVIDSGHHMAEDNPEQLTAVLTEFFLPS
+>GCF_023573625.1_01528
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000139.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db74bb50320c278539d260e3a194e709690bcd38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000139.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_01604
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>GCF_003691675.1_01316
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>GCF_005280335.1_01275
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN
+>GCF_005280335.1_01290
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>GCF_020097155.1_01198
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER
+>GCF_023573625.1_01531
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000141.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3314de3dedf3b8085144376be62e411e22617b94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000141.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01636
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSSKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADTLRIDKDVQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
+>GCF_003691675.1_01341
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFDVNTTVKDAKAEDFDGLVMPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRRLTSYPSLKTDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>GCF_005280335.1_01259
+MTENAAQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFDGIVLPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRKMTSYSSLKTDLKNAGAQWVDEEVVVDAGLTTSRSPEDLDAFNAKL
+VEELAEGKHEDQTA
+>GCF_020097155.1_01168
+MTENAVQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADAMRVNKDAQAFVRAFFDQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>GCF_020097155.1_01210
+MAVDLQGKRVTILAADGVERVELDQPREALDRAGARTEVLSVDEGEIKARENDLDPAGTF
+GVDGLVAEASGADYDALVLPGGTVNPDKLRIDEDAVAFVRDFAENGKPVVAICHGPWTLI
+EADVATGRTLTSFPSIRTDLRNDGANVVDQEVVVDKNLITSRSPEDLPAFSEAIVAQLAG
+TTTKEEETS
+>GCF_023573625.1_01565
+MTENAVQNAPLSGKTVAFLATDGVEQVELTSPWEAVIAAGATPVLVSPKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADALRIDTDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDSGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000146.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41b80b820c4f2fe1b75359ad390abe519fb15c07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000146.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_01795
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>GCF_002008305.4_02050
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSRWQTTTYAAVWERV
+RRIAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPDGVRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETGGLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>GCF_003691675.1_01756
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSGVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>GCF_005280335.1_01081
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>GCF_020097155.1_00730
+MNSATAPVLGTPSTMGDDEQLTTSRLFRDAARTYPDQSITHRTIDGEWKVTDYAATWERM
+QRVAAGLASLGVGPRDRVGLLLWNDLRHFECYFAVPLTGATMVQLNLRLAPQDLAYVIGH
+SGARTIVVDATLLPLAEALGPHLPEDTRWIVATDGALPDSWAGRADTMSYEDLIERSAPI
+EDAPDMDERSASGACYTTGTTGRPKGVFYSHRATWLHAFAIAANTGMTMDDTVMLLTPMF
+HAQCWGLPYASVAVGARVVLPGRFTMQDTALLTESLVEHGVTVAPAAPAILLPMLHYLEG
+MEETPHLPGLRFLCGATEPPVALMQGFDRLMGAEIIHAYGATETSPVVSVNRLRPALAER
+LSEDEQWDLKRYQGLVVTGVDVKVVDPMGQPLPPGERNVGEVMIRGPWITRSYFENPEAT
+EKGFDDEGYWRSGDVGHLSEEGYLKIADRMKDVVKSGGEWISSIDLENHLLTVPGVSEAA
+VVGVPHPTWQERPIALVVRTAGADLSEEQVKAALGARFASWQVPDRVLFVDELDRTSVGK
+LDKKRLRQVYADALAQGDGPGAPSA
+>GCF_023573625.1_01984
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALHAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRGDVLSYEALLDGQEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000147.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49a5b7a266d617e7fa2e81e99f4b39c9948beafc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000147.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01809
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>GCF_003691675.1_01506
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>GCF_005280335.1_01065
+MQTPATVHLVRHGEVHNPDRVLYGRLPEFGLSELGRQMADGVAAWFLERAEQTGRRPDVV
+AASPLTRAQQTAEPIAAALGRPLATEPDLIEAENDFEGMSQVAASLKRNPRLWPKLRNPL
+RPSWGEPYRQQAARMLAVVDRVRDEAEAAGGPGAEAVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVFEEGRALPRVEYHEPNQALLKDASSLPGA
+>GCF_005280335.1_02644
+MSDKLLHLVRHGEVHNPDRVLYGRLPGFRLSEPGHRMAEAAALELAGSDRVVARLLASPL
+ERTRQSARPIASALGLEVSIEERIVEPANVFEGMVNSGSDSAFRQPRYWYRFVNPFRPSW
+GEPYRQIAARVREAMDEAWETTRDGDIVMVSHQAPIWIAHLDVAGKPLFHNPATRRCELS
+SITSFEKRGERWFEVDYRTPAAGLVDDAVDVGAV
+>GCF_020097155.1_01000
+MQTLATVHIVRHGEVHNPDRVLYGRLDGFGLSELGQRMAVGVAEWFLDRATELQRRPAIV
+AASPLLRAQQTAAPIAGAFATQLRTEQDLIEAENTFEGMSDVAATLRRSPRLWPLLRNPL
+RPSWGEPYRQQAARMLAVVDRVKDEAVDALGPGAEAILVSHQLPIWVTRLAVEGRPLAHD
+PRRRECSLTSVTSLVFEDGRALPRVEYHEPNAALLKDASSLPGA
+>GCF_023573625.1_01730
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFEERAAQTGRAPAVV
+AASPLTRAQQTAAPIAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAAEGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRWRECSLTSVTSLVYEEGRRVPRVEYHEPNQALLKDASSLPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000148.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7371af214d7d7a3bb24467a7f6351cdc47a820ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000148.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_01830
+MTAPLTSPPAATASPDPVDVAVIGAGQAGLAAGYFLARAARDVDRGRRAGPAPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVTAVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPDGVRWDHDAGASH
+GWPAASRAAARVRGTEHPVDDVVWCTGFRADLRHLRSLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILAGLTAG
+>GCF_003691675.1_01527
+MTAPLTSPPAATASPDPVDVAVIGAGQAGLAAGYFLARAARDVDRGRRPGPAPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVTAVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPDGVRWDLGAGASH
+GWPPDSRAAARVRGAEHPVDDVVWCTGFRADLRHLRGLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILTGLTAG
+>GCF_005280335.1_00744
+MAGAVDVLVVGGGQAGLAAGFYLHRLGRDAGRDRGGPAPSFAVLDANDQPGGAWQYYWDT
+LELFSPADYSSLPGYRMPAWTGPGNPSAAHVVDYLRSYEDRYGLPVHRPVTVHAIEDHPD
+GGYLTRTDRGTWTSRAVINATGSWRRPFVPRMPGAEDFTGSQLHTTGYRGREPFAGQRVV
+VVGGGNSGAQIAADLLPAAAEVTWVTRRPPRYLPDDVDGRALFALATGHVQATRRGEPSP
+GGVGSLGDIVAVPPVRAARDAGRLQAQPTFSGFTPTGIRWDDGRKLEVDTVLWCTGFRPD
+LAHLRPLRPAMEGTVPATAGDPPTRSRDRDGLFFLGYGDWCGPASATLIGVGAPARATAT
+AAARHVLSGG
+>GCF_005280335.1_01038
+MTTRTAPASPPSAVDVAVIGAGQSGLAAGYFLARAAREAERGRRPGPPSSFVLLDASPGP
+GGAWPHHWDSLRLFSPAEHSSLPGRRMPPSPGPDTPGADHVVAYLADYEQRYALPVRHGV
+RVTRMEHDADAPHPFTLHREDGPPVAARAVISATGSFTRPFLPAVAFGDGFRGEQLHSSA
+YRRPGPFAGRRVLVVGGGNSGAQIAADLLLAGVETTWATRRPPRFMPDDVDGRHLFQTAS
+ARVLGRSEARVGDLGDIVMLPPVRRARDEAGLHAVPMVSAFIPDGARWDPDAGAVHGWAA
+SSRLAAEVRGAERALDAVVWCTGFRADLRHLRGLDLTHRSSGVPATRREVPTASADVPGL
+HLLGYDDWCGAATATLVGVGVHARGAVDDVLAGLAAG
+>GCF_005280335.1_02335
+MGHYLNRAGLHPLLVDRAPALGHSWRSRWNSLRLFTPARHNRLADLLFPGDPEAYPGKDA
+VADYLQDFARHQSLTPATGTAITDLHGRLGAFTATTATGRQLRARSVVVATGAFGTPFLP
+DWAARDGRGPRQLHAKNYRTPASVPGQEVLAVGGGNTGVQIALELAATGKRVHLSTGRPR
+RHLPQRLGGKDMFWWLTRTGAMSAPAGSVPGKWLRAHDPIIGTDRAALTGVNIRTRPRAT
+GLQGGIVGFADGTRYTPEVIVWATGYRHADRWIRIPAALDPTGVLHAPEGVSPVAGLYTI
+GRSWQRNRGSALLGFVSTDAAPLAQTILTALAKAP
+>GCF_023573625.1_01751
+MTAPLTSPPADAASPDPVDVAVIGAGQAGLAVGYFLARAARDVDRGRRPGPPPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVAEVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPEGVRWGHDAGASH
+GWPAASRAAARVRGAEHPVDDVVWCTGFRADLRHLRGLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILAGLTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000152.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d7b393e1c457bf29dfed15458dbba12697bc709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000152.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_01939
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>GCF_003691675.1_01635
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>GCF_005280335.1_00920
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+>GCF_020097155.1_00854
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA
+>GCF_020097155.1_02134
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR
+>GCF_023573625.1_01858
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000154.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5428ff8106412c2a6e0bf78b658e974c45b85674
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000154.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01983
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
+>GCF_003691675.1_01677
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA
+>GCF_005280335.1_00875
+MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA
+VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART
+KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFVF
+>GCF_020097155.1_00810
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWARTR
+DARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA
+>GCF_020097155.1_00823
+MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS
+IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR
+RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL
+>GCF_023573625.1_01909
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000160.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c415804ef613a2c84850cfff4d883c63543c32d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000160.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02072
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST
+>GCF_005280335.1_00736
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT
+>GCF_005280335.1_00740
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN
+>GCF_005280335.1_00741
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS
+>GCF_020097155.1_00488
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA
+>GCF_023573625.1_02000
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000165.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af49c20c787abd8601b27847ac4071f2040a490d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000165.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_02162
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVRTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGW
+LLDTYLRGLRP
+>GCF_003691675.1_01875
+MILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGWLLDTYLR
+GLRP
+>GCF_003691675.1_01876
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPRP
+SSPRPSV
+>GCF_005280335.1_00595
+MRADARANRQDLLAAAGRLLEEQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARVSGILHAFLDGGGSADRRWRRLAEELAAVNLTSLVTAGDDLEAADRPQEALIVEAE
+QVIISLTDRAVTEARRAGLVALGVTGTRYLTGLLAVTRPPAGELLARHADQRDWLLGVYL
+RGLRP
+>GCF_020097155.1_00518
+MQEEDTPPAEAMGRAEDAVMGLADRAVDLAREAGLVGDDVTGRAYMNGLIAVTRPPLPAL
+ESCRDDLEDWLLTVFLRGLRPAA
+>GCF_023573625.1_02107
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLMGPDVTGADYLLWVMRFLARGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000168.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4757e93caca148d3433948de8b56d16e01afe9a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000168.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_02252
+MTAQTPATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLGAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGRQIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>GCF_002008305.4_02276
+MTTETPTLAAPEIPATMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWP
+YRGHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVN
+AGEYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLTDYLAASDVLGTGWYAAVAAQAGPG
+KTIAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQV
+RELTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEG
+GPAPVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>GCF_003691675.1_01951
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSRAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>GCF_005280335.1_00489
+MTAQTPATPAVPETMKAVIMRAPGDVVVEEVDTPRVAKPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPADPDRLADYLAASDVLGTGWYAAVAANAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIAFSRHEDRAALAREFGADVIIAERGEEGAAKVKE
+LTNGYGAHGVCEAVGTQESMDQALASVRPGGHVGFVGVSHDQTIDGSRLFGLEIHLEGGP
+APVRRFLPELIERIQAGEIQPGRVFTARMPIDDAAEAYKAMDERREIKVLLEV
+>GCF_020097155.1_00435
+MTAQTPTTPAIPETMKAVVMRAPGDVVVEEVDTPRVVQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>GCF_023573625.1_02183
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYQAMDERREIKVLLEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000169.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bbe86dfb4b8f98978cd54afc84884b0746e3e01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000169.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02265
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPVVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGVRGHL
+>GCF_003691675.1_01960
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRRVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPEVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGGGGPSMTANGLLRSPHAARDREGVDSRGSPGVRTEVLEDLQVEKP
+LVRAGGLGEHRLVGADVDDLPHTEAGGLLRLKDRQVSVAGDAVDLGEPPRGPHLVCRPHH
+GPHTTQRDRPGGAAVVVMGDDPACRGQGPSLTHSPGGQQDQLVDFPHGDRVTAAFLLPVR
+ERGAADGADGDVHGRSVGAGPHPGARGASSPVMLGIGLEARRVKARTTHPHRVHRIDAMT
+RTGAFTIAGLAAFAISTGILVLLLITGSETPRETMAFFALIIGCYALSALCFAAAKRVLL
+ALLSGALAVVSFPLALFIGYVVEMLQSQQ
+>GCF_005280335.1_00469
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPLVTRPEAEEAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDE
+ATAREKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVARMDARNTASARLAETLGMRREAHHRQDWWSKGE
+WTDTLVYAMLASDRG
+>GCF_005280335.1_00641
+MAERFRGRGLGAQILAALTRHVFETMPAVDRFEGQTREDNIPMLRAFRRAGWVKEAHYRR
+GWPVEGGEPLASVAYAVLRQDWETGTTTPVPADVDVPSRRKRDVGAESNGHIPDWPMRTE
+RLTLRPHREDDLGWLQEMYAQPEVVRHLLDEPWDEPTARQKLVRRIEWNDLAGPSGVASL
+VIEHAGVPVGDVILWLTNRERGVAEIGWALDPRHAGQGFAREAAAAMLALGFEVHGLHRV
+VAQMDARNTASARLAEAIGLRREAHHRQDWWSKGKWTDTLVYATLSSDRD
+>GCF_020097155.1_00419
+MDVTFTPLDPAGADRDALVALLTENVWPFHMRPRITRSEAEEAVDGGAWEDEDHRTLWIE
+HPEHGRVGVVRLDELTDPTPLFDLRVTERFRGRGLGAPILTALTRLVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVEGGEPLASVAYAVLRQDWETGTTTPVPAEVD
+VPPQVEHGEGAAAVGPAPDWPLRTERLTLRPHREDDLGWLRDMYARPEVVRHLLDEPWDE
+ATARQKLAKRIAWDGLAGPSGAVSLVVEHRGVPVGDVILWLTDRERGVAQIGWALHPEHA
+GQGFAREAAAALLTLAFETYDLHRVVAQMDARNTASAQLAEAVGLRREAHHRQDWWSKGE
+WTDTLVYATLASDRG
+>GCF_023573625.1_02198
+MVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTAITRHVFETMPAVDRFEGQTREDNVPM
+LRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVDAPPPAGRK
+EGAAEGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDEATARAKLA
+KRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHAGQGFAREA
+AAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGEWTDTLVYA
+MLASDRGVRGHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68e3eb0e305ac0d74087550a972610b3a6c8b900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000178.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>GCF_003691675.1_02010
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>GCF_005280335.1_00419
+MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH
+HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI
+LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ
+GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV
+DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI
+AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA
+REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL
+GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR
+CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN
+IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK
+WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT
+LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV
+>GCF_020097155.1_00371
+MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH
+LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL
+HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG
+EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE
+DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA
+FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK
+EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW
+LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV
+YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE
+EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN
+APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ
+VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI
+>GCF_023573625.1_00005
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..269b97a53ff369ecbab1d14913cb10d9d32d6e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000183.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00014
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
+>GCF_003691675.1_02032
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR
+>GCF_005280335.1_00383
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR
+>GCF_020097155.1_00364
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG
+>GCF_023573625.1_00014
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..492aa1c26872ae26be4b7e8b2abd6584a3ccdd98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000184.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>GCF_003691675.1_02033
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>GCF_005280335.1_00382
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA
+>GCF_020097155.1_00363
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA
+>GCF_023573625.1_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6814526f225df60889d9e60548ae115b41fd03b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000185.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG
+>GCF_003691675.1_02034
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG
+>GCF_005280335.1_00381
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR
+>GCF_020097155.1_00362
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG
+>GCF_023573625.1_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c12c83815216a1347cea3bd9d10c000e057f9e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000187.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>GCF_003691675.1_02036
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>GCF_005280335.1_00379
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD
+>GCF_020097155.1_00360
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD
+>GCF_023573625.1_00018
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1145a4e24eb0bcc2e29eaf3138fca61c9e4f0604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000193.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT
+VMELEA
+>GCF_003691675.1_02042
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA
+AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>GCF_005280335.1_00372
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
+>GCF_020097155.1_00354
+MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA
+HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD
+ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV
+MGLED
+>GCF_023573625.1_00024
+MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV
+AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ
+DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT
+VMELEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000194.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f4bf2e676095097db78051d343dc88987be919a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000194.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00032
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>GCF_003691675.1_02049
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
+>GCF_005280335.1_00366
+MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>GCF_020097155.1_00304
+MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA
+PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV
+MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG
+LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP
+EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL
+AHIPDQENRAAAPSDTYHY
+>GCF_023573625.1_00031
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000195.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2372ad60b25402f4bb5abcc5cd7505b4b759c571
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000195.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_00033
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVA
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV
+VPAAVQSVLTEDNAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
+>GCF_003691675.1_02050
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV
+VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
+>GCF_005280335.1_00365
+MTRIPAPDEAAAAPSSPLDNALAQLAAAVRTLGYDEGLHQTLAAPRRELSVSIPLRRDDG
+AVEVLRGYRVQHNISRGPAKGGVRFSPDVDLDEVRALAMWMSWKCALVGVPYGGAKGGVS
+IDPRRYSKAELERVTRRYTSEIQPIIGPEVDIPAPDMGTDEQTMAWMMDTYSVNVGHTTL
+GAVTGKPVSLGGSLGRASATSEGVVHVALAALRDRGIDPQGATAAVQGFGKVGAGTVELL
+AAAGVRVVAVSDQYGAVRCEDGVDFATLSAHVAETGKVVDCPGTEAMDADELLLSDVDLV
+VPAAVQGVLTAQNADRVRARVVVEGANGPTTGEADRILNENGVLVAPDILANAGGVIVSY
+FEWVQANQAYWWTREEVAERLERRMVLAWEAVQAAAREHDLTLREAATVLAVKRVAEAHR
+TRGLYP
+>GCF_020097155.1_00463
+MTSASSPLANALAQLERAVETLGYDEGTHQLLANPRRELSVSIPLRRDSGEVEVFHGYRV
+QHNFSRGPAKGGVRFSPSVDLDEVRALAMWMTWKCALVDVPYGGAKGGVAIDPRTYSQAE
+LERVTRRYTTEILPIIGPEKDIPAPDVGTDEKTMAWMMDTFSVAMGYTVQGVVTGKPVSL
+GGSLGRAEATSRGVVHIALAALKHKGIEPAQATASVQGFGKVGAGTVEFLADAGVTVLAV
+SDQYGAVRREEGIDYAALAAHVAETGSVVDCPGTEPMDPAELLTMEVDVLVPAAVEGVLT
+KDNAGDVKAKIVVEGANGPTTGEADAILNENGVLVAPDILANAGGVIVSYFEWAQANQAY
+RWTLQEVNDRLAARMRTAWDGVLAASQKHGVSLREAATVTAVKRVKEAHEIRGLYP
+>GCF_023573625.1_00032
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQKQLWDTGSVKDTPGTAPMDADELLEMDVDLV
+VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000196.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e301823ed5a80f623d012e7087947455867dc3d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000196.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00034
+MHAITPGTWNLDPAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>GCF_003691675.1_02051
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>GCF_005280335.1_00362
+MAQVTTGTWNLDPAHSDVDFVVRHAGISKVRGTFAAVEGVLVVAEDFNASSVEVTVDVAS
+INTKNEGRDQHLRSGDFFDVEQFPTMTFRSTEVRGAAEEFTLVGELTLHGVTRTVELEAE
+LGGQDVDPFGTTRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLPEAD
+AQA
+>GCF_020097155.1_00303
+MAQITPGTWNLDAAHSDVDFVIRHAGISKVRGTFHTVDGQLVVAEDFNQSSVQVTVDMAS
+INTKNEGRDQHLRSADFFDVEQFPQMTFRSTEVRGEAEDFTVVGELTIHGVTKTVELEAE
+FGGQDKDAFGATRVGFEAKGEISRKDFGLTWNAATEAGGVMVSDKVKIEIGAAFVLPEA
+>GCF_023573625.1_00033
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGLLVSDKVKLEIGAAFVLPEAD
+AQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000197.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8eb24eedac60b02c107cb5b3586d6104d39f8e9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000197.fa
@@ -0,0 +1,88 @@
+>GCF_002008305.4_00035
+MRRIPRTGPLDEGPGLLTLFSAFMDTPSDAARVAAEERARALIDEQFRRAGWSVQDGAQK
+NLMASAGVAVREVTMRAGHGRVDYLLYVDRRPVGVIEAKPVGTTLAGVEWQSGMYADGLP
+DDALKRAVVVDGRLPFVFESTGSESYLTNGYDPNPRARRVFSIPRPEYFSQLMRDAEADP
+DAPTWRGKVRAMPPLQTEGLRPAQIDAVRGLERSLAEQRHDRSLIQMATGAGKTFTAITA
+AYRLLAHGGFRRILFLVDRNNLADQTLAEFENYRLPGDGRRFTEVYPVDKLRRAGMRDSA
+NVVISTIQRVYAGLQGKEVPDSDDPMLDEFVPDRPVTVDYSADLPPESFDLVIVDEAHRS
+IYGVWRGVLEYFDAHVVGLTATPGKQTLGFFRQNLVSEYTYPQSVADGVNVDFDLYRIRT
+QISEEGSTIEAGTVVPVQDKSTRIERFETLDEDLDYTRTQLDRAVVSTNQIRLVLEVFRD
+RLFTEIFPGRTEVPKTLIFAKDDNHAESIVRTVREVFGRGNEFAAKITYSARDPKGQLQA
+FRNSPALRVAVTVDMIATGTDVKPLECVLFMRDVRSAQYFEQMKGRGARTIPDADFQAVT
+PDAATKTRFVIVDAVGVTEHDFVDPPLNRQKAVPLKKLLEKAASLTITEDEAATLASRLA
+KLELELSDSERQELDDVAGGSVRQMVKDLVAAVDADEQASVRAEAAARGEDEDRALEEHI
+ERAVTPLAANPDLRMRILELRRAHDRVIDEVSADVLLDAYGVVDADKARSVVESWSAYLE
+EHRDEITAVQVMFEAGEGRLQYAQVAELAERIKRPPYSWTPEILWKAYESLDAGRVRRSD
+HHTLTDLVSLLRFATGTDDELVPFADRVRENYAGWLLAQEQAGAEFSDTQRWWLDRMVEV
+IGASAELTVDDLEGAPFTDRGGIDGAVRDLGPRAGLLIEELNEELTA
+>GCF_002008305.4_00190
+MATGTGKTCTAVALVDQMARAGWVKRVLFLADRQALVKQAADAFVEHGFVGTTVNLLKNR
+HGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAHRSVYAKYGEIFRHFDALL
+VGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLVPPRGVSVGTTFLRRGTRY
+DQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDRVLSTLREHGHKVAGSERL
+GKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYPDALLDDFKTPGKAPHIAI
+SVDMLDTGVDVPDVVNLVFFKLIRSKTKFWQMIGRGTRLRPDLYGPGRDKEDFLVFDWCQ
+NLEFFNQDLPESDGFTQRSLTQRLFEDRLALVVALDALDDDAGAPAAVGPEERAVRELRR
+TAAEELQAAIARLTLENVLARPLRREVEEFQRPEAWTSLSAQAAERARALAGVVTGLPGE
+DVDAKRFDLLIVRRQLADLTGEAGTAERIRATVQSLGENLLSKDAIPAVKEQIILLEAVA
+GEEWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQLEEVDVVRPTPGVDI
+ERFWAKVSEPLRHNESSLALQKLRHGKQLTEPDLESLEQLLRSIGAEDAHLAAAKSEGEG
+QLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQARIRFLGHMVEELTANGVLDAGRLFESP
+YTDDAPEGPFGLFEEAQVYSLRERLDFVRTSAMVPGPEANAGGDEARGVVA
+>GCF_003691675.1_02020
+MAVDITYDEALIEEIAARFDLRDPNKNALTEIVQRIADGGIGYQEMVADLATGVGKTFLM
+SSLIEYLAQQGVRHVLVVTPGSTIQRKTLANFDAASAKYVAGADIAPFVVTPDNFQAANV
+GSVLRNPQRLKVFVFNVQQLIRPTDKVSRKVRSEDENLGDALYSHLENADDLFVIADEHH
+VYREKAKAFSAAIRDLNPVALVGLTATPDKDDYGKVVFQYTLGEAIADGYVKVPVIVYRK
+DGTKDERTQLRDACQLLGHKEKSYAVYRETNRDAPTVKPVLFVVCQTIEHATEVGQLLAQ
+SGMIGDGSQVLEITSQSSDVALEALAKVEEPDSPIRAIVSVNMLREGWDVKNIAVIVALR
+RLASQTLTEQILGRGLRLPFGARTGIADVDQVDLVAHDSYQQLLAQKDVLRQRIQLPSTA
+VEVDDQGFATTTEVDPNQPVPVEPLAGSSQHDQIGGSGGSSSLAPAPGQWTLFDWEEDDS
+AQGEDYQPNPGLIFEETEQRVESQVPEPQYRVKDAPQIIFPRREPRLVHSPFSLSDIPDG
+DAQKAGAAFVKEVPTFIFRDALEAKRKGDQVEIISTPQGTSEAQQTLAGLDVVQAELTEA
+IMQQPEVPAERPSKNAAKRLVKAFMKGAGVTNDEETAQWGTKRRQQAVEGMRTMIRDKIT
+SRPRQEKFEFVKIELPLEPVTVAADAVKAHNVVKFKKGLQYVGWEKNVMPVATFDAGTTE
+WELARLMDRDPNIKWWVRVYVGGQAFIPTPEGRYFPDFIALDVDGVHWLIEGKADDHAKD
+DSVLRKKKAAENWARAVRDDGDFGTWRYMFATESNIKNSAGSWNALLMSTKPE
+>GCF_005280335.1_00209
+MSSNFDFLAPVWPRVHENAVRAESYLHADPRSACFYARRTVELVVEGIYRLRNLPEPYKA
+DLAARINADAFLHEADPRIVQKLNVIRQRGNDAVHKLPDIDPRTAAFVLTELHHVLLWAA
+FRHSAAGPALDMQARFAPALAPQAAPLTREEVVQLNDLIEKKDAEAAAALAASEQAREQL
+EADLAAARAELTAAKEAAGAVVDPRDYTENDTRDLFIDQLLNEAGWPLTAARDREFPVTG
+MPTPTGDGFVDYVLWGADGKPVALVEAKRTTASVQLGQDQAARYADALEARFGRRPVIFY
+TNGVEHYLWDDAAGYPPRQVRGFYTPAQLDTLIQRRAGRRPLAQTPVKAEIAGRPYQERA
+IRAIGEAFENKRRATLLVMATGTGKTRTAVALVDQMARAGWVKRVLFLADRQALVKQAAD
+AFVEHGFAGTTVNLLKNRHGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAH
+RSVYAKYGEIFRHFDALLVGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLV
+PPRGVSVGTAFLRRGIRYDQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDR
+VLSTLMEHGHKVADGERLGKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYP
+EAMLDDFKTPGKAPHIAISVDMLDTGVDVPDVVNLVFFKLVRSKTKFWQMIGRGTRLRPD
+LYGPGRDKEDFLVFDWCQNLEFFNQDLPESDGSTQKSLTQRLFEDRLALVVALDALDDDG
+GAPAAVGPEERAVRRTAAEELQAAIARLTLENVLVRPHRREVEEFQRPEAWTSLSAQAAE
+RARALAGVVTGLPGEDVDAKRFDLLIVRRQLADLSGEGGTAERIRATVQSLAENLLSKDA
+IPAVKEQIILLEAVAGEDWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQ
+LEEVDVVRPTPGVDIERFWAKVSEPLRRNESSLALQKLRHGKQLTKQDLESLEQLLRSIG
+AEDVHLAAAKSEGEGQLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQAQIRFLGHMVEEL
+TANGVLDAGRLFESPYTDDAPEGPFGLFEEAQVYSLRERLDLVRASAMVPGPEANADGDE
+ARGVVA
+>GCF_023573625.1_00190
+MSSNFDFLAPVWPRVHENAVRAESYLHTDPRSACFYARRTMELVVEGIYRLRGLPEPYKA
+DLAARINADAFLHEADPRIVQKLNVIRQRGNDAVHKLLDIDPRTAAFVLTELHHVLLWAA
+FRHSAAGPALDMQARFDPALAPQAAPLTREEVVQLNDLIEKRDAEAAAALGASEQARAQL
+EADLAAARAELTAVKEAAGAVVDPRDYTENDTRDLFIDQLLNEAGWPLTDTRGREFPVTG
+MPTPTGDGFVDYVLWGADGKPVALVEAKRTTASVQLGQDQAARYADALEARFGRRPVIFY
+TNGVEHYLWDDAAGYPPRQVRGFYTPAQLDTLIQRRAGRRPLAQTPVKAEIAGRPYQERA
+IRAIGEAFENKRRAALLVMATGTGKTRTAVALVDQMARAGWVKRVLFLADRQALVKQAAD
+AFVEHGFAGTTVNLLKNRHGEGRIYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAH
+RSVYAKYGEIFRHFDALLVGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLV
+PPRGVSVGTTFLRRGIRYDQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDR
+VLSTLMEHGHKVADGERLGKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYP
+DALLDDFKTPGKAPHIAISVDMLDTGVDVPDVVNLVFFKLVRSKTKFWQMIGRGTRLRPD
+LYGPGRDKEDFLVFDWCQNLEFFNQDLPESDGSTQKSLTQRLFEDRLALVVALDALDDDA
+GAPATAGPEERAVRELRRTAAEELQAAIARLTLENVLARPLRREVEEFQRPEAWTSLSAQ
+AAERARALAGVVTGLPGEDVDAKRFDLLIVRRQLADLTGEAGTSERIRATVQSLAENLLS
+KDAIPAVKEQIILLEAVAGEEWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADT
+LTQLEEVDVVRPTPGVDIERFWAKVSEPLRRNESSLALQKLRHGKQLTEQDLESLEQLLR
+SIGAEDVHLAAAKSEGEGQLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQAQIRFLGHMV
+EELTANGVLDAGRLFESPYTDDAPEGPFGLFEEAQVYSLRERLDFVRTSAMVPGPEANAG
+GDEARGVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000201.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e349ab8a72c2c16e25e853e261076227476dbc42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000201.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00043
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>GCF_003691675.1_02056
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>GCF_005280335.1_00357
+MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL
+LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM
+LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA
+WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF
+TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD
+>GCF_020097155.1_00299
+MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG
+DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA
+GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES
+VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI
+VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS
+SRPGADPPMRDELAD
+>GCF_023573625.1_00038
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000202.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c479fb31b65e99bcae092bea4d58a0be089fef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000202.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00044
+MGGVDTAQQTTAQDTAQDPASTTPRTVTVTGAAGNIGYALLFRIAAGGMLGPDTSVRLRL
+LEIPAALGAAEGTAMELADAAFPLLADVEVTDEPARAFDGVQHALLVGARPRTKGMERSD
+LLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPDVPAERFTALTRLDH
+NRAVAQLAARAGVAVTDVAGVTIWGNHSATQFPDLTHARVRVDGTWRPALEVVDPVWAGE
+EFVPRVARRGAEIIEVRGASSAASAASAAIDHMCDWTLGTGVDADGASRRTSAAVVSDGS
+YGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVAELEAERDAVRGLGL
+L
+>GCF_003691675.1_02057
+MRRAGVSSAGERGHDGGVDTALQTTAQDTAPDPVSTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VPAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
+>GCF_005280335.1_00356
+MRARRRAGLFSAGVRGYDGRVSTVSAPSRAPRTVTVTGAAGNIGYALLFRIAAGGMLGPD
+TPVRLRLLEIPAALRAAEGTAMELADAAFPLLADVEVTDDPAVAFDGVQHAMLVGARPRT
+KGMERGDLLEANGGIFGPQGRAINDHAADDVRVVVVGNPANTNALIAAAHAPDVPAERFT
+ALTRLDHNRAVAQLAARAGVAVTDVDGVTIWGNHSATQFPDLTHARVRVAGAWRPALEVV
+DPAWAAEEFVPRVAKRGAEIIEVRGASSAASAASAAVDHMRDWTLGTGAGAGGAGTDAGP
+RWTSAAVVSDGSYGVPEGLVSSFPVTSDGGAAWRIVPGLAPDESLLPGTGGRLAATVAEL
+EAERDAVHGLGLL
+>GCF_020097155.1_00298
+MTQDTLRTPATVTVTGAAGNIGYALLFRIASGQLLGPDTPVRLRLLEIPAAVRAAEGVAM
+ELADSAFPLLASVDVTDSADAAFDGTTHALLVGARPRTAGMERADLLRANGGIFGPQGAA
+INASADASVRVVVVGNPANTNALIASAHAPDVPAERFTALTRLDHNRAVSQLAARAGVGV
+ADVDGITIWGNHSATQFPDLTHARVRMSGDDGAPVWRPALEVVDPAWAAEEYIPRVAKRG
+AEIIEVRGASSQGSAASAAIDHMRDWSLGTGVDADGAPRRTSAAVVSDGSYGVPEGLISS
+FPVTSDGSGAWTIVPGLEPDESLLPGDGGRLAATVAELEAERDAVRALGLI
+>GCF_023573625.1_00039
+MRRAGVSSAGERGHDGGVDTAQQTTAQDTAPDPASTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VQAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000203.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ddc1b0f5fafd6df62808fc68e58ba0be911c86f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000203.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00045
+MPALSLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIVALRDARDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVVVDTATDDVLIAHPMRVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLMARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPADVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>GCF_003691675.1_02058
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>GCF_005280335.1_00355
+MPALPLPPRRPRLIATDLDGTIIGYRHTRSGYLSPRTVAALQEAHETGVEVVFVTGRPLR
+WLGALSEQLGQVGPVICSNGAVVVDTATDEVLLHHSMDRDAVWDAVGRLRALDRSATFGA
+ETLDGFFWESAFSEWGELEEGFRTAQRLEGVLPAHVDVVKLMARSSTMDPDVFLAAAREE
+LGALLNATHSAPGVSLVEMAAPGVHKAATLAEFAARRGVDARDVVAFGDMPNDTEMLAWA
+GLGLAVASGHESLLAVADAVVGECDDDGVAQAIELLLELPAE
+>GCF_020097155.1_00297
+MSALPASARRPRLIATDLDGTVIGYAHTRTGRISPRTVAALRRAHAEGIVVVFVTGRPLR
+WLGPLRAQLGEVGPVICSNGAVVADTATDEVLLHHALDRAAIDHVVRRIRALDPAATFGA
+EALEGFFWEDAFASDELGQTRAASLEAALPGDATVVKLMAKSGGIEPDVFLAAVRELGDG
+LVTATHSAPGMSLVEMSAPGVHKAATLAAFARGTGVEAADVVAFGDMPNDAEMLAWAGLG
+LAVASAHASLRAVADGVVGACDDDGVAAAIEALLALPEA
+>GCF_023573625.1_00040
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000209.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30f1d369fb4f16658116cfa43fa65285da20fcd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000209.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00056
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>GCF_003691675.1_02069
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLTAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>GCF_005280335.1_00339
+MVSTDMDTTTQTPDERTLLRAAGLRVTRPRVAVLTALGECPHADAATVLAAVRRELPAVS
+HQAVYDSLHTLTDVGLVRSIQPAGSTARYEIRRNDNHHHLVCRDCGTVVDVPCHTGQAPC
+LEARTDHGFLIDEAEVYYWGLCPSCRADPGAAAS
+>GCF_020097155.1_00279
+MSTVTVEQPEESALLRSVGLRVTRPRVAVLQGLRRHPHADAGSLLSAVREDLPQVSHQAV
+YDCLHVLTDAGLVRSLQPAGSPARYELAAHDNHHHLVCRGCGDLVDVPCQTGVAPCLHAP
+EDHGFLIEEAEVYYWGLCPDCRSGGYTTTSDGTPAPAPPAP
+>GCF_023573625.1_00051
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000215.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d1a3bcc77c7ddf6f5c63739414f47313777c5fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000215.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00065
+MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA
+GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL
+LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
+>GCF_003691675.1_02078
+MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG
+MERFELV
+>GCF_005280335.1_00330
+MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR
+ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ
+RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS
+GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR
+LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF
+NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV
+PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV
+AILENHQNADGSVTVPVALRPYLGGMERFELV
+>GCF_020097155.1_00272
+MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV
+VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM
+GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR
+LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA
+RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL
+RPYLGGLERFELV
+>GCF_023573625.1_00059
+MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000216.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..269f967988bb4236d1286ccd8992f6737bdf989d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000216.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00066
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
+>GCF_003691675.1_02079
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGID
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGLGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPTAA
+>GCF_005280335.1_00329
+MEKKLVCLDVDGTIVDHDGHLHEPVREAVKAVVAAGHHVVIATGRSRGATLPVAQSLGIE
+AGYMVCSNGGVTLRLDPALEDGYEVTDCRTFDPRSVLSQLRSRLPGAKYAVEVPDGSFLS
+TERFQDMSFGVAAEGTTFEELKNTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLHVAPEHTVAVGDGRNDLEMLAWAGRGVAMGQAVREVK
+EAADEVTASVDDHGLADVLWSLVPEADRPEGVRVQEPAAA
+>GCF_020097155.1_00268
+MTKKLVCLDVDGTIVDHDGRLHEPVREAVRAVIEAGHHVVIATGRSRGATLPVAESLGID
+SGYVICSNGGATLRLDRALEDGYEVTDLRTFDPQSVLAQLRDRLPSAKYALELPDGSFLS
+TERFQDMSFGVAAEGVGFEELMATTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASALEALRTVLHVDVADTVAVGDGRNDVEMLRWAGRGVAMGQAPDEVK
+EAADEVTGGVDEHGLATVLRTLL
+>GCF_023573625.1_00060
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRAATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEITDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKMAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000220.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..073c14506de4c266cb2f7db523d10737e85b3fba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000220.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00071
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARRVALAAAAREAGQGGAAPGAGTAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWA
+GDEFTRLRVDPPGRDPRVVSLDLDTLAALPAAVRHRVIARAARAAGGQAPPRERILAVDT
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>GCF_003691675.1_02084
+MPRPEARDPGPTPAGGAGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGSCRADAGPG
+RAGNRPRGLVALSGGADSLALAVACAVLVGTRDGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARREALAAAARDAGQGRAAVVLTAHTAD
+DQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAGLTWFED
+PHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWAGAEVTR
+LRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAVDALVTGAR
+AGCTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>GCF_005280335.1_00321
+MPSGSAAPPALESWPPRGRWPEPLHRAVAALRPVLAAHDGGALIGLSGGADSCALAVAAA
+ALRGTRAGAALGPVGAVVVDHGLQAGSADVAEAAARVARTLGLEPVLVRRVAVREAGDGP
+EAAARRARRGAFADAAREAGAGLVLTAHTADDQAEQVLLGLARGSGTRSLAGIPAGGALP
+GGTALARPLLGLTRADAEAICRWAGVRWWEDPHNADPALLRSRVRTRVLPALEDLADGLG
+PGVREGLVRTAAIAAEDAAALEQWAACALAECRVRGEAGPGPGAEPGDDPGAGTGRSEAP
+GRGDVVVRLDLAAFAALPPAVRHRVLGLAVVEAGGPRPTRERTLAVDALAVPADPGAGGP
+RGPWSCPAGWK
+>GCF_020097155.1_00263
+MSSPFVRDVVAVPGAPTLPALAGPWPPRSRWPEPLHRAVESVRAVRAEHPGPVLVALSGG
+ADSLALAVACAVLAGTRAGERLGPAGAVVVDHGLQDGSAAVAAAAARTARALGLAPVTVE
+AVTVTPAGDGPEASARSARRTALARAAEGVGEGTPALVLTAHTADDQAEQVLLGLARGSG
+TRSLAGIPAHGALPGGVALARPLLGLSRADTEAICRWAGLTWFTDPHNADPALLRSRVRT
+RILPALEDPDTGLGPGLRAALVRTAAIAAEDAAALDAWADDALARLRLPAPETDRPAPVL
+LDLDALAALPAAVRHRVHARAARAAGAGTPSRERILAADALVAAAHAGGGSAGPVELGHG
+VTVRRVAAGEGGVGGRKEGGPSGCARLAYIPRPADR
+>GCF_023573625.1_00065
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGRRFGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLAPVTVTRVEVARTGDGPEADARRARRKALAAAAREAGQGDAVPGAGAAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVVRPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDVGLGPGVRAGLVRTAAIAAEDAAALDAWA
+GDEVARLRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAADA
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000226.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd53a6447cf7281be977a553d94c27b225cce872
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000226.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00079
+MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL
+QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH
+>GCF_003691675.1_02092
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
+>GCF_005280335.1_00314
+MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR
+RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL
+QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD
+>GCF_020097155.1_00255
+MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR
+RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL
+LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD
+>GCF_023573625.1_00073
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000233.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ca95d0ccb8a2277c22c0643b01fbe6673b0f4b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000233.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00088
+MSTAHEPFRDATPHSGAHTPPPTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_003691675.1_02101
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_005280335.1_00303
+MSTPYEPIRDATPHAGAHTPPPTQAEFRAEHESLGEMFKSLSSRLSTLVSQEIALAKAEA
+TESAKKAGTGAGLLAGAAVGGFFLLMFLSLALMWALGSAMHLGWAALIVAVLWGVCAAVL
+ALMGKKHLEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_020097155.1_00248
+MSHATPNGGAPRHADPAAHQSTPAAGAHTPPPTQAEFRAEHESLGEMFSSATEKVSLLMR
+QEIALAKAEATDSAKKAGKGAGMFAGAAVGGFFLLMFLSLALMYALGSLMPLGWAALIVA
+VLWGVVAAVLALQGKKNIEKIKGLPQTQETLQEIPETLNPAKETR
+>GCF_023573625.1_00083
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000237.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..120c3fa45bdc9ad5e374be7648907c25a3f2d9a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000237.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00092
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV
+SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG
+>GCF_003691675.1_02105
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTDVTDPELLEKNLFPMVSEEQMEKSLAKLAAEVG
+>GCF_005280335.1_00299
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTAVTDPELLEKNLFPMVSEEQMEESLAKLASAVA
+>GCF_020097155.1_00244
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTDVTDPELLAKNLFPMVSEEQMEESLAKLASEVG
+>GCF_023573625.1_00087
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV
+SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d029ce3d71784f92479aedaf1ffc04107be9e27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000247.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00103
+MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA
+ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPA
+>GCF_003691675.1_02116
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR
+DDDGGLTFPD
+>GCF_005280335.1_00287
+MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL
+PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA
+ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA
+LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA
+GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR
+DDDGALAFPS
+>GCF_020097155.1_00233
+MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP
+RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA
+LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA
+LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG
+TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH
+DDGALAFPA
+>GCF_023573625.1_00098
+MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL
+PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA
+ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA
+LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA
+GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR
+DADGGLTFPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00d6eaa77234ce1809f7d3b4a34e80ab2c4d324a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000249.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00106
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
+>GCF_003691675.1_02119
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARAYLPRV
+>GCF_005280335.1_00284
+MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA
+ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT
+VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL
+SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL
+KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL
+VMLLRPMMVDLLEATGAPHDEARAYLPRV
+>GCF_020097155.1_00225
+MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA
+ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV
+LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL
+SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL
+KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER
+LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL
+VMLLRPMMVDLIEATGASHAEALTYLPRV
+>GCF_023573625.1_00101
+MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA
+EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS
+VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL
+SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL
+RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER
+LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL
+VMLLRPMMVDLIEATGAEHDEARGYLPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4342b735ebc95e4d4e19997af1d8650c35372716
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000250.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00107
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>GCF_003691675.1_02120
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>GCF_005280335.1_00283
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG
+>GCF_020097155.1_00224
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG
+>GCF_023573625.1_00102
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000257.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cd10f6340721419500502da192c4b4dac08cd21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000257.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_00115
+MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
+>GCF_003691675.1_02128
+MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
+>GCF_005280335.1_00272
+MPTPPTTSIETLRSGHPVVWSRPAAERPGTDLVLVLHGYGSNEVRAANRFFPMLPERCTG
+LAVRGGFEIDAAATEGPGDPGAHGWFLLDLMLQSDFAQVVAAAHRVFDVLASEEVAQARF
+RTVSVLGFSQGMAMATTLIRLRPEAFACGVGLSGFVVDNELLAVLDSPPEGPGPRPFFWG
+RDVEDPVIHPDAVAHTRAWAEEHTLLTVRTYPGVLHGIGPEAVRDVRIFLDHSLRAATPD
+T
+>GCF_020097155.1_00204
+MSTGSAPESEPLASGGHAVWSRPEHERAGTDLVLVLHGYGSNEVRAARRFFPMLPERCTG
+LALRGPFEIDAAAVEGPDDPGAHGWFLLDVLLQSDFAQVIAAAHRVYDALADDAVADAGF
+RSVSVLGFSQGMAMATTVIRLRPEAFACGVGLSGFAVDNELLAVLDSPAEGPGPRPFFWG
+RDAQDPVIRPDAVAHTAAWAEEHTLLTARTYPGILHGTGPEEARDVRIFLEHVLGGA
+>GCF_023573625.1_00120
+MSPTPTPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPDRCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..365bf0d943a72067d2bccb510a8ceac77a93cdc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000266.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00131
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
+>GCF_003691675.1_02145
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR
+TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE
+MRQPLLGQDEALTLLRTGLVPDRG
+>GCF_005280335.1_00254
+MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG
+RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF
+HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM
+LEFLRDEMRQPLLGREDALALLRTGLVPDQG
+>GCF_020097155.1_00651
+MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP
+ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH
+CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR
+TLIDGNSYAPRYEQEK
+>GCF_023573625.1_00139
+MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR
+TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA
+ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE
+MRQPLLGQDEALTLLRTGLVPDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000273.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d3f2e57c8776ec38f8e811fec79761b2e98d623
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000273.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00140
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>GCF_003691675.1_02154
+MGGMTDAQTPTVPTPEQDRERLKQLIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIEFDAVGGLTMGADPVATAMMHQAGTVGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>GCF_005280335.1_00244
+MGGMTDAQTPTVPTPEQDRERLKELIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGVQFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRDVVVLEDTSTTGGSALTAVEGVRRAGGRVQAVAVIVDRATGAAERVAE
+EADVPYLYAFGKDELGLD
+>GCF_020097155.1_00178
+MTAEHTSVAPTPEQDRERLRELIKELAVVHGRVTLSSGAEADYYVDLRRVTLHHEAAPLI
+GRVMLRLLEENGIEFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGMGRQ
+VEGPGVEGRRVVVLEDTSTTGGSALTAVEGVRKAGGDVQAVAVIVDRATGAAERVAEEAG
+VPYLYAFGKDELDLD
+>GCF_023573625.1_00148
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d8783e87b854fbdaece081d844b4df3d28a4d05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000277.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00144
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>GCF_003691675.1_02158
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>GCF_005280335.1_00240
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS
+>GCF_020097155.1_00174
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG
+>GCF_023573625.1_00152
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000280.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b240c1d8c21bbc0d06d288cc89ef74132d13c67c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000280.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00148
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>GCF_003691675.1_02162
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>GCF_005280335.1_00235
+MTTQPHHSTPASAEQLQHDWDHNPRWAGIERTYSPDDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGDFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYHERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>GCF_020097155.1_00820
+MTEQTVQQIAQEIQKDWDTNDRWTHIERTHTAEDVAKLRGRVQEEHTLARRGSEKLWEQL
+TSEHAKGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYPANS
+VPAVVRRINNALLRADQIEWSEGIKTVEDYLVPIVADAEAGFGGPLNAYELMKGMIASGA
+SGVHWEDQLASEKKCGHLGGKVLIPTGQHVRTLNAARLAADVAGVPSVIIARTDAEAATL
+ITSDVDERDAEFITGERTAEGFYKVKNGVEPCIARAKAYAPYSDLIWMETGTPDLELARK
+FAEAVKSEFPDQMLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYTFQFITLAGFHALNH
+SMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAISTAVNPESSTV
+ALKESTEAGQFH
+>GCF_023573625.1_00156
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7201dc9ea10d6b82823467030f63658e693261c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000281.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00149
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA
+>GCF_003691675.1_02163
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
+>GCF_005280335.1_00234
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA
+>GCF_020097155.1_00819
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA
+>GCF_023573625.1_00157
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000288.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0cc09a39343acfe371a38581e484c51b66b87d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000288.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00179
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD
+>GCF_003691675.1_02175
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYELFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD
+>GCF_005280335.1_00222
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNATPVIGNGVVVNLEALFEEIDGLESRGHSCAHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEVAEYFLGYAERLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIESIPVCVAYDVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGAREFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIDG
+>GCF_020097155.1_00168
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPLIGNGVVINLEALFEEIDGLEARGHSCANLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATFLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRMTGGEFGVNT
+GRPRRTGWYDAVLAHYAARVNGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDEV
+VQVRGLIED
+>GCF_023573625.1_00176
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWAEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..487990686a25117917b43929c814769f75ac3dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000291.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00182
+MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR
+>GCF_003691675.1_02178
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
+>GCF_005280335.1_00219
+MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI
+IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA
+RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR
+>GCF_020097155.1_00164
+MNTQAHGAHAVQTVGGTAAPQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIVAF
+ELWRAATGLLSDGPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAARSAA
+RYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS
+>GCF_023573625.1_00179
+MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI
+IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA
+RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25c6638b1c039634cc1a95f1113fc8e61ab0c9c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000294.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00185
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>GCF_003691675.1_02181
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT
+>GCF_005280335.1_00216
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>GCF_020097155.1_00161
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS
+>GCF_023573625.1_00182
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000302.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10101b1e6119446c193e883d162a426b6c0277ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000302.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00197
+MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH
+RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW
+TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA
+GRWLVRGFVVVVIVGLPLALWLGAFAAR
+>GCF_003691675.1_02193
+MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH
+RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW
+TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
+>GCF_005280335.1_00202
+MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR
+WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV
+NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR
+WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR
+AGRLLVYGFVAVFMVALPLATWIGAYLAR
+>GCF_020097155.1_00150
+MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW
+GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN
+RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW
+TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT
+GRLLVYGFVALFVIGLPAALWIGAFLNR
+>GCF_023573625.1_00197
+MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH
+RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW
+TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c2ae764ba5cfe3f5ef49d2d0c4788329350e947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000303.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00202
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST
+>GCF_003691675.1_02197
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST
+>GCF_005280335.1_00190
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR
+>GCF_020097155.1_00144
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR
+>GCF_023573625.1_00204
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000305.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e8f01d86c02de1816f7ea2f10e7dc7f54b755cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000305.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00204
+MSAALTTPAATTGPEARERSGHDDGDTGARRRQRPRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>GCF_003691675.1_02199
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
+>GCF_005280335.1_00198
+MTVLDRPGGRTAVGLIVPALLLLLWWALTAAGVFSGVQLPPPAWVAEAAVDLAARGTLWH
+HIAISVQRVLVGFLIGGALGLLVGSVLGLSRWADALLAPTIGALRAVPSLAWVPLLILWM
+QIGEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAYGYHGVRLLGTVQLPAVVPA
+MFSGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKISDW
+LLGFVERWAVRRWA
+>GCF_020097155.1_00140
+MSTALTTPAATTGPEARERSGHDDGGTGARRRQRSRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>GCF_023573625.1_00206
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000308.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acbb1f305bfde9aeecd33c2915132f930a4fdb29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000308.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>GCF_003691675.1_02203
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>GCF_005280335.1_00181
+MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK
+NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD
+EGPQTR
+>GCF_020097155.1_00127
+MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK
+DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA
+>GCF_023573625.1_00210
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD
+EGPLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000312.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12fcb01f3208c09f994209b93d52b17c3f5a70ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000312.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_00214
+MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR
+>GCF_003691675.1_02207
+MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR
+>GCF_005280335.1_00169
+MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ
+GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT
+RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA
+>GCF_020097155.1_00120
+MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG
+AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA
+AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA
+>GCF_023573625.1_00214
+MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..933dbfdb3b35149b7642fbac3a20f68625b82b2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000314.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00218
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV
+CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL
+EPAWLGLTPPMTWEEFARAPASSSLDDKVT
+>GCF_003691675.1_02212
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
+>GCF_005280335.1_01604
+MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV
+LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD
+AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR
+LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD
+RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW
+LALVPALTWPEAAATSGTP
+>GCF_020097155.1_00616
+MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL
+VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA
+AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA
+DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT
+VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS
+>GCF_023573625.1_00219
+MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV
+VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV
+HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL
+PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD
+RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL
+EPAWLGLTPPTTWEEFARAPASSSLDDKVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000315.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcba9b07be50a549510707dc07bfa3661e27bbf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000315.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00220
+MPEPHTAPAPSETLPPAVVALPADVWRAHARAHRERIARRTDPLVALRMRGQKHPVQDFL
+FGYYTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGATPRGEWKHYRRVEAGEVAGAV
+VDGRPVGGWLVDVAAVLADRASGVAFTRELLARTAERAPRLGCFGLHEWAMAYRSDVHGV
+RHSQLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMRKMEQ
+PGCLHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDLTGVDDLSDGRGG
+YAAVRIEEPAGRAEYARRQREFAARGQSLRVRLLAVLDAAAGAAPGARPDTEWTSSARP
+>GCF_003691675.1_02233
+MPEPRTDPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAGGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDP
+>GCF_005280335.1_00160
+MAGTCLHTPPPSPAAPRTAPTDPTAVVVLRPEEWLARSAAHRERIEARTAPLLELHGRGE
+RHPVQDFLFGYYTHSPAALARWHPGAGVVLADPDGAAAAAEAERDGAPHRGGWRHLRATE
+PGEIPGAEPDGRPTVGWTVDADAFAADRATGIAFTAELLERTAARPARLGCFGLHEWAMA
+YRSDLHGVRHSRLPLRLGAEGTDAVVESQRIRCTHFDAFRFFAPEARGLNEGADGVLPTR
+AGMRDMEQPGCLHAGMDLYKWAYKLLPWVSSDLVADCFDLAWDIRALDMRASPYDLRGVT
+DLAGGDYPPVRIETPEGRAEYVRAQRGFADRGQALRARLLAALAPLLGDDARG
+>GCF_020097155.1_00118
+MTSAAPSPVPLVLAPEDWRARARAHRERIAARTAPLMARRTRGEPHPVQDFLFGYYTLTP
+GALQRWHPGAGVVLADDDGAAATAEAAELGTAPRGEWRHWRRVEPGEVVGVVLDGREVGG
+WTVDVPAFLADRASGVAFTRELLERTAGRPARLGCFGLHEWAMAYRSDVHGVRHSQLPLR
+LGAAGTDAVVEDQRIRCTHFDAFRFFAPEAVPLNEGAEGVQPTRAGMRDMEQPGCLHAGM
+DLYKWAHKLLPLVDSDLVADCFDLAWDIRRLDMEASPYDLTGVDDLSDGLGGYTPVRIET
+PEGRAEYARRQRGFAERGQALRARLLAALEAGARAAGDRRPTEDPSTPDPEEHHG
+>GCF_023573625.1_00221
+MPEPRTAPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEAAPYDLTGVDDLSDGRGGYAA
+VRIEEPAGRAEYARRQREFAERGQALRARLLAVLDAAVGAAPGTGPDAEWTSSSARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbf993debfd01f56ac0d801dacb182d76d52cf61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000318.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00225
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_003691675.1_02238
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_005280335.1_00155
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF
+NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_020097155.1_00113
+MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF
+NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>GCF_023573625.1_00226
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000319.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e6d54dc824cc259769386f8c21739c1b062803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000319.fa
@@ -0,0 +1,107 @@
+>GCF_002008305.4_00226
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD
+ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA
+SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG
+DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR
+PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA
+WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA
+EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP
+VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG
+FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA
+TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG
+GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA
+AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL
+EERPNDA
+>GCF_003691675.1_02239
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN
+AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD
+RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP
+RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS
+ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV
+GRAVVERVLGGRLLEERPNDA
+>GCF_005280335.1_00154
+MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG
+SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP
+PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP
+EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS
+SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR
+QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA
+PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ
+AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD
+SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG
+RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP
+VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA
+TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA
+GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP
+RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA
+REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE
+ERANSA
+>GCF_020097155.1_00112
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV
+SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL
+PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA
+LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP
+SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV
+AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS
+EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS
+AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD
+EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE
+AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE
+TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG
+PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD
+PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR
+EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA
+GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE
+PGL
+>GCF_023573625.1_00227
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLVQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAPDGGGSAEN
+AEGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQPVAEAPEGDAAAGATGSER
+PQQPPQPGRPEPAEVGARSEDARRPEAGSRPEPEGRPEPEGRPQAQDRTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDTRGQSGARPAGPARTD
+RPERPAPPQGRPDRPAAQPNRPAPAPGPAPREPESSRPAPPRSAAPSTAEDDPAPPAAPP
+RATQQRQTPQPSPAWTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDPPVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDSDATPRAAAGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLD
+ARAAAIHAAREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVE
+RVLGGRLLEERPNDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000322.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d83ac8dac2f52c5a57a6b2e9ecf19fb6dafe8bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000322.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00231
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE
+NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
+>GCF_003691675.1_02244
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE
+NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
+>GCF_005280335.1_00150
+MANVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRTHGGIEWVHTRHEEAAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAALEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHAMRGKDRIEYD
+NPYDVGLTGLLGFSSGYHALKDAETLLILGSSLPYRQFYPEDATVIQVDVRGDQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNASSSFLKKARRHYAKTRKDLDELAAPDRRTVHPQYVA
+RVLDEAASEDAVFLPDVGSPVVWAARYLTMNGRRRIIGSMTHGSMANAVTQAIGAQAVDR
+TRQVVAMAGDGGLAMMLGELLTFVQNGLPVKTLVFDNDSLNFVELEMKAAGLVPYATDLQ
+NPDFAAVAEAMGLKGFRVERSKDLPAVMAEFLAHEGPALLVVKTERQELTIPPSIEFEQA
+KGFALYALRTVLDGKGTQLVDLAKANLRQLF
+>GCF_020097155.1_00107
+MATVAKHIVETLSASGVRRMYGVPGDSLNALTEALRQHTDMEWVHTRHEEAAAFAASAES
+QLTGELAVCAGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQELF
+RECSVFVEHVSDVSQMPQLLRIAMRAAVEQRGVAVLVIPGDVALQDLDAKPEVIRATRSH
+VVPDEDSLREAAEALNSCKRITILAGSGAAGAHDEVVALADRLQAPVVHALRGKDHIEYD
+NPFDVGLTGLLGFASGYHAMKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVS
+VDIPLVGGVRETAQALMPLLKGNSSSAFLKKALKHYDKSRKGLDSLATPSRGTIHPQYVA
+RLLDEAADDDAVFIPDVGSPVIWASRYLTMNGRRRIIGSMVHGSMANGITQALGAQAIDR
+SRQVVVMAGDGGLAMMLGELLSFVQNRLPVKTVVFDNDSLNFVELEMKAAGFVPFGTGLQ
+NPDFAQVAEAIGIKGFRVDRAKDLPDVMREFLAHDGPALLLVKTEPQELTIPPSIELEQA
+KGFALYALRTVLDGKGTQLIDLAKANLRQLF
+>GCF_023573625.1_00232
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNDLPVKTLVFDNDSLNFVELEMMAAGFVPYGTDLQ
+NPDFAAIAEAAGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000323.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b79cc663afed421dba9ae7576027646bc4dd3a6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000323.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00232
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDRTKLAMVSLEKTVGADQTEYERVRDDVAAGVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>GCF_003691675.1_02245
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAARVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>GCF_005280335.1_00147
+MSTPSPIGLLLDVDGPVASTQTRTVPDGIVATLVRLAGRGVPVGFNTGRSADFLLHSVIG
+PLRAAGLPADAPFFAVCEKGAVWFPFSAVPAGTLPEVTVDAPAPAWVRTDPAMALDPGLR
+ERIWELNRERAGDLQFVDRTKLAMVSLEMRVGADQAAYEAVRDDVAAGVEEMLAERGLAD
+EVRVDPTVISVDVEHRSSGKDLGVDRCRALMAEAGVPVPGRWFTAGDSRTDYAMADRLHA
+IGLAVEHLDVRPADGIPATPYPVLTAADLAGRGVGNAEDVHERAGESLLRWVERDLLD
+>GCF_020097155.1_00105
+MTSPSPIGLLLDVDGPVASTETRAVPEGIVTTLVRLAAARVPVGFNTGRSADFLLHSVIG
+PLRAAGLPEDAPFFAICEKGAVWFPFSDVPAGDLPAVTVDAPTPGWVRTDPAMAVDADVR
+DAIWEINGERAGDLQFVDRTKLLMVSLEKTVGADQDAYVQVRDDVAAGIEDLLRERGLAE
+DVRVDPTVISIDVEHRTSGKDLGVDRCLGMLAEVGVAVPERWFTAGDSRTDYAMADALHA
+MGAPVEHMDVRPADGIPERPYRVLTAADLAERGVGQAEDVHERAGESLLRWVERDLLA
+>GCF_023573625.1_00233
+MRTPSPIGLLLDVDGPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHSVIA
+PLRDAGLPDDAPFHAVCEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAAGVEGLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLTVEHMDVRPADGVPEKPYGVVTAAILAERGIGDAEDVHERAGESLLRWVERDLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000324.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7f9355a3dc013c87aa8fd72684db8d915dadca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000324.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00233
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>GCF_003691675.1_02246
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>GCF_005280335.1_00138
+MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT
+PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV
+SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL
+GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA
+WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD
+GGDDPVDGRR
+>GCF_020097155.1_00103
+MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT
+SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI
+VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW
+VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG
+LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG
+GDPVDGVR
+>GCF_023573625.1_00234
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8594e8a29a17c2fe0568d0c2a7d4e192668dcbfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000331.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00241
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS
+>GCF_003691675.1_02254
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS
+>GCF_005280335.1_00128
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR
+>GCF_020097155.1_00095
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG
+>GCF_023573625.1_00242
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41fe2a7bb3074ef8249762b4a016fc25341b9ec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000332.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00244
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG
+>GCF_003691675.1_02256
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG
+>GCF_005280335.1_00125
+MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA
+ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY
+VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL
+AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA
+AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS
+AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL
+VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS
+>GCF_020097155.1_00094
+MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR
+AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG
+FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF
+ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA
+PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL
+EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT
+VEEVSDEAVAAHFGPGEDAPLRLR
+>GCF_023573625.1_00244
+MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000338.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77e77d1443fb5d8731b683b05ce8ab093092933d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000338.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00256
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>GCF_003691675.1_02270
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>GCF_005280335.1_00113
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV
+TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV
+PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK
+YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA
+ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG
+KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>GCF_020097155.1_00081
+MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV
+SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV
+PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK
+YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE
+AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG
+KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA
+EGTSVQVDLRGRGEPFTVVPLPFYTRAR
+>GCF_023573625.1_00255
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000339.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cad27644d81695cdae5ecd3ab8fe93e3c7c6bc10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000339.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00257
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>GCF_003691675.1_02271
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>GCF_005280335.1_00112
+MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG
+GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM
+ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY
+QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA
+YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG
+>GCF_020097155.1_00080
+MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD
+GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE
+QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD
+ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG
+DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG
+>GCF_023573625.1_00256
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000342.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaa4ffe449661d1df5ab6c2882e9261bea85f50d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000342.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00263
+MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA
+>GCF_003691675.1_02276
+MPQTGHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA
+>GCF_005280335.1_00100
+MSQTAPASQNHDAVPALALAIAGSEATGGAGAQADLKTFQELGVFGIIALTCIVSFDPKD
+DWNHRFFPVPTEVLEHQLEAVQQDYPELLRTVKLGMQGSPEVIRTSAAALRRQEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVHSVDDLVAAARRI
+HEVSGAAVLAKGGMHLPGPDAVDVFVDADTVEVLSAPKIGEAGVSGAGCSLAAAVTAELA
+KGATPLEAARRAKEFVRSGIEQAVAGRTPFAALWQGGLRGA
+>GCF_020097155.1_00071
+MTTTTTTPRSVAPALALAIAGSEATGGAGAQADLKTFQELGVFGILSLTCIVSFDPADDW
+NHRFFPVPQDVQAAQLEAILADYPDELRAVKLGMQGSPETIRTTAEALRGHAWDHVVLDP
+VLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMAVRTVEDLTAAARRIHE
+ISGAAVLAKGGMHIEGLDAVDVFVDADHEEVLATPKIGDSGVSGAGCSLAAAVTAELAKG
+AEPVEAARRAKAFVTAGIAQAVEGRTPFAALWQGGLRETPEAGR
+>GCF_023573625.1_00261
+MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVGAGIAQAVEGRTPFAALWQGGLRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000343.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8efc10a66fc43facf410dbd95fa908511f99a85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000343.fa
@@ -0,0 +1,22 @@
+>GCF_002008305.4_00264
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>GCF_003691675.1_02277
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>GCF_005280335.1_00099
+MLEFLTGTGLATSAGLNAYIPMLALGLLDRFTGLVDLPAGWTWLSADASLWILGVLLLLE
+VVADKFPGVDAVNDAVQTVVRPAAGGIVFASGVGTETTAVHDPGTLFGGSGWVSVLIGAG
+IALAVHLAKAGTRVGANTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLVVAVVVG
+LWLLARRFRARRTRGRAAAAAGGSEWTA
+>GCF_020097155.1_00070
+MLALGLLDRFTPLVDLPPAWAWLSSDVALWVVGILLVLEVVADKIPAVDAVNDVVQTVVR
+PAAGGITFASGVGAQTVTVQRPDTLLDSQVWVPTLIGAAMALLVHLTKAGTRAAANTVTM
+GTAAPLLSTAEDASAVVLTAAALFLPVLVLVVLLAVLVGLWAVPRRFRAGRRGGRRATMA
+S
+>GCF_023573625.1_00262
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLAADASLWILGVLLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRDRRTRGRAAAVPGGPEWTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000345.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b46d4288faa677db2b709905ea6347f37fe21886
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000345.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00266
+MSAEQNSTQTPGHRTAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEALADGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHQASEHGVHAAFARQPEALQ
+ILTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>GCF_003691675.1_02279
+MSAEQNSIQTPGYRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPEALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>GCF_005280335.1_00097
+MSTEQNSTQTPAYRAAHVPAGQDLGHRWSTRVADHEDPADRRAIRQIAELTFESSAEADL
+VEELAGGGEGWLPQYSLVAMTASIPGTDLQSDPMGYGTLVRAHVGEAEVLALAPHGVLPE
+HQGEGAGTAIVNALLQKAQGDGEKVVVVYGWPEYYAKFGFRPGVEHGVTAAFADQPEALQ
+VLTLQDDAEVPSGEFRYPPAFGAENAQVAGRA
+>GCF_020097155.1_00068
+MSTEKGSTATPTYRAAHVPEGQDLGHRWSTRLAHHDDPADRRAVRQIAELTFESSAEADL
+VEELVASGEGWLPQYSLMAMTASIPGTDLYSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLEKAQKDGEQAVVVYGWPEYYAKFGFRPAAEHGVTAAFATQPEALQ
+VIALQEGAEIPSGEFRYPPAFGAENAQVAGR
+>GCF_023573625.1_00264
+MSAEQNSTQTPGHRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAQVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPDALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000346.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbc3cfca6b7e743e9dd29bb7df5c98e31a3f3672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000346.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00267
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>GCF_003691675.1_02280
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>GCF_005280335.1_00096
+MARMSTPAEDTLTALIHLLDREGYDAVTADQLAREAGMSRASFFRNLGGKEEVVFADHAT
+LLAHLEELLRGTGLGVREALDEAVLQVFRHHTRDPERAQARARLLRGSQALRTRELLTSH
+RYEELFSAWLADALPDTPARGGVAVGLAAAVVAVHNRALRAWLHSPDDDAEAGLRADLAE
+VVARLTAEPSAAERTLEAVRRLLG
+>GCF_020097155.1_00067
+MNPMTAVPEDTLTALIHLLDRQGYDDVTVDQLAREAGMSRASFFRHVGGKEEVVFADHEQ
+LLPRLEDLLHSTSLPLPTALREAGLQVFRHHVQHPERARARARLLRGSRALRTRELLASH
+RYEQLFSRWLAERLPDTPTRGSVAVGLAAAVVAVHNAALRGWLHAEAPDPTAAEAALGAQ
+LDEVILRLTREPGEAEVRLAAVRALLD
+>GCF_023573625.1_00265
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69739aab5595d05db84a99514ad224cb056f79fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000351.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00277
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR
+>GCF_003691675.1_02292
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
+>GCF_005280335.1_00076
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS
+>GCF_020097155.1_00061
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA
+>GCF_023573625.1_00276
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5b002bded5e44c5aefa0981080ea0c1f3b04bdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000364.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00298
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR
+LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM
+AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV
+>GCF_003691675.1_00006
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH
+>GCF_005280335.1_00056
+MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR
+LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL
+AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA
+>GCF_020097155.1_00034
+MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR
+AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF
+AELDRQRVRDLVSLPAEFLGLRRLPGA
+>GCF_023573625.1_00305
+MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR
+HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL
+AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000366.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d97c7bf164391ba36ff9a3da1ea64fd85a86d02d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000366.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00300
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>GCF_003691675.1_00008
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG
+EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>GCF_005280335.1_00054
+MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS
+PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA
+GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP
+LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH
+NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG
+EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR
+DAVLAIVRAER
+>GCF_020097155.1_00032
+MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ
+TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN
+PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY
+LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA
+NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA
+KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY
+YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL
+ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG
+EAKDRATMETVRDAVLAIVRAPR
+>GCF_023573625.1_00307
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6f2df0ad7c67f88fa4a64de010c1cb378c740f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000369.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00305
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>GCF_003691675.1_00020
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>GCF_005280335.1_00032
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI
+>GCF_020097155.1_00028
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR
+>GCF_023573625.1_00312
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e121053ca2e85a0098ee11bb2a95cdb79bc285d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000370.fa
@@ -0,0 +1,61 @@
+>GCF_002008305.4_00306
+MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA
+VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG
+>GCF_003691675.1_00021
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
+>GCF_005280335.1_00031
+MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY
+GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA
+VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE
+WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD
+GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG
+>GCF_020097155.1_00027
+MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV
+WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA
+VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP
+VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP
+GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY
+LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH
+PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG
+AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR
+IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ
+VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS
+GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA
+RVALGG
+>GCF_023573625.1_00313
+MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR
+TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY
+GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA
+VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA
+FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG
+VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF
+LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV
+ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE
+GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA
+WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD
+GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e389132d3dcf8ed8b302180beccd075a75ed15f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000372.fa
@@ -0,0 +1,72 @@
+>GCF_002008305.4_00308
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR
+>GCF_003691675.1_00023
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
+>GCF_005280335.1_00029
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR
+>GCF_020097155.1_00025
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR
+>GCF_023573625.1_00315
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000378.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70e43a53e009f1e6140ae16957f4859f185d2907
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000378.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00317
+MVEKARRLRARTTPGSVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGGEPVTAVEMAERLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRWAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRSGGWPVLGGPHQWRRGELSVRWAAVAPSS
+>GCF_003691675.1_00032
+MVEKARRLRARTTPGPGPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGDLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS
+>GCF_005280335.1_00020
+MVEKARRLSASTTPGRVRGPQGHITRGTTAAQRMRRVDRWLTDVHGALLRRTDRPLAVDL
+GFGAEPVTAVEMFTRLRAVNPALELTGLEIDPARVARARERAGGVPGLSWAVGGFELPVP
+RPPTVVRAFNVLRQYREEDVPAVWALLCAGLAEDGVLVEGTCSEDGRRATWVDLRRDGPA
+SLTLALRLGSFERPSDVAARLPKALIHRHVPGEPVHRFLAEADAAWAAHAPLAAYGTRQR
+WLASVAALREAGWPVLGGPRQWRRGEMSVRWEAVAPSS
+>GCF_020097155.1_00016
+MVQKARRLTLPDGGRARPGARGGPQGHVTRGTTAPQRMRRVDRWVADVHGPLLRRTAAPL
+LVDLGYGAQPWTAVEMLTRLRAVQPSAELVGLEIEPERVAHARATAPALPGLSWERGGFE
+LATSRPPTVVRAFNVLRQYREEDVPAIWDLMASRMAPGGVVVEGTCSEDGRRAAWVDLRA
+DGPASLTLAMRLGAFERPSDVAERLPKALIHRHVPGEPVHRLLADADAAWALHAPLGAYG
+TRQRWIAMVRTLKDAGWPVLGRESRWRRGELTVRWDAVAPGVG
+>GCF_023573625.1_00324
+MVEKARRLRARTTPGPVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000379.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc15c4efa0fe0460fafde0daebc30769677abd79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000379.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00319
+MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV
+FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>GCF_003691675.1_00034
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>GCF_005280335.1_00018
+MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV
+FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP
+>GCF_020097155.1_00014
+MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD
+EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL
+FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT
+TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA
+>GCF_023573625.1_00326
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000382.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd01539bdef41039f7b4bbfd283ca433a8508277
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000382.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00322
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>GCF_003691675.1_00037
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>GCF_005280335.1_00015
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA
+LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ
+DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG
+GEH
+>GCF_020097155.1_00011
+MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL
+GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV
+WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ
+H
+>GCF_023573625.1_00329
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000388.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf5f03acbd9c4860e31a05955e1a2d2acc04ce6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000388.fa
@@ -0,0 +1,69 @@
+>GCF_002008305.4_00331
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES
+TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV
+LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP
+>GCF_003691675.1_00047
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP
+>GCF_005280335.1_00004
+MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA
+GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP
+AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE
+ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV
+HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS
+PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV
+FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE
+AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS
+QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY
+GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL
+WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT
+NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC
+>GCF_020097155.1_00005
+MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG
+DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL
+GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT
+HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES
+EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF
+LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW
+ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA
+VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV
+SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD
+EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW
+AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG
+VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED
+GQWQGQPAYLTLNVPPLTTLWLQPDED
+>GCF_023573625.1_00338
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44a59395ba36d440fd69b5e0e50ae37f88c076c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000392.fa
@@ -0,0 +1,48 @@
+>GCF_002008305.4_00339
+MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD
+RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL
+RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL
+ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL
+DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW
+DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA
+AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA
+LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF
+>GCF_003691675.1_00055
+MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG
+RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
+>GCF_005280335.1_02673
+MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE
+HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT
+DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA
+RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL
+HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL
+RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV
+GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR
+AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF
+>GCF_020097155.1_02485
+MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA
+VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE
+RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ
+SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT
+AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH
+RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW
+EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT
+VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL
+DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF
+>GCF_023573625.1_00346
+MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG
+HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000393.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..524ad33a069d67f6ad5bfe8edd0d69e29987bf84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000393.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00340
+MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE
+PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPTG
+>GCF_003691675.1_00056
+MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE
+PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPIG
+>GCF_005280335.1_02629
+MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR
+HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL
+LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT
+VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA
+LLGAGPRG
+>GCF_020097155.1_02484
+MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS
+PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN
+TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ
+PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA
+RELA
+>GCF_023573625.1_00347
+MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR
+HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP
+VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP
+ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL
+ADAPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01cac661a14527c9f0397d965535fbb2e2656839
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000394.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00341
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>GCF_003691675.1_00057
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
+>GCF_005280335.1_02628
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE
+MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA
+KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR
+GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE
+LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV
+>GCF_020097155.1_02480
+MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD
+MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA
+KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR
+GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE
+LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV
+>GCF_023573625.1_00348
+MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE
+MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA
+KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR
+GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE
+LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05017ada762a5eefe3bdc5427417da9575951139
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000395.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00342
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL
+PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP
+>GCF_003691675.1_00058
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP
+>GCF_005280335.1_02627
+MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV
+SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR
+LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS
+ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ
+GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA
+AAEAMDSAQWHRLWTAARGAPLP
+>GCF_020097155.1_02479
+MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG
+ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV
+DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL
+ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG
+SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP
+ARIASCAQAADAAARMDGAQWHRLWTAARGETLP
+>GCF_023573625.1_00349
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000396.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed60bc745b01c9b496c5c861c3812754baf50b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000396.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00343
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>GCF_003691675.1_00059
+MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>GCF_005280335.1_02626
+MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL
+QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP
+DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA
+>GCF_020097155.1_02478
+MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL
+QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD
+GTREEDQYMAVEQDGEPVYGAELVESPPIGG
+>GCF_023573625.1_00350
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f8782b5b3647da36afbf43ce620a2fd94d3e509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000398.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00346
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>GCF_003691675.1_00062
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>GCF_005280335.1_02623
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED
+>GCF_020097155.1_02475
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG
+>GCF_023573625.1_00353
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc3f3942d30d753ab9393b3ec471f6924353759b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000399.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00347
+MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN
+GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG
+TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD
+>GCF_003691675.1_00063
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
+>GCF_005280335.1_02622
+MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG
+GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE
+APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG
+TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG
+>GCF_020097155.1_02474
+MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG
+TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA
+GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY
+SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD
+NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG
+>GCF_023573625.1_00354
+MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN
+GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE
+ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS
+ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG
+TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..616f3e4e4618dd3a6aa7a215ed6254a0b28a25d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000401.fa
@@ -0,0 +1,59 @@
+>GCF_002008305.4_00351
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>GCF_003691675.1_00067
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR
+>GCF_005280335.1_02610
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>GCF_020097155.1_02469
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR
+>GCF_023573625.1_00358
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d6fe2d33ad3944b44a8da365c21775e53eb9a52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000403.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00353
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>GCF_003691675.1_00069
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
+>GCF_005280335.1_02608
+MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE
+AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN
+>GCF_020097155.1_02467
+MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY
+QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER
+>GCF_023573625.1_00360
+MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT
+AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000405.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64d7bfdff4f2ad5dd5d12f46ecf8e60ce9daab91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000405.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00356
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYAGDPTAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVCDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
+>GCF_003691675.1_00072
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWTEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
+>GCF_005280335.1_02605
+MTVLIDPPAWPAHGTVFAHLVSDASLEELHAFARAAGLPERAFDRDHYDVPAHRCEELVA
+RGAVPVSGRELVRRLVASGLRVPARGRAEKRDAVLARRWAALFEGTGARAEAVDAAGRDL
+RERWAQPHRHYHDRSHLLAVLEAVDLLERAGADPGPEPRAVRLAAWFHDAVYAGDPAAPA
+GQDEADSAALAARMLAAPALAVPAAVVGEVRRLVMLTASHDPAPQDAAGALLCDADLEVL
+GRSPEAYRRYVQAVRRDFAHVPDADWARGRAAVLESLLGAERLYRTAPGRARWEAAARRN
+LEAELADLRP
+>GCF_020097155.1_02464
+MAVLIDPPRWPAHGTVFSHLVSDASLEELHGFAAAHGLSPRAFDLDHYDVPAHRHAELVA
+AGALAVDGGELVRRLIRSGLRVPARRRDGRAEPVLRRRWARLFAGTDASPDAVTAAGAEL
+LGRWSEPHRRYHAPAHLLAVLQAVDLLSAAGEDLGPHPLAVPLAAWLHDAVYTADPARGP
+GADEEDSARLAERLLAAPGLALGDDVVAETARLVRLTAEHRPAPDDAAGAVLCDADLEVL
+GRAPHDYEAYVDLVRADFAHVPDEAWRTGRAAVLEGLLGADRLYATAAGRARWEDPARAN
+LERELAAHRPALS
+>GCF_023573625.1_00363
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000406.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8d871265c0e34aa563c28363313c0e2bb5ef315
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000406.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00357
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>GCF_003691675.1_00073
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>GCF_005280335.1_02604
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVGAMEAHLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAAQQYQDAEAANAAMFRH
+>GCF_020097155.1_02463
+MTIVQIDVEDLRAKSGAVEGSIARLQTEVNTMEANLRQLEGTWRGQAAANFQGVLTEWRA
+TQARVEESLGGIRRAMDLAATQYSDTEAANAAMFRL
+>GCF_023573625.1_00364
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a77ca6697d0ce88a06a60448ed2186ba790772a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000410.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00362
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG
+>GCF_003691675.1_00078
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG
+>GCF_005280335.1_02599
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG
+>GCF_020097155.1_02458
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG
+>GCF_023573625.1_00369
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000411.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..302ec8a8ae88b5b8c7d10deda4085be2a90a1fe3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000411.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00363
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV
+AALLRCIDHVVERLG
+>GCF_003691675.1_00079
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
+>GCF_005280335.1_02598
+MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG
+ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV
+ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+SALLRCIDHVVEQLG
+>GCF_020097155.1_02457
+MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE
+ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD
+NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV
+ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+TALLACIDHVVARLG
+>GCF_023573625.1_00370
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..848b80b363537b8032de69a36451d58071230d37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000414.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00368
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED
+>GCF_003691675.1_00084
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
+>GCF_005280335.1_02593
+MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA
+AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT
+GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR
+PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV
+MLWAGRRRREPAARRR
+>GCF_020097155.1_02452
+MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF
+IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF
+AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL
+TAIRWVLLAVITVAVVVMLWAGRRRRPRT
+>GCF_023573625.1_00375
+MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT
+LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV
+IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA
+ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab42fcdf85893ccdcde56c4c5d7adb9798449734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000415.fa
@@ -0,0 +1,79 @@
+>GCF_002008305.4_00370
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>GCF_003691675.1_00086
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>GCF_005280335.1_02592
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED
+>GCF_020097155.1_02451
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG
+>GCF_023573625.1_00377
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000418.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f15d9ab7ddda663a2e8aa0b0b99fc89618b2d67a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000418.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00373
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>GCF_005280335.1_01002
+MIRVLVADDEALIRGAVEALLALEEDLDVLPGVGTGDDAVAAARALVPDVCLLDLEMPGL
+DGVEAAREILRSVPTRVVIFTRHARPGVLRRALAERVSGFVPKSTPAEALADVLRQVAAG
+RRYVDPEIAASALSGERSPLTDRELDVLRAGRTAARVEDIAERLHLAPGTVRNHLSHAMG
+KLGVRTRHEAAERAWEEGWI
+>GCF_005280335.1_02589
+MNDIRIVLADDEKLLRTALATLLEMEGGIRVEEVAADGNEAVEAVRRIDPDLLVTDMEMP
+GLDGVAAVETLRETHPDLPVVMLTRHARPGVLRRALKAGVAGFVTKSAEPEEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>GCF_020097155.1_01177
+MRESADPAPSPASPPAAGLGPGAPLRLLLADDQALVRGALAALLDTEPDLTVVAQAASGD
+EVADAVETHDVDVALLDIEMPGVDGLEALRRIRDRGLGCAVLMVTTFGRPGYLERALAAG
+ARGFVVKDTPAEQLADAVRAVARGERVVDPSLAVDTLAAGPSPLTPREVDVLREALTGAS
+VRAIAGRLHLSAGTVRNHLSAAIGKTATSTRGEAATVARDRGWL
+>GCF_023573625.1_00380
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000425.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f71bf03227a0f428d8b1db4188a5493fca3c62c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000425.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00383
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASLFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIAATDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGAVAEDAATE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>GCF_003691675.1_00098
+MTDTTVPLIILALYIVFVVGVGIYARRKATSDSSRDYLTGSGDVGVWVNGFAIFAAFATG
+GTMLGNIGLSYVGGWGYITAYNAGVALGYVITTFFLAKTLKNMNVATVPEFIRKRFHGRT
+LNILVPIILMATLVAYVVAQMKVGGLLGEQLFGFPYEWSVIVVGLVYIFYTFYGGMRAVT
+LTDFVQGLLMISVVVICGGIAFGQHGGPANLYEMAVAIRPKWEGTEQFPLISYIGAFIIW
+ATVNAVLPHTVMRIFAAKNERQGRASLAIGLGLYVLTAIATTIFVVAAVIIVQGEEELAS
+ADSTFLIFLAEQTPSWVAGLAFAGIFAAVMSSVSAMLLALGGAFAYDLVAELRPSMSDRS
+KRRLTSISVLGFGILTLVLSLNPPELLTLLYTAAMGMLASGLFFPTLLGIWWKRMNSSGA
+LAGLIVGVGSYLFLLWGTGMPSLSQVTVSIPLSLLACIVVSLMTKPPTDAEMERITIAHE
+REFLIQGQDDLIETAERH
+>GCF_003691675.1_00107
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSALKERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPIFRGEATASEDGATAEDEIPE
+TAAELASNRGWVLLLGAVVLGLAIVVPNVVAALTIAYDILVGGLFVAIVGGLVWQRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>GCF_005280335.1_02572
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLVGQ
+DVWQRVFTARSPRVAQVGGATAGLYCIVYGVAGALIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGATAEDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTLGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDAAARERL
+>GCF_023573625.1_00389
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTVGLFALMLPLSLANAGGWGAMQERLGAEFFSWDGIGVQSIVTYSVVYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIIYGVAGAVIGMAARTVTADIATQDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATASEDGATAGDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTPPTDP
+AVLEAWRVRSRHGVDAVAGASLTRNPGACDPPMPARWSGQTMRRRAILPQAPPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000426.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..636511990d6a69085eb54a2924bde6a170ece131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000426.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00384
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>GCF_003691675.1_00108
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>GCF_005280335.1_02571
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI
+VLWTLVGHA
+>GCF_020097155.1_01754
+MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV
+AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG
+GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA
+LVLWILAGRT
+>GCF_023573625.1_00390
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e18575638203667341346dd49fc5f154bae48e80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000428.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00388
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>GCF_003691675.1_00112
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
+>GCF_005280335.1_02568
+MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQTD
+>GCF_020097155.1_02439
+MTEHTTPSMQRPDPAVGPGSMFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLAVGGEPDI
+VPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTARRADTAEE
+IAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD
+>GCF_023573625.1_00394
+MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA
+VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR
+RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000429.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c393e1d51811b6b08ac5e4c0828750e2a149220a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000429.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00389
+MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA
+IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
+>GCF_003691675.1_00113
+MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADEDGAYLTRGDGPERPLAEVARPAPAGGERAQNLVTSYPAGEA
+IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
+>GCF_005280335.1_02567
+MSATVPSPAALRRIALDAAGAVSADLAAAFRRPSAAGPGPEAKSTHHDLVTVHDRRTEAR
+LVAALTTAVPGSAVLGEELGGRDGAGEAARLTWIVDPIDGTSNFAHGFAMFSVSVAATVD
+GEVVAGVVLDPVSGLAFSADDHGAWLARPGEAERPLADVARPAPAGGERAQNLVTSYPAG
+EALALEGEDALRRFGRLVSAHATVRRTVSGALELAYTAAGWADAALYVDTKPWDVAAGQL
+ILRRAGGRWLTPDPAAPLSGRLVDDGPRAHTCPFALAVAPGREVPTTAAVLGDIVASRAA
+DHV
+>GCF_020097155.1_02438
+MVSSDSGPRSAAGSPLAPSPARLRAIGLEAARAVAPALAAAFRTPDAAAATKRNHHDLVT
+AHDRATEEALVATLTAAVPGSAVLGEETGVTAPPADAGVPRVRWIVDPIDGTSNFSHGFD
+LFSVSIAAEVDGEVVAGVVLAPAAGLEFSADDAGAWLGEAPLPLRAAPDGGERALNIVTS
+YPAAEALAREGEAALRRFAQLVDAHATVRRTVSGALELAFVAAGWADVTLAVDTHPWDVA
+AGQLLVARAGGTLVAADDAGPAPALVPHLAPHLLAVGPGRRAPTARAVLAGLVADRAAE
+>GCF_023573625.1_00395
+MSPALPRPAELRAIALDAARAVAGDLATAFRSPTATGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA
+LAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGSWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000431.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84a30f73dc4bfb66d129a5daf92752d62d99faa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000431.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00392
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>GCF_003691675.1_00116
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>GCF_005280335.1_02564
+MTGPRAVEVRIPLRWADMDAYGHINNIAVVQLLEEARVAAFGVPANTGAGGGEAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVEAVKAASVHVGYALHDGVDDTLCAT
+ASSVMVFVDGETGRPVRVTPEQRAALQG
+>GCF_020097155.1_02435
+MTETTTSSAARDGAGRWVEVSVPLRWADMDAYGHINNIAVVQLLEEARVAVFGVPANTGA
+GGGGAPPVDLLEGVPEGVRTFVSEHTVKYRAQMPYRPVPLRVRVGVAAVKAVSVEVAYEL
+YDGVDGTLCVTARSVMVFVDGASGRPVRLTAEQRAALAG
+>GCF_023573625.1_00398
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bce206a793db57c57573f9bea84182ae4e075bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000439.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00401
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG
+>GCF_003691675.1_00125
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG
+>GCF_005280335.1_02556
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG
+>GCF_020097155.1_02425
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG
+>GCF_023573625.1_00407
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000441.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b83a94ce99da846f272fbe4e5b329aa9937644b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000441.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00404
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>GCF_003691675.1_00127
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>GCF_005280335.1_02552
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR
+LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKRALLAHEAAHAG
+>GCF_020097155.1_02420
+MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE
+LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR
+QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG
+SYLYGSAAKAALLAHEAAHAPA
+>GCF_023573625.1_00410
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTDAKQALLAHEAAHAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98541393245268bb8ac77b2787306daa60438734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000442.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00405
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP
+VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>GCF_003691675.1_00128
+MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR
+>GCF_005280335.1_02551
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF
+EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS
+RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>GCF_020097155.1_02419
+MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG
+APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL
+SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF
+EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR
+VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS
+RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV
+VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS
+PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF
+GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR
+>GCF_023573625.1_00411
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b548b673ce5ad905bf6c6ad9001e5b8a54f9b6e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000443.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00406
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>GCF_003691675.1_00129
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
+>GCF_005280335.1_02550
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>GCF_020097155.1_02418
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD
+>GCF_023573625.1_00412
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c74ecac95bf574f4192c20cc846dc11074758679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000447.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00414
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA
+AEHEADAPRR
+>GCF_003691675.1_00134
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
+>GCF_005280335.1_02545
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA
+AADREAADTRR
+>GCF_020097155.1_02413
+MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD
+LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD
+AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA
+KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA
+ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA
+EGR
+>GCF_023573625.1_00417
+MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE
+MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD
+AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI
+SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS
+PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS
+RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG
+ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA
+AEHEADAPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000451.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00cd49297fde00b2f631b8b4bd7087eb276fc229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000451.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00420
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>GCF_003691675.1_00141
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>GCF_005280335.1_02539
+MTQTPDINTQPLSEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTALMDHGDTL
+MGLSLAHGGHLTHGMKINFSGKNYKIAAYEVEPDTYRIDMDKVREKALEAQPKVIVAGWS
+AYPRQLDFAAFRSIADEVGAKLWVDMAHFAGLVAAGLHPNPVPHADVVTSTVHKTLAGPR
+SGFILSTEEFKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLQGAQIL
+AERLTAPDMTELGISVLTGGTDVHLVLVDLRESQLDGKQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVAEIVAAALKPSPDVQALRARVVKLTEDFPLY
+DGLEGW
+>GCF_020097155.1_02408
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEQW
+>GCF_023573625.1_00423
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000452.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a83ceb12088eb7d712213349a2e7d077872a4321
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000452.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00421
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVTPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>GCF_003691675.1_00142
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDIQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVGLAGKHVLVIGRGVTIGRPAGL
+VFTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>GCF_005280335.1_02538
+MTAKVLDGKATAAALKEELRERVSALTERGHTPGLGTVLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEEILAVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRRHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTQNLDELLGQADVVIAAAGSAHMVRPEQVKDGVIVLDVGVSCV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLSNVVEAAERAADAEDWAGER
+AEA
+>GCF_020097155.1_02407
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTLGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIRSIQKELPGDATEEQILDVVRELNEDPECTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>GCF_023573625.1_00424
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAAEDDGRAGER
+AGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000453.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6492c398f5163dea855855471c7cc1ec48224f89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000453.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00422
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD
+>GCF_003691675.1_00143
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD
+>GCF_005280335.1_02536
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD
+>GCF_020097155.1_02406
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD
+>GCF_023573625.1_00425
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2380a12bf399fabb3ebbca65112d2abb3e9319d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000455.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00425
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>GCF_003691675.1_00146
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>GCF_005280335.1_02532
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG
+>GCF_020097155.1_02402
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS
+>GCF_023573625.1_00428
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000456.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..273aebeb5a0c92feae88ba69621e45398223f4c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000456.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00426
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>GCF_003691675.1_00147
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>GCF_005280335.1_02531
+MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV
+RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR
+LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR
+SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA
+PLVVDYRF
+>GCF_020097155.1_02401
+MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG
+RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR
+TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL
+PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT
+LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP
+LVVDYQF
+>GCF_023573625.1_00429
+MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11b938f8ebdf21b395bd9341f5e31f47992c6772
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000461.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00432
+MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV
+LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV
+LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG
+>GCF_003691675.1_00153
+MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY
+ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS
+VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV
+>GCF_005280335.1_02525
+MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA
+RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV
+AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG
+>GCF_020097155.1_02396
+MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL
+QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV
+GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG
+>GCF_023573625.1_00435
+MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE
+ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG
+MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6f84ea5b73cbc66601b13d6f01a2fbdf599592d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000462.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00433
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF
+>GCF_003691675.1_00154
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
+>GCF_005280335.1_02524
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF
+>GCF_020097155.1_02395
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF
+>GCF_023573625.1_00436
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5411f0119a1028dc6a8c20187fc6f68f0e89091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000463.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00434
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_003691675.1_00155
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_005280335.1_02523
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP
+YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_020097155.1_02394
+MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP
+YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>GCF_023573625.1_00437
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000466.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d25adcf59a0cbfa73640ff0e0f16a5e199acdada
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000466.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00437
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>GCF_003691675.1_00158
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>GCF_005280335.1_02520
+MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT
+TDHAQEVKKAVEALKAEGVDEVL
+>GCF_020097155.1_02391
+MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR
+DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL
+SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG
+LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT
+TEHAQDVKRTVESLKAQGADDVL
+>GCF_023573625.1_00440
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000467.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a386052c3d142a33de81277b26173c28a3201a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000467.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00438
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>GCF_003691675.1_00159
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>GCF_005280335.1_02519
+MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG
+YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT
+AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG
+VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE
+VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA
+WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH
+>GCF_020097155.1_02390
+MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA
+EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH
+TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE
+GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI
+AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD
+EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF
+AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR
+>GCF_023573625.1_00441
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1f6845c8ed0603443e070f8cefaa6bbad15907b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000468.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00439
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGAVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
+>GCF_003691675.1_00160
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASGSGAAESEAIATVDGVGSD
+NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEKAYGITTSEAESNEPSEFTPNVTAMVNA
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTAEGFSDNVQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGMEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+KNVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVADVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIVSGELKVGSEYSPEA
+>GCF_005280335.1_02518
+MGTATPSAEGRRRLLLPAAVLGASALLLTACGQAPEASNSSEPAGSASATGAAAEVGSDN
+SDYTGCIVSDEGGFDDRSFNQSSYEGLKAAEEEFGIEIREAESNSVGEYVPNLNAMLDAD
+CNLVVAVGFQLGDTMKPIAEENAETKFVGVDVTAPGFPENVRNIIYDTAQGAFLAGYLAA
+GMTETGTVATYGGMEIPTVSIFMDGFARGVEHYNEVKGEDVRVLGWDTENRTGSFIGDFS
+NQNAGKTNTANFINEGADIIMPVAGPVGLGTIDAVKEANGGGKDVKVIWVDSDGYETTQD
+GEVILTSVMKRMGDAVKQVIAEDINDEFTSEAYVGTLENDGVALAPFHDFEDAVPQELKD
+ELEALEAGIVSGEIEVGSEDSPEA
+>GCF_020097155.1_02389
+MGIVSPLAGRRRLAVPAALLSSGLLLAGCGAPPAENSGSASGSGAAVSADAAAGSDNKDY
+KSCIVSDAGGFDDRSFNQSSYEGLKAAEEAYGIETNKAESKDASEFTPNVNAQVNAQCDS
+IIGVGYMLGDTIKPIAQKNPDIHFLGVDVTADGFSDNVKKLTYDTAQAAFLAGYVSAGMT
+KTGTVATYGGMEIPTVTVFMDGFAAGVEHYNEVKGKDVKVLGWDREAKTGSFTGDFDNQA
+NGKTNTANFINQGADIVMPVAGPVGLGTLDAVKEANAGGKSVAVVWPDSDGYESTKDGAL
+ILTSVVKNMGQSVSDVIGQDLKGEFSADPYVGTLENKGVELAPFHDFDSKVPQELKDEVQ
+TLQEDIISGKVKVDSEYSPKS
+>GCF_023573625.1_00442
+MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD
+NNDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG
+DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA
+AGTTETGTVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF
+ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK
+DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK
+DELKDLEAKIISGELKVGSEYSPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce9b1d056b9db03afd9b4fc2613c93cbedd7b44f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000469.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00440
+MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP
+>GCF_003691675.1_00161
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP
+>GCF_005280335.1_02517
+MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL
+VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI
+RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA
+IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS
+LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA
+IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR
+EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF
+IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV
+DGDASRETLGLMMAGQTPESLATETATTEEGPRA
+>GCF_020097155.1_02388
+MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL
+LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI
+REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA
+IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV
+LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA
+IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD
+VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL
+FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI
+VPGDASREHLGLLMAGQTAEDTHQEGARA
+>GCF_023573625.1_00443
+MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL
+LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI
+REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG
+IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV
+LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA
+IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV
+APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF
+IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV
+PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000470.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caffa7753b6975cb3830382cf28943463ca71274
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000470.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00441
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPATTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYVAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+ALTGAGGHAAAPSTGVQEAAAAAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>GCF_003691675.1_00162
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTVLAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPPGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVHLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLVAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQAAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>GCF_005280335.1_02516
+MSQNPPQTPASEPVQPPGGAPVPAAGVTGADAPPAPERGSQESVLREILSGNAMVTALAI
+VLSLAISAVLIIVTSPDVIDAAGYFFARPMDTLSAAWTVVSDAYLALFRGSIVNYRADSF
+ADMIRPLTETLTVATPLIIASLGVAIAFRTGLFNIGGQGQFLIGAAFATVGGVYLDLPLG
+VHLLLVIVMGALGGLLWGAVVGLLKAYTGAHEVILTIMLNYVALHLVSYLLNTPFLRRAG
+TNNPISEQFPDSAAFPALLGDGFRLHWGFVMALVLTFLAWWMLERSTLGFRLRAVGANPA
+AARTAGISVKGGYVAAMAIAGALAGLGGVAHISGTEKVLTSGIAGQFGFDAITVALLGRS
+HPVGVLFAGLLFGALRAGGVTMQTQTGVPIDIVLVVQSFIVLLIAAPPLVRAIFRLPAPG
+SVRARANADVVTQPALAGAAVPGAAAEAVPAETGSATTSKGEGR
+>GCF_020097155.1_02387
+MSTAVASRPAGARTQEDGSALRRLASSNGAVTVLAVLLSLVISAVLIVVTDEDVQDAAGY
+LFARPQDALTAAWKAVSGAYAALFRGAVFNYEADTFTDMVRPLTETLTVATPLIIISLGV
+AVAFRAGLFNIGGQGQFIFGAMVATWTAVHLPLPFGLHLLVVLLAGVVGGVLWGAVVGVL
+KAWTGAHEVILTIMLNYVAVNVLAYLLNTPVLRRAGTTNPVSEFLPESGMFPKLLGDGYR
+LHWGFVLALLVTAFTWWLMSRSTLGFRLRAVGANPAAARTAGMSVKGTYVAAMAISGGLA
+GLAGMTHVSGTENALNTSVAGSYGFDAITVALLGRSNPVGVLFAGLLFGALRAGGVTMQT
+ETGVPIDIVLVVQSMIVLFIAAPPLVRGLFRLPAPGAARARRTADVVTQPAVAGAAVPGA
+AGLASVPSAQTQDAAATAVAADPADPVAGTGPHREKGQDL
+>GCF_023573625.1_00444
+MSTAAPQRPAPESDPRARPAPADSALRRVLSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQEAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000476.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..997a381f66da86c55be249763efb052317ed4bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000476.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00447
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>GCF_003691675.1_00168
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>GCF_005280335.1_02510
+MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA
+PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL
+AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV
+RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG
+>GCF_020097155.1_02381
+MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR
+ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT
+PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH
+LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP
+ERALRGAIACVRAGDWDALRR
+>GCF_023573625.1_00450
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD
+PERALRATVARVRAGDWAALRPSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000478.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9c5bbe523ab8b6aa9ce7a151e5b1bda2d234112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000478.fa
@@ -0,0 +1,51 @@
+>GCF_002008305.4_00450
+MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>GCF_003691675.1_00171
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
+>GCF_005280335.1_02506
+MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP
+TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>GCF_020097155.1_02378
+MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV
+ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA
+YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV
+AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR
+PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV
+KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS
+ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA
+RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA
+AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG
+IALSLRG
+>GCF_023573625.1_00453
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000481.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f21be268ea42832f7c02dc43d9e98b2b0d1c185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000481.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00457
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVAGVDLTEPYGPDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGAHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWSDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
+>GCF_003691675.1_00175
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVGGVDLTEPYGQDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTELDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
+>GCF_005280335.1_02490
+MSETSAAEAFGAPHATGTQHRLRRAGAEAVAVGLAGALRTYRVHGVDLTEPYGPESIPPA
+GNGIQMSPWPNRVAGARWELGGAEQGLDVTEPARGHAIHGLLRNTHFVAEASSEHAVTLR
+GEIHPQHGWPFRLTHRVTYELDADGGLTVTQELENHADAPAPVAFGAHPFLRIGDVPVPE
+LSLRVPADAWIRTGEDLIPVETLPVEGTDRDFRRGRPVGEDALDVCLTGLAPDADGRHRQ
+TLLAGDGRAVTLWSDHAFAYTHVFVTDRLPGRDVAVAVEPLTAPADALNSGEGLHRLAPR
+TRWSAQWGLTPHVPPHADEENRS
+>GCF_020097155.1_02374
+MTVPPAPDADAVFGAPRASGAQYRIARGGAEAVVAALAGALRTYRLDGVDLTEPYGPDMV
+PPAGNGIQMSPWPNRVAGGRWELDGAAQQLDVTEPSRGHASHGLLRNTHFTAESVAEDAV
+TLRGEIHPQHGWPFRLTHRVAYALDDAGALTVTMSLENHADAEAPVAFGAHPFLRIGDVP
+SAELTLQVPAREWIRTGEDLIPVETLPVDGGPQDFRSGRPVGAQGLDVGLTGLEADADGL
+HRARLLAPDGRSVTLWSDPAFTVTHVFVTDRLPGRDVAVAVEPLTAPADALNSGTGLHRL
+APGATLTARWGLVPDLAPAAPAAAPKEDAA
+>GCF_023573625.1_00457
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLASALRRYRVGGVDLTEPYGQDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c05d9227d0c0372355967a34438bf22ebb2b058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000484.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00460
+MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA
+>GCF_003691675.1_00178
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA
+>GCF_005280335.1_02487
+MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG
+VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP
+RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE
+SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA
+>GCF_020097155.1_02371
+MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG
+STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP
+VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE
+RLTHDDLLVQAVGRTVSTAAAAAAAAG
+>GCF_023573625.1_00460
+MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG
+TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP
+RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE
+ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b09e1b241a5a0541c19f344234700bfc7c5ad43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000493.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>GCF_003691675.1_00188
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
+>GCF_005280335.1_02477
+MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE
+KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL
+RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE
+>GCF_020097155.1_02361
+MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA
+AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA
+TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA
+EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG
+INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL
+RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA
+FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV
+IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE
+>GCF_023573625.1_00470
+MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA
+AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA
+TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA
+EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG
+INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL
+RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA
+FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV
+IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f813ccd33c9025c728682d15863dee40d2e5a47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000494.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>GCF_003691675.1_00189
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>GCF_005280335.1_02476
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV
+>GCF_020097155.1_02360
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA
+>GCF_023573625.1_00471
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000496.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..890aaf14929433c562e9814948dcdc82250b349c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000496.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>GCF_003691675.1_00191
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>GCF_005280335.1_02474
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR
+>GCF_020097155.1_02358
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG
+>GCF_023573625.1_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8202cc5c4f0838c3f6c518fd9d1898ecce57d77c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000497.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>GCF_003691675.1_00192
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE
+RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>GCF_005280335.1_02473
+MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL
+TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH
+RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI
+SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP
+DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE
+ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV
+TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR
+>GCF_020097155.1_02357
+MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI
+AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR
+NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA
+AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD
+PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL
+RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV
+DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA
+>GCF_023573625.1_00474
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000498.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..057e21fbeb09d67db8b041462d5a0648ef0506bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000498.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
+>GCF_003691675.1_00193
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP
+>GCF_005280335.1_02471
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR
+>GCF_020097155.1_02356
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG
+>GCF_023573625.1_00475
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000500.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e884aefa19a8d4aa6fa589d29e2a51bf2dd08e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000500.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00478
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
+>GCF_003691675.1_00196
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLLGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLRPRGRHR
+TPDAGV
+>GCF_005280335.1_02469
+MLSDLWSRLTGLVSMLWREVAKFGTVGAAAFVIDSLVFWWMMTGPLEGSNVKAKIVAGVV
+ATLFSWVANRYWTFREKRSSNKTRELVMFLLMNAIGLGIQAGCVFIAQYLMGVTDPGGLF
+IAGNVVGLFFGTVFRYFAYRFWVFKEELDVEPGFANDIAIITGQMPVLRDEQLHPHGRHE
+ARGRPAERHVRRDDGPARHRAS
+>GCF_020097155.1_02353
+MPTDLWHRFTGLVSMLWREVAKFGTVGAAAFVVDSAVFWWLMHGPLEGSNVKAKICAGVV
+ATIFSWVANRYWTFRDKRQNNVVRELVMFLVMNAVGLGIQAGCVAIAQYGMGVTDPNGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEELDEEPGFENDIAVITGQLPVLHAHDEHVPGLQH
+RHPRHDVEDGSA
+>GCF_023573625.1_00478
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000502.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18278c4e7838b6eb2b2eca15a48b8b74063b52ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000502.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00480
+MEQTQRVEDAHHADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAAPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
+>GCF_003691675.1_00198
+MEQTQRVEDTHRADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAVPVSQDWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
+>GCF_005280335.1_02467
+MEHTQRVEDTHRAESAQAAAPRPRGVPSDWFLDPADPLAGADAATLEDQATALLSAHDLE
+DEAGTPSATVTALFPGDAGQPVEAAPVADDWAAIPGLVTEPVEGELAWQVDALCAQTDPE
+AFFPEKGGSTRDAKRVCEACVVKDQCLEYAMENDERFGIWGGLSERERRRLRRARA
+>GCF_020097155.1_02351
+MQNTQRVEDVARAERAPAASRSRGVPTDWFLDPADPTAGGRATAGLAAESLEDQATAFLA
+AHDLDDAGTPAATVTALVPRPAEAPAVDDALVPDAWQPVPGVVMEPAEGELAWQVDALCA
+QTDPEAFFPEKGGSTRDAKKVCAACDVRRECLDYAMANDERFGIWGGLSERERRRLRRER
+G
+>GCF_023573625.1_00480
+MEQTQRVEDTHRADPAQAPAPRPRSVPSDWFLDPADPQADVSGVSLEDQATAFLTAHDLD
+GETGTPAATVTALFPGDARPVEAVPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEA
+FFPEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000503.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43588fbecfc857e8a436314be48fe5b2259387c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000503.fa
@@ -0,0 +1,22 @@
+>GCF_002008305.4_00481
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPTGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
+>GCF_003691675.1_00199
+MARMTAPASSDPLDPLPFRAGDAAGAEPGVEGGPAKAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
+>GCF_005280335.1_02466
+MDRLAALEAPGLRHVTARVERIPDRLDERLRALRAGAERDEETLFARAERQGQDGVVITL
+FERPLRDAADPEDLDGAVYGVALSRCAEALGVDPQVLDPGWGRA
+>GCF_020097155.1_02350
+MARMPADPLAPLPPLPPARRDGRGPRPGLRRDVRGRGLRHPLPFGARAGRGRADALMDAV
+EKAVDRLAGLQAPGLRRVAARLERIPDRLDERLALQRARAVADEEGLFGRAERDGADGVV
+ITLFERPLTESADPADLEEAVYAVALSRCAAALGVDPQVLDPSWGRA
+>GCF_023573625.1_00481
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e172bf5d027e3978dd629dff0297f46d23c0be2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000506.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00484
+MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR
+>GCF_003691675.1_00202
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG
+ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL
+ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR
+>GCF_005280335.1_02463
+MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS
+PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA
+AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI
+LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY
+LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL
+FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA
+LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR
+>GCF_020097155.1_02347
+MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL
+AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV
+PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP
+GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM
+WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA
+GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM
+SQDRRAQLEATRLRWAREDAHGVR
+>GCF_023573625.1_00484
+MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL
+SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG
+ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA
+LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT
+HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV
+WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL
+VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000507.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df8beca9c31d9f32053f3be24ae5af52045f96fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000507.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00485
+MQNQSPVHESATELIGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPTTTSRTLLFLP
+LAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKAQ
+KSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGEV
+ISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVTV
+KIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVII
+TAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDAEAFTQWALDRELTLTPA
+EAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIED
+HAEDVEALYRR
+>GCF_003691675.1_00204
+MQNQSPVHESATELVGMPPADSTITDLIVASCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL
+PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA
+QKGGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE
+VISCVSGASALSPDLVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT
+VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVI
+ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP
+AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE
+DHAEDVEALYRR
+>GCF_005280335.1_02462
+MPRVFEKVESGVATKAQKAGTGKVYQAARSTAITWSKALEEKKFGSGRGPSPALRARHAL
+FDRLVYRKIREALGGEVRTCVSGASALSEELVHFFRGAGVPIVEGYGLTESTAPATVNVP
+GAHRVGTVGLPVPGVTVKIAEDGEVLLRGPVMFSGYHGMPEASAESHAEDGFFRTGDIGS
+LDEHGYLRITGRKKDVIITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALVTLD
+EEELTRWSLDRERSLTPAEAAKDPAVLETIQEAVDRVNEDVSRAESIRRIRILDHAFTED
+SGYVTPSQKLKRAQVIEDYAEDVDALYRGR
+>GCF_020097155.1_02345
+MQHASPISESSTDLYGLPAEDTNITDLILSSCAEDPRASVYAVRNGAGAWLDVRFDAFLG
+QVRDVAKGLIAHGLQPGQRVALFAPTCYEWAVLDQAVWFAGAVSVPIYETSSAAQVAHIL
+GDSQTHAAAVGGDELAATTREAARQAGIDVTVFPMSEAALRVLARDGAAVTDEQLEAART
+TATLDDAASVVYTSGTTGRPKGAIITHRNFAAASINVLNFAAGVVDYHPGTNSRTLLFLP
+LAHVLAHAVQVICLYARIQMAHSGSTKTLQEDMASFHPTWLLAVPRVFEKLEAGIAAKAE
+DGGRGPVYHAAKRTAIEYSEALEAQTHEGGPGPSRALRARHAVFDTLVYGNVRKAFGGEV
+LSCVSGASALSPELVHLFRGMGIPIVEGYGLTETTAPATVNIPAAYKVGTVGLPVAGATI
+RIADDGEVLVKGPIVFAGYLRQPEATAESMDGDFFRTGDLGTLDEDGFLRITGRKKEVIV
+TAGGKNVYPTPLEEIIRQHRLVQHVVVVGDDRPYVGALIVLDPDELKRWSLDRERTLTLE
+EAVADEGVLAALQEAVDQANATVSRAESIRRIRVLDHELTEDSGHVTQSQKLKRAQVLAD
+YADEIEQLYRGR
+>GCF_023573625.1_00485
+MQNQSPVHESATELVGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL
+PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA
+QKSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE
+VISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT
+VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDGFFRTGDIGALDEHGFLRITGRKKDVI
+ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP
+AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE
+DHAEDVEALYRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000510.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbdc8d697850ef8f49ccaef7ad566e38726f1026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000510.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00490
+MAHASETPLAYRAPAQQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDIASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVA
+ALARAVSENTARVYGSF
+>GCF_003691675.1_00211
+MAHASETPLAYRAPAPQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCTEHGWHMSFAGPV
+TFKANDELREALRTAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>GCF_005280335.1_02457
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEFPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAAEGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLVPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>GCF_020097155.1_02341
+MATTTSAQSASTQSASTEPGIPSAYRPPATPADLGDGPARDTREEKSGRKRRLEYPPAPE
+PLPVPVVDNHTHLDFRDGLVRVDVHQAMDAAEAVGVVGAVQVACDVESARFTVEAIEAES
+RLLGAVALHPNDAARLTARGEFEEAFAVIAELAEHPRVRAVGETGLDFFRTTDEAGHAAQ
+EESFRRHIRLARELGKALQIHDRDAHDDVVRVLLEEEADGGLPPHVVFHCFSGGPDLART
+CAERGWHASFAGPVTFKANDDLRDALRLLPRELVMVETDAPFLTPHPHRGRPNAPYLIPV
+TLRGMAEARGEEVAELAAAVAENTARVYGEF
+>GCF_023573625.1_00489
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..858c36075cd975d98376fb9f01b4caba93375174
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000512.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00492
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEVSA
+>GCF_003691675.1_00213
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
+>GCF_005280335.1_02455
+MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV
+QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE
+LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS
+GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP
+RTRGEALGIEAFARIAEHGPRRAAGEGSA
+>GCF_020097155.1_02339
+MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV
+LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT
+AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA
+VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA
+AS
+>GCF_023573625.1_00491
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000514.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e328a01dabc39c206a9022c272dcac65bc3e17e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000514.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00494
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKPRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDEAGGPARGAGPVRGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAALGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLRAAELAEGD
+>GCF_003691675.1_00215
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+PDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMADAGGPARGAGVARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
+>GCF_005280335.1_02453
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPTHTVRQAVVGDVEDHVWASDPKVRDVLGGLLDGLDLEQTV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKDRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWILARAERARQAAVVEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDSVSLAKTATARLGKDVLDLEHVGLSLGEKR
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLEPDSGRVKRGKTVVTATLTQDVKE
+LDEVAHLRVAEVMAREGSAFQVGDKEMSAGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDAAGASGGPARGAGAARGRNDVVGTCAGMGGPEEDTGP
+TEAERRLARKEMARLEKQMTRLRDSRSVLEARMAELGQAQDFDALTAASADLKDLDAQLD
+VLEEEWLQAAELTEGD
+>GCF_020097155.1_02337
+MAHLLGAENIGISFGTRTVLDGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVHVGVLDQRDVLDPQDTVRRAVVGDVEDHVWASDARIRDVLGGLLAGMDLEQRV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLAGHLNARWRPNDGGLVVVT
+HDRWFLDAVCTRTWEVHDAAVDPFDGGYAAWILARAERARQAQVTEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDTVSLAKTATARLGKDVIDLEDVTLTLGDRT
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLQPDSGRMKRGKTVVSATLTQDVKE
+LDEVADLRVAEVMAREGSAFQVGDREMSPGQLLEMLGFGPTRQWTAVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGRVRDLPGGVDQYLELRVLMDDAGGAAPAPGSSRGRGDAQGTCAGMVVDIPEVSEAER
+RQARKDMARLERQMQRLRESRGGIEARMAELGQAQKYDELGAATAELTAVDAELEDLEEQ
+WLEAAERDA
+>GCF_023573625.1_00493
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKARDVLGGLLDGFDLDQPV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIQDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDDAGGPARGAGAARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..668eed496e7b3eb2a21497d0a15cfb5afb0d6ac2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000520.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00505
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
+>GCF_003691675.1_00225
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA
+>GCF_005280335.1_02445
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT
+>GCF_020097155.1_02329
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA
+>GCF_023573625.1_00504
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000522.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7567ca411d4afc715149d6ffa2fe9f77c04de734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000522.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00507
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPIPDFDVTARKRRQDMTRTDLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGLLELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLRHRS
+DLGAPRTAETPTTGPNRTPGGAQ
+>GCF_003691675.1_00227
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAGEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHAGDPDGEPIPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
+>GCF_005280335.1_02443
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEADLHVVVSTDSEEIAEVAR
+RYGADVPGLRPAELAQDETPTEPVVEHALAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VAQFRETGVDSLVGVVPVSPFLWRHAADPADPPVCDFDVAHRKRRQDMDRPDLRFRENGS
+LYVTRPWVYDELHNRLGGRIGMFELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLQRVP
+DRTQLHGTSTATLGDAL
+>GCF_020097155.1_02327
+MSILCVIPVRGGSRGLPGKNIRMLGGHPLVAWTIQAALDAEADLHVVVSTDSEEIAEVAR
+KYGADVPALRPAELARDDTPTEPVVEHALAAERARGVEPEAVMLLQATSPLRLPGTLDRA
+VAAFREPGVDSVVGVVPVSPFLWRHAADPAAAPVADYDVDGRKRRQDMDRADLRFRENGS
+LYVTAPWVYDERHNRLGGRIALLELDDLEGVDIDTELDFALAEQQMDQYLAVQKLLQTRP
+DLTRTAGGAL
+>GCF_023573625.1_00506
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPTPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ad6835355864e0b02ed352f33d3ae84ab7bd402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000523.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00508
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE
+ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_003691675.1_00228
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE
+ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_005280335.1_02442
+MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG
+ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI
+GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG
+TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV
+KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED
+AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_020097155.1_02326
+MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG
+AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI
+GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV
+KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK
+VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA
+DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR
+YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM
+DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
+>GCF_023573625.1_00507
+MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE
+ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI
+GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA
+TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV
+KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA
+PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK
+VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD
+DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR
+YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD
+DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA
+EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL
+SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS
+FIPEIWQGHINNGEGFWTALDRLEQWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000527.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..980be4ba26c3144a72c36079c84f1bd28d3dc543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000527.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00516
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGIRDILVITTPQDAEQ
+FQRLLGDGSQFGVSLTYVQQPSPDGLAQAFVLGEEHIGVDHVALVLGDNIFYGPGMGQQL
+RRHTDVEGATVFGYWVKDPTAYGVVEFDTNGKAVSLEEKPAQPKSNFAVPGLYFYDNDVV
+EIAKDLKPSPRGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFTDLNDASNFIHAVE
+SRQGLKVGSPEEAAWRQGLLTDDQLRERAERLVKSGYGRYLLDLLDSGR
+>GCF_003691675.1_00236
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAQQ
+FQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDEHVALVLGDNIFYGPGMGQQL
+RRHAQVDGATVFGYWVVDPSAYGVVEFDDAGKAISLEEKPEEPKSNYAVPGLYFYDNDVV
+EIAKSLKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLELLESGR
+>GCF_005280335.1_02435
+MKGIILAGGTGSRLHPITHAISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAGQ
+FQRLLGDGSRFGISLTYVQQPSPDGLAQAFLLGEEHIGDDHVALVLGDNIFYGPGMGQQL
+RRHTEVHGATVFGYRVADPTAYGVVEFDGTGRAVSLEEKPTAPKSHYAVPGLYFYDNDVV
+EIARALKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLDLLENAR
+>GCF_020097155.1_02317
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAEQ
+FQRLLGDGSQFGVSLSYVQQPSPDGLAQAFILGEEHIGDDRVALVLGDNIFYGPGMGQQL
+RRHTEVEGATVFGYWVADPTAYGVVEFDGAGKAVSLEEKPKEPKSNYAVPGLYFYDNDVV
+QIAKDLKPSPRGELEITDANRVYLERGMLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGSPEEVAWRQGLLTDDELRQRAEPLVKSGYGRYLLGLLDRADPIGRSSR
+>GCF_023573625.1_00515
+MNPDRTALNLHHRIGPMKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILA
+GISDILVITTPHDAEQFQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDDHVAL
+VLGDNIFYGPGMGQQLRRHSEVDGATVFGYWVADPTAYGVVEFDGDGKAVSLEEKPAQPK
+SNYAVPGLYFYDNDVVEIAKELKPSARGELEITDVNRTYLERGALNVEVLPRGTAWLDTG
+TFKDLNDASNFIRTIESRQGLKVGSPEEVAWRQGLLTDNELRERAEPLVKSGYGRYLLDL
+LETGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..868dc844a1e09414ef18be93a74fd1051cfbdbfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000535.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00533
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>GCF_003691675.1_00254
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>GCF_005280335.1_02419
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR
+>GCF_020097155.1_02301
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR
+>GCF_023573625.1_00533
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000543.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08f7ed9b4a9c77ffac1d39a729ce19a86d371b62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000543.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00543
+MIPHDDGAAGLGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAAAGVDAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAS
+RQGVLHSGHWLGLVLPESGAGSGMAEEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGEDFTRLWEPSNAQR
+>GCF_003691675.1_00268
+MIPHDDGSAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAAAGVEAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAG
+RQGVLHSGHWLGLVLPEPGVGSGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR
+>GCF_005280335.1_02404
+MRHDDGAAGPGVRPRLVLGSASPGRAEVLTRARVPFRVVVSDVDEAAVGAAAPEADPCEL
+AVLLAEAKGRDVAARVAAAGVDGPTLVLGCDSVFEFDGRAHGKPYEPEVAVARWRAQAGR
+SGRLHTGQWAGLLLPGEDGAVPDAETSTCVGADVRFAAVDEDTVRAYVATGEPLHCAGAF
+TIDGAGAALVESVDGDPNAVIGLSVVVLRAQCEELGLRFADLWEKC
+>GCF_020097155.1_02287
+MSTLPHGGGAPAALVLGSASPGRAQILRRALLPFRTVVSRVDEEAVGAASPGATPAELAR
+LLAEAKAEAVAGVVAAEGVDRPTLVLGCDSVFELDGQALGKPWEPETAIARWRAQSGRSG
+TLHTGQHVILLTPGTDAAGAPASGATVSAGVAFTDVDEATIRAYVATGEPLQCAGGFTID
+GAGAALVESVEGDPNAVIGLSVSTLRRQCSVLGVDLSALWGSSNCDA
+>GCF_023573625.1_00546
+MIPHDDGAAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAGAGVEAPTLVLGCDSVFEFEGRAHGKPYEPEVAVERWRAQAG
+REGVLHSGHWVGLVLPEPGVESGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73df7424598026f1c17b21d42fed4b85ff1e6100
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000544.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00544
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>GCF_003691675.1_00269
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>GCF_005280335.1_02403
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA
+>GCF_020097155.1_02286
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA
+>GCF_023573625.1_00547
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000545.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..912cefec9baa0c7d5d85dc0a36af298150ee4008
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000545.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00545
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>GCF_003691675.1_00270
+MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>GCF_005280335.1_02402
+MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR
+AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ
+>GCF_020097155.1_02285
+MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR
+RPDRSLVRRGDLGLWARPGEDQWRRAAGRR
+>GCF_023573625.1_00548
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000547.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ed4010dc63ac1fc8347e7bd3703ff1ba32dfd2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000547.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00548
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGLVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVLTDRRILQGAGIGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR
+>GCF_003691675.1_00273
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVVTDRRILQRAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTRTWPAPVPTGDLR
+>GCF_005280335.1_02398
+MRLEPGEQVMVRTRTHPRALLRPAAVLVTVAFLLGLAMGVLARPDLPGILTQNRALLETA
+AWAVAVLALLPGVLLPVLRWATRRTVVTSRRIVQRTGLGGGADVAMSLVSIADVQRRRRG
+SGAGDLHILFQERARQVHWRLRDVPEAARFEEALAHLTRQARVASWPAPAPTGGPR
+>GCF_020097155.1_02282
+MRLEPGEQVVVRTRSHPRVLVGTAARLTGTAFLLGLAMGLLARPGLPSPLRAAVPWLEAV
+VWAAAVVAVLVGVVRPLLRWATRATVLTSERLVQRPGLGAGPEAAMPLVSIADVQRRRRG
+ASSGDLHILFQDPLRQVYWRLADVPEAERFEQVLAETTRAARDRARPAMPAWGGVL
+>GCF_023573625.1_00551
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTIRPLWRWVFRRTVLTDRRILQGAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f64b69f6e3266168d8d99b2d4e2ee625e5bd3143
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000549.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00550
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>GCF_003691675.1_00275
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>GCF_005280335.1_02396
+MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA
+AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR
+WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS
+SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG
+GRDNVTAVLVRIP
+>GCF_020097155.1_02280
+MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG
+HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL
+ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR
+NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER
+LVEAALWRGGRDNITAVLVRIP
+>GCF_023573625.1_00553
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51a123a66149f82a135a05570c98e238f0b84949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000552.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00555
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>GCF_003691675.1_00280
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>GCF_005280335.1_02390
+MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS
+NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE
+>GCF_020097155.1_02273
+MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE
+NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE
+>GCF_023573625.1_00558
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55595f36ccbc68d158893fb1fb679229fbeba58d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000554.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00557
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_003691675.1_00282
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_005280335.1_02388
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG
+ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>GCF_020097155.1_02271
+MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT
+LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV
+ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG
+AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV
+GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD
+LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA
+SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD
+GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT
+RGQADAGRVREIVLERLGVA
+>GCF_023573625.1_00560
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000558.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6edb03f1bd9406a476e6a55f0f304c06b8ea681e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000558.fa
@@ -0,0 +1,43 @@
+>GCF_002008305.4_00561
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVAGWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDVEDILADLERGFAAAARRGDDDAGERA
+>GCF_003691675.1_00286
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLADDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
+>GCF_005280335.1_02382
+MVASASLYGGTQNLFKHTLAKVGIETTFVQDPDDVAAWTAAVRPNTKAFFGETLGNPRGD
+VLDVAAVADAAHAAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIV
+DAGTFDFAQHAERFPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSA
+ISPFNAFLVNLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRY
+LPKGAGAFVSFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQR
+AAGVTPGLVRLSLGVEDLEDILADLERGFAAAASAGERE
+>GCF_020097155.1_02266
+MSTQPTPRRGFSTTQIHAGTDAPHAFGATALPIYQTTSYDFPSAQVAADRFALADLGPIY
+TRIGNPTQSAVEEKIAALEGGVGALLLASGQSATTFAILNVAGAGDHVVASASLYGGTQN
+LFKHTLARVGVEVTFVQDPDDLDAWRAAARPETKAFFAEALGNPRGDVLDVAGVAAAAHD
+AGVPLIVDNTLTTPYLLRPFEHGADVVVHSATKYLGGHAAAMAGVIVDSGRFDFARDPER
+FPGFNEPDESYHGLVYARDLGVGSPLGANLAFVLKARVQLLRDYGSAISPFNAFLVNLGL
+ETLSLRMDRAVASALAVARHLEGHPQVESVSHPGLESSPWHARAQELLPRGAGAFVSFEI
+AGGAAAGAAFVDGLELHHHVANIGDVRSLVVHPASTTHAQLAEDEQRAAGVTPGLVRLSL
+GLEDVEDILADLDKGFAAAAAALDAADAAEQD
+>GCF_023573625.1_00564
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTKAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVERVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000559.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fff85b8750b958bd68972136baca8c722efd9031
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000559.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00562
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRTLAL
+>GCF_003691675.1_00287
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL
+TEYGQVADTLKRTLAL
+>GCF_005280335.1_02381
+MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA
+LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP
+WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA
+ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER
+RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV
+GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL
+TEYGQVADALRDSLAL
+>GCF_020097155.1_02265
+MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA
+GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD
+TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ
+AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD
+YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL
+DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA
+ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL
+>GCF_023573625.1_00565
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRALAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2090f9fd0c171aef03948357bc6b781b435bdcaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000566.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00573
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGGAAPPSEA
+>GCF_003691675.1_00305
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDGGDAAPASEA
+>GCF_005280335.1_02360
+MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA
+RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR
+PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR
+>GCF_020097155.1_02251
+MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP
+DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL
+AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR
+>GCF_023573625.1_00574
+MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT
+VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG
+ADLLAVLDREDAAPSSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000567.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec0397bd8acd3780c557c88253c0940d27afec32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000567.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00574
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG
+>GCF_003691675.1_00306
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG
+>GCF_005280335.1_02359
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG
+>GCF_020097155.1_02250
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG
+>GCF_023573625.1_00575
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000568.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ad074b8ed5f42db0244c1cad5751a4d1e26611a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000568.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00575
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>GCF_003691675.1_00307
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>GCF_005280335.1_02358
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI
+>GCF_020097155.1_02249
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL
+>GCF_023573625.1_00576
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000573.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51659539fc352f4737d2df2444cd2e490ff4a118
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000573.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00608
+MSSACGCEAPTPGAPEEPEEHRPWWRDAAILLPVLSGVAFIAGLVLEWSGAGLVATVVFW
+VGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEALE
+DKAMDRARAGLRALLKLVPETATIRQGGATVQVEAKDLHPGQVLVVRPGERIATDGIVRT
+GRSSLDTSAITGESIPVEVGPGDTVSAGSINTSGALEIDATAAGTDNSLTTIVHLVEQAQ
+TEKGARARLADRIAKPLVPGVLVLAVLVAALGSLFGDPELWITRALVVLVAASPCALAIA
+VPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLTTPGLTE
+DQVLGWAAALEQHSTHPLAAAIIAAAPDAPGAKAVTETAGHGITGRIDGATITVGSPRWL
+DPGPLAAQVQQLEDQGMTVVIIHRDGTVAGAIGVRDELRPEVPAVVTTLTGQGIGLTMLT
+GDNARTARAIAAQAGIGDVRAELRPEDKAAAVGQLTGTRPTAMIGDGINDAPALAAAEVG
+IAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIMNQNIVLSLLIIGVLLPLAI
+TGMLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALASLTDRQAQRSTVG
+>GCF_003691675.1_01768
+MSAACGCEAPTPTPGAPEEHEEHRPWWRDAAILLPALSGLAFLTGLVLEWSGAGLVATVV
+FWVGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEA
+LEDKAMDRARAGLRALLKLVPETATIRAGGATVEVEAKDLRPGQVLVVRPGERVATDGIV
+RTGRSSLDTSAITGESIPVEVGPGDTVSAGSINTAGALEIDATAAGTDNSLTTIVHLVEQ
+AQAEKGDRARLADRIAKPLVPGVLILAVLVAALGSLLGDPELWITRALVVLVAASPCALA
+IAVPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLAAPGI
+TEDQVLGWAAALEQHSTHPLAAAITAATPDTPAAEGVTETAGHGITGRLDGATVTVGSPR
+WLAPGPLAAQVQGLEDQGMTVVIIHRDGAVAGAIGVRDELRPEVPTVVTTLTGQGIDLTM
+LTGDNARTARAIADQAGIDDVRAELRPEDKATAVHQLTGTRPTAMIGDGINDSPALAAAE
+VGIAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIINQNIILSLLIIAVLLPL
+AITGVLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALEPLTDRQAQPATTG
+>GCF_005280335.1_00728
+MRATTHTPVEELETDDEHETPWWADRAVLIPIASGVAFVAGLACEWSGAQSAALVLFWVG
+LLLGASTFVPGALRKLATGKLGIALLMTMSATGAVILGHVEEAAALAFLYSIAEALEDRA
+MDRARAGLRALLKLVPQSATVLTDGHSASVPARDLAAGQVMLIRPGERIATDGIVRSGHS
+SVDTSAITGESIPVEVGPGDEVSAGAINAAGALQVEATAPGTDNSLTTIVSLVERAQAEK
+GQRARLADRIARPLVPGVLVLAVLVALIGSLAGDPQTWITRALVVLVAASPCALAIAVPI
+TVVSAVGSASKFGVIIKSGAIFERFGDIGHVAFDKTGTLTRNQPTVTAVVPAADVTEQQV
+LAWAAALEQHSTHPLATAITHAAPHNPRRPGHHRGSRPRNPRHRRRRRSAGRQPPLGRPR
+RPHLPGP
+>GCF_005280335.1_00729
+MLVGSPRWVDPGDLTYRVRDLEAQGMTVVVVHRDGAVAGAIGVRDELRPEVPEVITTLAG
+QGIDVTMLTGDNERTARALAAQAGISDVRAELRPEGKSAAVGELSVRRPTAMIGDGINDA
+PALAAADVGIAMGATGSDAAIESADIAFTGQDLRLLPQAIAHARRGRRIVNQNIVLSLLI
+IAALPPLAITGVLGLAAVVLIHEVAEVLVILNGLRAARTHQPTRGH
+>GCF_005280335.1_02365
+MVPVFSGVAFLTGLVLEWAGLEVPALVLFWIGLLLGASTFTPGAIRKLFKGKLGIGLLMT
+ISAVGAVILGYVEEAAALAFLYSIAEALEDKAMDRARGGLRALLKLVPETATIRRDGASV
+EVPAKDLAVGQLMLVRPGERIATDGIVRTGRSSLDTSAITGESIPVEVEPGDTVSAGAIN
+TAGALEVETTAAGTDNSLTTIVDLVEKAQADKGDRARLADRIARPLVPGVLILAALVAII
+GSLLGDPELWITRALVVLVAASPCALAISVPLTVVAAIGSASKFGVIIKSGAVFERFGVI
+RHVAVDKTGTLTRNEPAVTAVLTAEGVTEKQALAWAAALEQHSTHPLAAAITAAAPGAPA
+ADGVTEQAGHGIEGTLDGARITVGSPRWLDAGTLGEQVAGLEEQGMTVVIVHRDGTPVAA
+IGVRDELRPEVPEVVRTLAAQGIGVTMLTGDNARTARALAAQAGIGDVRAELRPEDKAAA
+IAELGEKGAVAMIGDGINDAPALAAADIGIAMGATGSDAAIESADVAFTGHDLRLLPRAF
+DHARRGRHIINQNLILSLLIITALLPLALFGVLGLAAVVLVHEIAEVVVILNGLRAARTR
+KSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000574.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4293476adcb8746fc992c4631427ed8095276c61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000574.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00612
+MTTPTIPTDHPIEHRVDTGPASEEAGMPVAARHRPFGVVLLVTGVVGWVASAILVLERLA
+LYENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVIATAMVVLSGARPG
+RGYWAGLQAGVTLGMGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFILLTARNLAHGVI
+PAPPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGL
+>GCF_003691675.1_00328
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTMR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
+>GCF_003691675.1_01772
+MTDRLTEPTAPSAASPVSAAGPAPAPAWFTGRRAFGLVLLVTGAVGWIASATLVLERLAL
+YENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAMVVLSGARPGR
+GYWLGLQAGVTLGIGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFLLLTARNLAHGVIP
+APPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGF
+>GCF_005280335.1_02343
+MRTPATDTDSPVKTEPLTDLPTERAADPDPSAPAPVPAVARHRPFGLVLLVTGVVGWVAS
+AILVLERLELYEDAGHITSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAM
+VVLSGARPGRWYWAGLQAGVTLGMVFVAWLWFQALFVIHILCLYCMIVWAAMIPLFILLT
+VRNLAHGVIPAPPGVVRFATGWAGTLIAVAYVTVTGSVFVQFLPAFTGY
+>GCF_023573625.1_02009
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTVR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000576.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a195f5c549aba431376acbe0ecc5d437b8e9b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000576.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00636
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQLRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>GCF_005280335.1_00408
+MLCILPLDQSLHQTRSDSDFYREFVDHPRVIRVLALSGGYTRAQATTLLARNHGVIASFS
+RALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>GCF_020097155.1_02192
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIQLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDD
+>GCF_020097155.1_02193
+MTLPERADFYREFVDHPRVIRLLALSGGYTRAQATTLLARNHGVIASFSRALTEGLSTAQ
+SPAQFNTVLDEAINAIATASRT
+>GCF_023573625.1_00595
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVIGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000579.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..081521a36c41ae67fc99a7bbe1d7d1d800ae7f6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000579.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00642
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>GCF_003691675.1_00379
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>GCF_005280335.1_02320
+MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR
+GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA
+VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL
+SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI
+RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>GCF_020097155.1_02183
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>GCF_023573625.1_00612
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83565138c329c0ed2f31890f947720f9f91a62fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000582.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00647
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>GCF_003691675.1_00384
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL
+DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL
+>GCF_005280335.1_02316
+MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT
+VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI
+NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA
+ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL
+DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL
+>GCF_020097155.1_02175
+MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT
+VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI
+NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA
+AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV
+AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF
+CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL
+DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL
+>GCF_023573625.1_00617
+MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT
+VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI
+NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA
+AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI
+AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF
+CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL
+DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000585.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7f2edf59bbf6cd89066c0e28abffea62dcab0d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000585.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00652
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAERAEAPAAEAAPQGE
+>GCF_003691675.1_00389
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVPYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAAPQGE
+>GCF_005280335.1_02311
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQGQEVIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMSKTPSAVWVVDTKKEHLAVDEAKKL
+GIPVVAILDTNCDPDEVTYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQSAAE
+PMAEWERELLEQHNAQQAEQAEAPAEAQAQAEEASAEAPAQAEEASAGAPAQAE
+>GCF_020097155.1_02168
+MSVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLTYIDRAYEFVKQT
+VAHGGTILFVGTKKQAQEAIAEQATRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEAI
+DFEDVAGSTHTKKELLLLNRELEKLQGNLGGIRDMARTPSAVWIVDTKKEHLAVDEAQKL
+NIPVVAILDTNCDPDEVAYPIPGNDDAIRSVTLLTRIVADAVAEGLIARQGGKSGDSSAE
+PMAEWERELLEQHNAEQAAQAEAPAAEAAESEAPAAE
+>GCF_023573625.1_00622
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAEQAEAPAAEAAPQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68804dbed79e75bd4339416a2e58d5a7bbcd1dd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000587.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00654
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_003691675.1_00391
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_005280335.1_02309
+METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD
+RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG
+VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
+>GCF_020097155.1_02166
+MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS
+IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ
+VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY
+TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL
+GEEIGTSVTP
+>GCF_023573625.1_00624
+METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD
+QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA
+IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG
+VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV
+TRALLGEPIGTTVTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000588.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..904827667f05156fb7b6f087899e63d2420763c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000588.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00655
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>GCF_003691675.1_00392
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>GCF_005280335.1_02308
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSYTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRVVMPELTEERRKEYVKLVKSK
+AEEHKVSVRNARRKAKDALDKAVKDGEVGEDEGARGEKDLDAMTKKHVDLIEEMAKNKEQ
+ELLEV
+>GCF_020097155.1_02165
+MIQETLTSAQEQMERTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDVSALRNIEKALSDSEVGANPSNDGKVIRVVMPELTAERRKEYVKLVKNK
+AEEHKVSVRNARRKAKEAIDKLVKDKEIGEDEGARGEKDLDALTKKHTDLIEEMAKKKEA
+ELLEV
+>GCF_023573625.1_00625
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08376560ef2719938a9f30b26d88aa0819ba28c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000591.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00659
+MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>GCF_003691675.1_00396
+MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
+>GCF_005280335.1_02304
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD
+KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEETR
+>GCF_020097155.1_02160
+MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA
+EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY
+GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD
+KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS
+PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP
+PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA
+>GCF_023573625.1_00629
+MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA
+ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF
+GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD
+KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS
+PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP
+PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000592.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44aa81a65ee68767ab7383a20d2d20e6e69e625e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000592.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_00660
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
+>GCF_003691675.1_00397
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAESDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLAMV
+>GCF_005280335.1_02303
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGSEGETLEVGAPLVTFTVEGAGGDGGDTESGGRVPTLVGYGAAPDTGKPGRRARRGGSA
+GSATSAAPAGEPERGRAPSTSEEAPAGAARPQPEAAEPERADEAPEAQPASGTSGERPRC
+TPPVRLYARREGVDLTAVSGSGVGGVITRADVEAFLAGGGAPAAEPTASAAAPAEAGTSG
+GVRTLGGRPRTESVPVKGVRKATASAMVASAFTAPHVTEFLQVDVTETMELLAELKASRE
+YRDVKLTPMTLAAKACLVAMERTPDVNARWDQASGTILQQNFVNLGFAAATPRGLMVPNV
+KDAQAMSLTELADAIRELTGRAREGRLSPAELSGGTFTLTNVGVFGVDAGTPIINPGEGA
+IIAIGQVRRTPWEHRGEIVLRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTM
+V
+>GCF_020097155.1_02159
+MTRTVFRLPDLGEGLTESDLVTWRVSAGDDVVLNQVLAEVETAKAVVEVSSPYAGTVAEL
+HAQEGQTVDVGSPLVTFDLPGDDAAPSDGPAADGRVPTLVGYGAAPESGAPARRRRRPAS
+SAGESTPETGTSAEPAPAPAESAPAERPRSTPPVRLLARRLGVDLESVTGSGDHGVITRA
+DVDAAARAASDSAGSEAPAEADAAPGVRTLGGRPRVVVEQVRGVRKATAQAMVSSAFTAP
+HVTEFLTVDVTESMELLDELRRDRAFRDVKVTPMTLALRACVLAMERTPEVNARWNGQDG
+TIERRHFVNLGMAAATPRGLLVPHVKDAQALDLRGLAVEVAALTERARAGTLTPAELTGG
+TFTLTNVGVFGVDSGTPIIHPGEAAILCLGAVRTQPWEHRGQIALRQVVTLSLSFDHRLV
+DGEQGSRFLADVGAMLRRPGMTLALV
+>GCF_023573625.1_00630
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPVGEPARGQAPSTSEAAPAGAGRPQPEAAEPARADAAPEAVRGAASGERPRCT
+PPVRLYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAATPPQSDAESGSTGGV
+RTLGGRPRTEAVPVKGVRRATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFR
+DVKLTPMTLAAKACLVAMERTPDVNARWDEAAGTIVRQNFVNLGFAAATPRGLMVPNVKD
+AQAMSLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAII
+AIGQVRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000597.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4db99a801c430819d29237feef4319470e7c7a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000597.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00669
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAVLLIAGAGIMTVWTLALFGFDFNALLGAAVEKNPKGEA
+ILEPGLQYGASALTRLDFVSLGLALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>GCF_003691675.1_00406
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>GCF_005280335.1_02293
+MSALTPLLQAAPEAVGSPAVNIGIFLAFVVVTLVIVIRASKTSSSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIAIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGVMTVWSLAMFGFDFNAMLGAAVELNPEGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERIMAAPGGQNSAAPLLAFELGGSILLGVISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHQLTPNEEVRIGKITVVVIGLLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGAPTSMI
+PGADFAIFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>GCF_020097155.1_02155
+MSTFALPLAAAVGDPVVNIGIFVAFVAVTLVIVIRASKKNASAADYYAGGRGFSGTQNGT
+AIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMADVL
+SFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNITDKGGQALVIVIVGVLMI
+VYVLVGGMKGTTYVQIIKAILLITGAGVMTLWSLALFGFDFNAMMGAAVQLNPQGEAILE
+PGLQYGKNFTTRLDFLSLGLALVLGTAGLPHVLMRFYTVPTAKEARTSVVWAIVLIGAFY
+LFTLVLGYGAGALIGPEKILAAPGGVNSAAPLLAFELGGSILLGLISAVAFATILAVVAG
+LALTAAASFAHDVWGSVIAKEPLTPEEEVRIGKITVVVIGVLAIVGGIAAQGQNVAFLVA
+LAFAVAASANLPTILYSLFWRGFTTRGAVWSMYGGLIASIVLIVLSPVMSGAETSMIPTA
+DFAVFPLKNPGIVSIPLAFVLGWLGSVTSKDVEDPDKQAEMEVRSLTGVGAEKPVAH
+>GCF_023573625.1_00639
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNTSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERITAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000603.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f27f25b6263037b63decf6767eb5dd57840958a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000603.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00675
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
+>GCF_003691675.1_00412
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
+>GCF_005280335.1_02287
+MVAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPVQALATNKMGSVFGTATSAITYRRRL
+RQDLSTALPMAAVAFVAALAGAVVAASLPAGVIRPVILVALIAVAVFTAVRPGLGKTAGV
+GPERRTAVARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKIVNLATN
+LGALAFFIPAGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLVVVAALIVKVG
+ADTLAPLLL
+>GCF_020097155.1_02149
+MELFGPVELSVGIVLLVLAAGFSAGWIDAVVGGGGLLQLPVMLLVPGLSPVQALATNKMG
+SVFGTAASAATYARRVRPDLRTALPMAAVALLCSLGGAVVATVLPAAVIRPVILVALVGV
+ALVTALRPQWGLTQGLKHAGTAHALRALAVGAVVGFYDGVLGPGTGTFLILGLVGVLGYD
+FLQASAKAKIVNLATNVGALAFFLPAGHVVLGLGLLLGAANLTGGYVGARMAISRGTGFI
+RTVFLVVVCALILRLAWDVFAPLLG
+>GCF_023573625.1_00645
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b7dc3515b5262769d3591e0167b99cbb2a2506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000606.fa
@@ -0,0 +1,81 @@
+>GCF_002008305.4_00679
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>GCF_003691675.1_00416
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>GCF_005280335.1_02284
+MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS
+KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG
+EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR
+PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP
+GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ
+PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA
+RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP
+VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG
+KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI
+IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE
+VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC
+GIGLGSFNDIKEGDVIETFEMREKPRA
+>GCF_020097155.1_02145
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK
+PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA
+SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS
+KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP
+AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG
+GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA
+DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE
+AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG
+AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH
+AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL
+EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG
+RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA
+QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI
+HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA
+LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL
+KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV
+>GCF_023573625.1_00649
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000607.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a05873810fdef42fbf9bc19a7f1e87d2dd38374f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000607.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00680
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>GCF_003691675.1_00417
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>GCF_005280335.1_02283
+MADPARAGRLAQRIKVLVAEALRRSVKDDRVEAVTVTEVRVTNDLQHATVYYTVLGDEAT
+AAAAHEGIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGATYAGEADPYRTSEPGSEADDAPRA
+>GCF_020097155.1_02144
+MADPARAGRLAQRIKVLVAEALRRAVKDERVEPVTVTEVRVTNDLQHATVYYTVLGDEAV
+VAAAQEAIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGAQYAGDADPYRTSGDDDEQD
+>GCF_023573625.1_00650
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRSAEPDADADDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000608.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c161bee0471d9c740fa2c3145e395d1f6403dfb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000608.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00681
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>GCF_003691675.1_00418
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>GCF_005280335.1_02282
+MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR
+AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL
+AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA
+>GCF_020097155.1_02143
+MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG
+LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV
+AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV
+DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT
+ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV
+ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR
+>GCF_023573625.1_00651
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000611.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0104e58b74ed36365899f54af74ac910410e6f97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000611.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00684
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>GCF_003691675.1_00421
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>GCF_005280335.1_02279
+MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS
+VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV
+VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG
+DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE
+AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV
+EKLVAQMTQDVEQARAILAATPSDR
+>GCF_020097155.1_02140
+MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV
+VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV
+VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD
+VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV
+WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE
+KLVAQMHQDVDQARAVLAAAPQPAGRV
+>GCF_023573625.1_00654
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000612.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e051cfc600c58722266439c63134550f1b2eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000612.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00685
+MSAPEPGAPPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
+>GCF_003691675.1_00422
+MSAPEPGAPPAVPNLPGRPARVRRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
+>GCF_005280335.1_02278
+MTGPGPGVPRLPGRPARARREAGNPFADAGGEHYDAVRPSYPAEAVAWVLEGLGQGLDRG
+LDVVEVGAGTGLFTRSLTALPVERVRSVAAVEPAASMRAVLERDVAAGSDGRVRAVPGTA
+EATGLPEASADVVVAAQAWHWVDPAAGSAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTR
+IMHAGDVHAARPELRRFAAPFGAEEHARWTWTLPQTAADLHGIMASRAYWLRASETTRAK
+MSANLDWYLHEHLGHGPDEAIVVPYVSVAWQASST
+>GCF_020097155.1_02139
+MSERGLPDSGAAPRPAGGYVPALPSRPAITRTGGVNPFEVSPEQGEQYDAVRPSYPAAAV
+DWVLDGLGAGLDVVETGAGTGLFTRRLAERPAERVRSVAAVEPSEAMRAVLERDVAAGSA
+GRVRAVDGTGEATGLADGCADVVVAAQAWHWMDAERASAEAARVLRPGGRLAAVWNQLDV
+TVPWVHRLTRIMHAGDVHAAAPERRRFAAPFGPEEHARWSWSLTTTPAGLHALMASRSYW
+LRAREGTRARMTANLDWYLHEHLGHAAGEELTLPYVTVAWRAPAPAR
+>GCF_023573625.1_00655
+MSAPEPGASPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAVVDRVLAGIADGA
+EVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADAVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000614.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..629b4c0b5995a1e1eeae4aa8b0a4e0d1c42c33cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000614.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00687
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_003691675.1_00424
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_005280335.1_02270
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_020097155.1_02137
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>GCF_023573625.1_00657
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b4669548bbf9651f5f041db90f793741b4adae3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000615.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00688
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>GCF_003691675.1_00425
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>GCF_005280335.1_02269
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA
+>GCF_020097155.1_02136
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA
+>GCF_023573625.1_00658
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52a5d2bb661076793c5d0a6fba61bb1948981a45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000617.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00690
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_003691675.1_00427
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_005280335.1_02265
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG
+>GCF_020097155.1_02133
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD
+>GCF_023573625.1_00660
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d0e1464f2102add8649c725820f4cbc8b45a8ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000620.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00694
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_003691675.1_00431
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_005280335.1_02260
+MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD
+EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>GCF_020097155.1_00464
+MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL
+IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP
+LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE
+AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA
+IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI
+PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP
+GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH
+LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL
+EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ
+DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA
+>GCF_023573625.1_00664
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA
+GTWVNRKLRRRPMIIPVVLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000625.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8818dd712feca4ffc3f7a1aa863442c8e833ee06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000625.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00700
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
+>GCF_003691675.1_00437
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
+>GCF_005280335.1_02254
+MRVSEFQRLMDEEFGPGRAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCELHDIPE
+ERRLGRDVPPKR
+>GCF_020097155.1_02126
+MTEFQRLMEDEFGPARAGLVADSLHLPGFDATASEALAAGADPKDVWRAVCDLHEIPAER
+RLGRDVPPTR
+>GCF_023573625.1_00670
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..567647fdd8250cf09c9b3aba978016acb43a0fcb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000627.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_00705
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS
+DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT
+RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR
+EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS
+KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR
+AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>GCF_003691675.1_00439
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD
+TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
+>GCF_005280335.1_02252
+MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS
+VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA
+AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED
+ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD
+RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA
+AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE
+E
+>GCF_020097155.1_02124
+MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA
+AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR
+GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA
+>GCF_023573625.1_00672
+MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA
+RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD
+IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV
+VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG
+LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE
+RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eb1c4fde87e18de2875f8b16ca24cc0989aeef6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000629.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00707
+MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV
+AEALAVVAGDAT
+>GCF_003691675.1_00441
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AEALAVVAGGAA
+>GCF_005280335.1_02250
+MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG
+VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT
+DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP
+RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS
+ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ
+ALAVVAGS
+>GCF_020097155.1_02122
+MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AAALAVVAGDAT
+>GCF_023573625.1_00674
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV
+AEALAVVAGDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000633.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a6852c37418ca3fd5689a8863cf46f9ff355f60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000633.fa
@@ -0,0 +1,54 @@
+>GCF_002008305.4_00714
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA
+AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAL
+>GCF_003691675.1_00445
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
+>GCF_005280335.1_02244
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR
+TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV
+VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI
+VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL
+EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK
+PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP
+DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF
+AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP
+DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS
+>GCF_020097155.1_02116
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA
+LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA
+GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL
+TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL
+LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR
+EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI
+GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV
+DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR
+LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA
+QEAASA
+>GCF_023573625.1_00678
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50ef63d82028171f3fe226d45bdd472aa90f1399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000634.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_00715
+MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>GCF_003691675.1_00446
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>GCF_005280335.1_02243
+MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR
+HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL
+PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK
+EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA
+ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT
+SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ
+DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD
+ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR
+FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA
+EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV
+AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA
+VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS
+>GCF_020097155.1_02115
+MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ
+AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV
+VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA
+WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV
+TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS
+VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD
+AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV
+APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP
+FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR
+RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR
+PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE
+RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH
+>GCF_023573625.1_00679
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000635.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f35df3ba92c5d7d9395047b9a15233956e1140e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000635.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00716
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRVTAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
+>GCF_003691675.1_00447
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRISAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
+>GCF_005280335.1_02242
+MATTDEQPAPLTDRQRRIVQTIRDAIAEHGYPPSMREIGDAAGLASLSSVTHQLGRLEQH
+GYIRRDPGRPRALEVLLDVDGTPLGEAAPPAAAAPSGLPAIPAWHTGAEDADTVPVPWVG
+RIAAGGPVLAEQQVEDVMAVPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQETAE
+NGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRAL
+>GCF_020097155.1_02114
+MATSPTPPPGGAQPLTDRQRRIVRTIRQAIAERGYPPSMREIGDAAGLASLSSVTHQLGQ
+LERFGYLRRDPGRPRALEVLRDEDGAAAVADAAPGAPEIPSWHTGASEDATVEVPWVGRI
+AAGGPILADQQVEDVMAVPRRLTGEGDLFMLRVVGDSMVDAAICDGDWVVVRRQETAENG
+DIVAALLDDEATVKTLRRRDGHTWLLPQNTAYEPILGDHATLMGRVVTVLRAL
+>GCF_023573625.1_00680
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPTAAPSSRVSAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQD
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..201431bad2b01695b5ae7af63066c2475f5417c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000636.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00717
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>GCF_003691675.1_00448
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>GCF_005280335.1_02241
+MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA
+VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI
+PATR
+>GCF_020097155.1_02113
+MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA
+TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL
+NGLEGRDPELGQELYVPPTR
+>GCF_023573625.1_00681
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48b30ff207b58b098cb82307bf6c3c29becfe854
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000637.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00718
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
+>GCF_003691675.1_00449
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT
+ALEEVLGETGHRS
+>GCF_005280335.1_02240
+MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR
+YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR
+ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE
+ALEAVLAEIGHRR
+>GCF_020097155.1_02112
+MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR
+YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY
+PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI
+YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR
+LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT
+GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD
+ALREIVEQDPAVVSAVDAD
+>GCF_023573625.1_00682
+MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR
+YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY
+PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV
+YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR
+LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR
+GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT
+ALAEVLGETGDRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..036aa540eb43aa8767bd0c3e6eb485e7783cbe86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000638.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00719
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>GCF_003691675.1_00450
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
+>GCF_005280335.1_02239
+MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMSGVPSTKGAL
+>GCF_020097155.1_02111
+MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRVHDVPSTKGAL
+>GCF_023573625.1_00683
+MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV
+RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP
+YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA
+FARALRAAVEDDPRMTGVPSTKGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85e7ed334e2cbeb0fb6fa908a1efc41df764c047
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000651.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00733
+MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>GCF_003691675.1_00464
+MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>GCF_005280335.1_02220
+MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV
+GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI
+RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA
+>GCF_020097155.1_02096
+MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA
+GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV
+RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS
+LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA
+>GCF_023573625.1_00697
+MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV
+GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000654.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..275a5317eabe53b00a3d5d3aa61391d076e6e788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000654.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00736
+MPRGAAHGAQAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
+>GCF_003691675.1_00467
+MPRGAVHAVPVPRGVHMGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
+>GCF_005280335.1_02194
+MTAGSGAAAAAPRRRRPRWRDDRGAAVAESTMVMTLVVLLFAALLQAGLVIHTRNVMIDA
+ASAGARYGALADRVPEDGVQRARELLAAGVPGQSGARIVAEPTSQDGVPVLRVTISSSLP
+GVGFLPGPIPVEVSGHAHRL
+>GCF_020097155.1_02093
+MEPAARPAVQGRPGPDRRAGDRGSVVAENAMVTALLVLLFAAVLQVGIIVHVRNVMIDAA
+SAGARYGALADRDPAEGAARARDVLSASVPGQSGAQVRSEPTTVGGVPVVRVTITSSLPG
+LGFLPGPVPIEVHGHAFRY
+>GCF_023573625.1_00700
+MPRGAAHDAPAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRNPEDGVQRARELLSTGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000656.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c5bba736e01a9e609f41fd902002e642e2d8f85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000656.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00738
+MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>GCF_003691675.1_00469
+MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>GCF_005280335.1_02192
+MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL
+GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD
+LLAAAGPFAGMLPLSVPIQATGDSRTSLSR
+>GCF_020097155.1_02091
+MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA
+DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA
+TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR
+>GCF_023573625.1_00702
+MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE
+ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000657.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..865b29eec9e56d5c9604bd12623626066dd03c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000657.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00740
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>GCF_003691675.1_00471
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>GCF_005280335.1_02189
+MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG
+EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI
+RWRAEQAKAAQED
+>GCF_020097155.1_02087
+MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS
+HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA
+EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI
+RWRAEQVKAAQED
+>GCF_023573625.1_00705
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000658.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb090371c7057cb36384c9812803b81a201120ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000658.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00741
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL
+>GCF_003691675.1_00472
+MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>GCF_005280335.1_02188
+MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA
+NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>GCF_020097155.1_02086
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>GCF_023573625.1_00706
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb3b09bb4c98e6670af4b38d9952b2639c47f509
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000660.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00743
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEGRA
+>GCF_003691675.1_00474
+MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>GCF_005280335.1_02186
+MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG
+WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRAAGEES
+>GCF_020097155.1_02084
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>GCF_023573625.1_00708
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c11932d6be962b25460c14f74b37d4370c26dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000661.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00744
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD
+>GCF_003691675.1_00475
+MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>GCF_005280335.1_02185
+MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL
+GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD
+>GCF_020097155.1_02083
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG
+DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>GCF_023573625.1_00709
+MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000663.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6408db76b9e57632fecf296cc57e285db3fab5fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000663.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00750
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGVVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEDSA
+>GCF_003691675.1_00480
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFMRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGEEAEGGA
+>GCF_005280335.1_02180
+MERPENPANRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLVDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRISVSGVDDVADASLSFSSIEGWRER
+GAIREFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHEDVLARLRPSGGGED
+>GCF_020097155.1_02075
+MDQTWNAARDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVSDADRAAEESI
+RSTLSRARARDLILGEEFGGNLSRTGRQWVVDPIDGTKNFVRGVPVWATLIALLIDGEPV
+VGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRIQVSDVDRVEDASLSFSSIEGWRERGAV
+REFLQLTSDVWRVRGFGDFWSYMLLAEGAVDVATEPELALHDMAALVPIVREAGGRFTSL
+DGEEGPFGGHALATNGLLHDEVLRRLTPGQD
+>GCF_023573625.1_00714
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2a776ccd7ce857c94aacaea2609d2e4e7b040fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000664.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00751
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>GCF_003691675.1_00481
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
+>GCF_005280335.1_02179
+MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL
+DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED
+SASSED
+>GCF_020097155.1_02074
+MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA
+PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV
+VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL
+DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR
+ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS
+ASSED
+>GCF_023573625.1_00715
+MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE
+RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV
+VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL
+DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER
+ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF
+DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED
+AASSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e58cf0fa5d6c50348cadc73a57bdd30a33b71e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000667.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00754
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG
+>GCF_003691675.1_00484
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
+>GCF_005280335.1_02176
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR
+>GCF_020097155.1_02071
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG
+>GCF_023573625.1_00718
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bffcdbe6004cc50affa4c6150ea88913ea7771c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000675.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00763
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>GCF_003691675.1_00493
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRTEGRTRGA
+>GCF_005280335.1_02167
+MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ
+QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF
+TEAEHTVEITGVCADCAATRAADAG
+>GCF_020097155.1_02062
+MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA
+LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE
+HGFSDPDHTVEITGVCAECRAAGRG
+>GCF_023573625.1_00727
+MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT
+LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE
+HGFTDADHTVEITGVCARCRAEGRTRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..978f3ebb6359856792af7e4b3ec70ec71b0bc2f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000690.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00781
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+ARETDPRLAR
+>GCF_003691675.1_00512
+MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA
+ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF
+AREADPRLAR
+>GCF_005280335.1_02149
+MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV
+RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF
+AREADPRLGR
+>GCF_020097155.1_02043
+MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP
+ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA
+AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE
+FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP
+AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL
+GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS
+VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV
+GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE
+IVRRETLDDLLRREVDPQNPA
+>GCF_023573625.1_00748
+MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP
+LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS
+GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR
+RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA
+ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV
+DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA
+PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV
+RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF
+AREADPRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa5df08b989fc410ba266ce50a0335a7fa9faca7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000693.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00784
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV
+AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>GCF_003691675.1_00515
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA
+TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA
+VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL
+VPCVAVDGVRVESLHHG
+>GCF_005280335.1_02146
+MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD
+VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV
+AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA
+AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL
+VPAVAADGVRVEPLHHG
+>GCF_020097155.1_02040
+MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA
+ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL
+PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI
+GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA
+SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL
+VPGVAAEGARVEPLHHG
+>GCF_023573625.1_00751
+MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA
+TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL
+PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV
+AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA
+VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL
+VPCVAVDGVRVESLHHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1125967474fdf0a6af96721a971ed6f4ac02cac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000696.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00788
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>GCF_003691675.1_00519
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>GCF_005280335.1_02143
+MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA
+GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR
+PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG
+DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA
+TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA
+EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL
+LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG
+ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG
+PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA
+PAPTPAPDGDDAADRAGREA
+>GCF_020097155.1_02036
+MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG
+RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA
+LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP
+STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA
+>GCF_023573625.1_00755
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA
+DPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000700.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9954b85a66cc60a2b976cc23324113bc26c9b919
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000700.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00792
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>GCF_003691675.1_00523
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>GCF_005280335.1_02139
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>GCF_020097155.1_02032
+MEISGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIN
+>GCF_023573625.1_00759
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000703.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34cd1695b2ca9a02b7688df722a62b10e1c8c159
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000703.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_00795
+MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI
+EQDQVAQEQITKQKR
+>GCF_003691675.1_00526
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
+>GCF_005280335.1_02136
+MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE
+NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID
+DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT
+AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA
+SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG
+DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL
+FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR
+QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG
+SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT
+KQKR
+>GCF_020097155.1_02029
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP
+SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG
+RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE
+REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI
+GQDQVVQEQITKQKR
+>GCF_023573625.1_00762
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000706.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c24d9e0a2a1c1d7fa36bb7e8c33693e662040c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000706.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00798
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQAHGGFFSVDHDRVVIAATSARLGDAAAA
+>GCF_003691675.1_00529
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQARGGFFSVDHDRVVIAATSARLGDAAAA
+>GCF_005280335.1_02133
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRAVDGGTV
+TAQAHGGFFSVDHDRVVIAATSARLGDAAAA
+>GCF_020097155.1_02026
+MAELNVEIVSEEKSIWTGTASAVSARTINGEIGILPGHTPMLAVLGDGEVVVRATDGGTI
+TAQANGGFFSVDDDRVVIAAATAQLGGAAA
+>GCF_023573625.1_00765
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQARGGFFSVDHDRVVIAATSARLGDAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000711.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc1f5797bc50668c3dcb5b61d4ae35a1d0fa75ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000711.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_00803
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRQLAAALF
+>GCF_003691675.1_00534
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
+>GCF_005280335.1_02127
+MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA
+ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA
+VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA
+ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED
+RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF
+>GCF_020097155.1_02020
+MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ
+LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP
+AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP
+VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA
+AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS
+EDPRVHASRRRLAAALY
+>GCF_023573625.1_00770
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000716.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95c2ac8ac7d2a3fd9b453c62ba4f59ad313db448
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000716.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00809
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>GCF_003691675.1_00541
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>GCF_005280335.1_02121
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR
+>GCF_020097155.1_02012
+MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV
+GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG
+FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD
+HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD
+>GCF_023573625.1_00778
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000717.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8444a67c3c99f8eeb7c8973326abb559b0788a01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000717.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00810
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>GCF_003691675.1_00542
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>GCF_005280335.1_02120
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED
+>GCF_020097155.1_02011
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED
+>GCF_023573625.1_00779
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25acb14d5cd9c4393fc21b8c68f76d690731337a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000718.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00811
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>GCF_003691675.1_00543
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>GCF_005280335.1_02119
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+>GCF_020097155.1_02010
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED
+>GCF_023573625.1_00780
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e065879a0fbcbe1a3f491271c03db780627b0937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000722.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00815
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
+>GCF_003691675.1_00547
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA
+>GCF_005280335.1_02115
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA
+>GCF_020097155.1_02006
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA
+>GCF_023573625.1_00784
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000729.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d3d5edec58b80a78e4c17819432cb10c7730b9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000729.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00822
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>GCF_003691675.1_00554
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>GCF_005280335.1_02108
+MPTPSSATTHDVVLIGGGIMSATLGVLLQRLEPTWSIALYENLDQAGLESSDPWNNAGTG
+HAALCELNYAPLGKDGTVDVTKALGINEQFWTSRQFWSSLVKDGTLQDPKTFINPLPHMS
+FVWGDAHADYLRTRYEAMSAQPLFAQMEHTEDPATIAEWAPLLIEGREDAGRIAASRVVG
+GTDVDFGSLTRQLVTAMAGAGADVRFGHKVTGLSRGTDGRWEVSVKNKAAGTEVVDRARF
+VFVGAGGGALSLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNRHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSIRPHNLTTMLDVAKDNMDLT
+KYLVAEVVKSQNKKVESLKEFYPEAEGGDWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HGDGSIGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGALKELIPSLGRTLNDDPALL
+AEVSASTDAALKLA
+>GCF_020097155.1_01999
+MWIPPDGVRRCTILALEHQEHIVSTPTSTTHDVVLIGGGIMSATLGVMLQKLEPSWSIAL
+YENLDQSGLESSDPWNNAGTGHAALCELNYSPLGKDGKVDTAKAKGINEQFWITRQFWSS
+LVKDGTLADPKNFINPLPHMSFVVGDAHADYLKTRYEAMSAEPLFADMEHTEDPDVIGEW
+APLLMDGRTGTERLAASRVPTGTDVDFGSLTRQLVTALAAGGADVRFGHKVTGLSRGTDG
+RWDVTVKNKAAGTEVRDRARFVFVGAGGGALGLLQNSGIPEIKGFGGFPVSGQFLRCTDE
+KVVNQHMAKVYGQAAVGAPPMSVPHLDTRFVNGKRSLLFGPYAGFSTNFLKSGSYLDLPL
+SIRPHNLPTMLNVAKDNMDLTKYLVTEVLKSNEKKVDTLHEFYPAADGSEWELITAGQRV
+QVMKKKGKLGGVLQFGTEVVSHADGSIAGLLGASPGASTAAPIMVKLLERCFPAKMAGWD
+AALKDMIPTLGRTLNDDPSLLAEVRSATDAALQLG
+>GCF_023573625.1_00791
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYETMSAQPLFAGMEHSEDPEQIRAWAPLLIEGRASGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGAEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000734.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ce86f34669b5db76f57c7bde5c06f5a192e8342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000734.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_00830
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRT
+HGPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEV
+DALAAQLTALTALCAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEVGAGH
+LAMVTLAPELPGALDAVGRLAGAGVVVAIGHTDASYETTRAAIEAGARMATHLHNACRPT
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDSMAAAGCGDGE
+FPLGPLRVRVHDGVARVVGADGAAGAIAGSTATVTGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLHHGTWVKAAAPAAAD
+>GCF_003691675.1_00562
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVTAVGAGDPPRT
+HGPVHELGDALLAPGCVDVHCHGGGGHAVESGPDAARAAAAAHARAGTTTVVASLVTDEV
+DALVAQLTALAPLRAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEAGAGS
+LAMVTLAPELPGALDAVGRLAEAGVLVAIGHTDASYEVTRAAIEAGARMATHLHNACRPA
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGD
+FSLGPLRARVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLRHGAWVEAAAPAAAD
+>GCF_005280335.1_02131
+MRPGGHARARRITPPLADHHVHGGAGVDLATSGAEDVRRWLAELRAAGASVVLGSLPALV
+PADLAAALERLRPLWEDGALAGVHLEGPFLSPARAGAQHPDALCAPDSAAGRRVRALLRA
+QPRGFVRTLTLAPELPGAREVAAELEAAGTVLCLGHTDAGPAEVAAALDWPRPRAAATPV
+ATHLFNGMRPFHHRDPGPVPTLLAAARRGRLRLELVADGAHVAPELMELILEDPDLAAQT
+CLVSDAIAATGAPCGTVHRLGPAVVHAAPDAPRLGEPAEDGQGSKATGPEDGGRAPLAGG
+RRTLVEAVTALLDADLDADAVLRAAVHVPRRSLPETPAPELEDGALVWDEGRPLVALPAA
+RA
+>GCF_020097155.1_02024
+MTASALLRTTAPWVGADPGATPVRVSAVWSAGPDGALLVWAGLAERVPQELWETAVDAPA
+LRLSPALTSHHVHGGAGVDLATSPAADVRSWLAAQRQAGVGAVVGSLPTLAEDALAAALD
+RLRPLWAEGLLAGVHLEGPFLSPARAGAHDPALLLTPPSPAGRRVRALIAAQPEGFVRTL
+TLAPELPGADALTRELTGTGVVVCPGHTDADGATTRAWLQTADDARAAATAAGLPAPTPV
+ATHLFNGMRGFHHRAPGPLPALLGAARAGRARLELIGDGVHVDDEVLTAILGDPGLAPAA
+CLVSDAVAATGATRGTAHRLGSLPIHAAQDGPRVGADEPTGPAEAALAGGAADLPEIVGR
+LLHSDLDPDAVLRAATHVPARTLGGSHAVPVGTPETTEHAAPGGDVLVWAPDGAVTVLRS
+QAAPGGRHHD
+>GCF_023573625.1_00799
+MPASVPHRPRAEQAPQAAASPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRTH
+GPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEVD
+ALAAQLTALTPLCAEGVLAGVHLEGPWLSPRHRGAHRAASLRAPEPEDVARLVEVGAGHL
+AMVTLAPELPGALDAVGRLAEAGVVVAIGHTDASYETTRAAIDAGARMATHLHNACRPTH
+HREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGEF
+PLGPLRVQVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPAD
+ALGLPDVGRLRVGSRADAVVFGPELEVRGVLRHGTWVKAAAPAVAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000735.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e7579f3012a094c97ab4b7109b0aa5629ba876b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000735.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_00831
+MSTTPRDARAAVPQVPTPASRPTESARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAVADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAERTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGDVKEIIPDLVAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_003691675.1_00563
+MSTTPRDARAAVPQVPTPASRPTETARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLVREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGTEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGYDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_005280335.1_02093
+MSTTPRDARAAVPPVPTPASRPEEQARPQERRPAVRPDTVEPRVPGEGNRVKPTLMTGSE
+GIIRALEELGVTDVFGLPGGAILPTYDPLMDSDQIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGSDAFQEADIVGITMPITKH
+SRLVTRPEDIPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRVDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDA
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPCARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLAAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRISALSGPEAAYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>GCF_020097155.1_01992
+MSTTPRATAPAASAGRDQRGPTRTETVEPRVPGPAAVVEPTVMNGAQGIIRSLEELGVED
+VFGLPGGAILPTYDPLMDSSRIRHILVRHEQGAGHAAQGYHLAGGRVGVAIATSGPGATN
+LVTAIADAHMDSQSVVFITGQVSSAAIGSDAFQEADIVGITIPITKHSRLVTRAEDIPAA
+LAEAFHIASTGRPGPVLVDVTKDAQQSEFEFSWPPRLDLPGYRPVLRGHPRQIREAARLI
+REARRPVLYVGGGVARGEAHEELRALAALTGAPVVTTLTARGVFPDSHPQHLGMPGMHGG
+VPAVAALQQADLLITLGARFDDRVTGHLPSFAPGAKVIHADVDPAEISKNRLADVPIVGS
+VKEIIPDLVAELGAGADLPDLAPWWATLERLRETYPLGFTAPDDGLMAPQQVISRISALS
+GPEAVYVAGVGQHQMWASQFVEYERPRQWLNSAGLGTMGFSVPAAMGAKVAQPQRTVWAI
+DGDGCFQMTNQELATCVINGIPIKVAVINNSSLGMVRQWQTLFYDQRYSNTDLNTGHGTA
+RIPDFVKLADAYGAAGLRCEREEDLDDVIRQALEIEDRPVVVDFVVSRDAMVWPMVPAGV
+SNDAIQIARGMTPDWDHED
+>GCF_023573625.1_00801
+MSTTPRDARAAVPQVPTPASRPTETARAQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000741.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40e4edc7005a5d1e8629bf738c64884cf3ea23e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000741.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00849
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH
+RLV
+>GCF_003691675.1_00571
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
+>GCF_005280335.1_02086
+MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG
+PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF
+LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE
+LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE
+LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS
+GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH
+RLV
+>GCF_020097155.1_01986
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT
+GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH
+RLV
+>GCF_023573625.1_00808
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000742.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..836d4f1d3814208cfc177757dcbf3257b4e953c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000742.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_00850
+MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT
+LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI
+VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG
+AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH
+>GCF_003691675.1_00572
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
+>GCF_005280335.1_02085
+MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML
+ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD
+RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG
+RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI
+FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG
+FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG
+SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV
+SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG
+GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV
+APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV
+VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA
+TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY
+VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH
+>GCF_020097155.1_01985
+MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR
+GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL
+FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL
+YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR
+GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT
+LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF
+KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI
+VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG
+AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR
+RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH
+>GCF_023573625.1_00809
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000743.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b88ef0c281b88b817f27713fc417befbe62fe804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000743.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_00851
+MVAPRTTPGGAPAAEASPARRTWQAARWWVRQLSGEGKYDAYVAHHRAHHPERAPMTERE
+FWRAEYARQEANPGSRCC
+>GCF_003691675.1_00573
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC
+>GCF_005280335.1_02084
+MAASGTCPTPTGGSAAEPAAARRAGDGTGPAAGSGLRAAWASARWWVRQLAGEGKYDAYL
+AHHRAQHPGVEPMSEREFWRDEYAKQEANPGSRCC
+>GCF_020097155.1_01984
+MAGIWASTRWWVRQLTGEGKYDAYLAHHRAHHPGEVPMTEREFWRDEYARQDANPGSRCC
+>GCF_023573625.1_00810
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000751.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfc21ae8350d67f030817e61bfeb84a963024df7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000751.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00864
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>GCF_003691675.1_00586
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>GCF_005280335.1_02071
+MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI
+DAYERARPSYKPTTLPARTAG
+>GCF_020097155.1_01965
+MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS
+AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV
+ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI
+AAYEAGRPSYKPTTLPARTAD
+>GCF_023573625.1_00823
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000754.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ed0a20f0a2b9acb76d35e5767232691821830f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000754.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00867
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>GCF_003691675.1_00589
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>GCF_005280335.1_02068
+MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL
+PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER
+GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG
+PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV
+HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA
+>GCF_020097155.1_01962
+MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV
+WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE
+GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT
+ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN
+SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA
+DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK
+SEGRHA
+>GCF_023573625.1_00826
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000757.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e451aaefb2ea011a6399b9d933d8896ebd0e76f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000757.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_00870
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRTGTLGETVAQ
+>GCF_003691675.1_00592
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAEQAAEGAQGPVAPGADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPAAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSGTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRAGTLGEAVAQ
+>GCF_005280335.1_02065
+MALLAVGIAAAVYVGGIARTIDQDTQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAE
+QAAEGAQGPVAPDRDEKADEQALDVLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQV
+MSIMRDMWVPIPGHGDHKVNAAYQYGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDA
+LGGVSVDNPAAFVSTGGIDFPAGTVQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAI
+VAAFLSRDTLSDPSRVQAAVEEFAPFLTLDDELGSSTLANLAWSLRDARDAPIVTSTVPS
+VGVGYTDTGEDVVWPDWAAIARLGEGIRTGTLGEAVAP
+>GCF_020097155.1_01959
+MSTAEPTATPRRRRRPLLIVLVALLVLLLAAGLTAALWLGGLGRTVDEGVQRFEGQALPE
+ESLRPAEPGSAAAPGSAADGRNASGVYSPSAPPPGTAPAGVDPATALAGPAGPAADEVAD
+GKAVDFLLVGEDSGVEGRDPNGRSDTLMWVHIPGDRSAVQVRSIMRDTWVPIPGHGDHKV
+NAAYQYGQIPLTVATVENMFQARVDHVVAVDMAGFQGLVDALGGITVDNPIAFTADDGHA
+YPAGAIQMDGATALVYARERYNLPRGDFDRVENQQRVVKAVFSKALSLDTLSDPGRVQQA
+VERFSPFLTLDSELHSGDLAALAWSMRNLRGSDIQTSTVPAAGVGYSADGQAVVWPDWAA
+IHEIGRQIRTSEAR
+>GCF_023573625.1_00829
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARIIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRTGTLGEAVAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000760.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0f25bef17f4bafd56c7272c4ee4dfcbd7463de9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000760.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00873
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>GCF_003691675.1_00595
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>GCF_005280335.1_02062
+MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC
+EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI
+LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL
+YLWQDER
+>GCF_020097155.1_01956
+MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC
+EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI
+LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL
+YFWQDEG
+>GCF_023573625.1_00832
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI
+LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL
+YLWQDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fb279b60c3841188528acf16285430a89c5c248
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000764.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00877
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_003691675.1_00599
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_005280335.1_02058
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>GCF_020097155.1_01952
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR
+>GCF_023573625.1_00836
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000765.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..623460b59b9f2674ccebb48f41e9bf7ce41dd946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000765.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00878
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_003691675.1_00600
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_005280335.1_02057
+MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>GCF_020097155.1_01951
+MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK
+GRKVADA
+>GCF_023573625.1_00837
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9b765500fa24aff91e3813bd3313d5e3561e3d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000769.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00882
+MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERVLRRVAGR
+>GCF_003691675.1_00604
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERLLRRVAGR
+>GCF_005280335.1_02053
+MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER
+ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG
+EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA
+>GCF_020097155.1_01947
+MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG
+EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR
+ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT
+LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA
+THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP
+SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA
+RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA
+>GCF_023573625.1_00841
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG
+EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000771.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa89f2fe9f7117b64a3ae5f3eed5364018a6d1a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000771.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_00895
+MSADPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEILERKQSELVRERIAWSGGERPTGITAL
+>GCF_003691675.1_00617
+MSAEPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEMLERKRSELVRERIAWTGGERPTGITAL
+>GCF_005280335.1_02042
+MSGSRPLDPAVVLDEAGMTYTVRSSDTGARRAGIGGMLRGVRGVRTDQVQALAPLSLIVD
+RGESVGIIGTNGSGKSTLMKLITGEIHPTTGRVYATSTPVMLGVNAALVRQISGEDNIRL
+GCLAMGMTTAEAAEKRDDVVRLAGLDDQALQLPLKAYSSGMASRLQFAIATSVDPDILLI
+DEALNTGDAQFRARTRARIDELRARAGCVFLVSHSLTTLKQMCSRVIWIEQGILTMDGNP
+EVVTGNYARYTRHRSNGADEVAERLLAEARAGVKRVAVRWAGGQRPSGVIAD
+>GCF_020097155.1_01940
+MTDTTVDYALVLDRVSMTYRVPSSAADSVAALPAWRRGLARALRQPPRVPVHALHEMTLG
+LEQGRTLGLVGRNGSGKSTLSQIIAGKLAPSTGRVLATATPMMLGVNAALVPAMSGRQNI
+VLGCLALGMAKDEVMAKTPEIAASTGLGEAIDLPIETYSSGMSARLRFAIATSRDPEVLV
+IDEALNVGDSQFRARAKERMQELKRKAGAVVLVSHDNKTILDSSNKVLWLDKGRPVMEGS
+PQRVMDRYEQYNEMLAAQKVDEARAFVEDLRTTYRPRVVLPATDMHLPSVQEVEFSPRHA
+L
+>GCF_023573625.1_00846
+MPNLTGLDNIRIGLLAMGLTPAEVHDRIPQVAELADIGKSIRMPMRTYSSGMRARLRFAI
+SVASQPDIIMIDEALATGDDAFRERSNQAMRDLIARSGTGFLVNHSAGVIREMCTRVVWM
+DEGAIIEDGDTLDVMQHYSYFMSALRKHGEEKALEARARYETTEAERIVALKGTTGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000775.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b86120dd7746a999c1c65939e9154ec2a2366f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000775.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00902
+MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG
+STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG
+KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL
+REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>GCF_003691675.1_00621
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD
+>GCF_005280335.1_02040
+MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG
+STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG
+KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL
+REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>GCF_020097155.1_01938
+MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE
+ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA
+LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV
+AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR
+AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN
+LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG
+GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA
+>GCF_023573625.1_00850
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000784.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9231df38e1afb199eb0671bb70b07428f6bc828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000784.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_00911
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>GCF_003691675.1_00630
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>GCF_005280335.1_02031
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS
+>GCF_020097155.1_01929
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP
+>GCF_023573625.1_00859
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000785.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aec259a3a5ad2639051fa064395ad9f5ff854b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000785.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00912
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>GCF_003691675.1_00631
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>GCF_005280335.1_02030
+MTGSERAPRAGARTAVRAGLDVEAGLAAPFLAAGGTDRVLVAGMDEVGRGALAGPVVVGV
+CAAWLPAEGEIPAVRDSKALTDRRRRALVPEIRAWAAAVALGEANPAEIDALGISAALGL
+AGRRAWAAVCAAAGQEPVALVLDGRDDWLTRSDPDAGPAPAPRPVPPVPTMLVKAEDRCA
+TVAAASIAAKVARDDTMIALHADHPAYGWAGNKGYGAAAHRAAILDHGAGEHHRRSWSLG
+LPAAPADEPPTLFD
+>GCF_020097155.1_01928
+MSPRPPVVRAGLDVEASLAEAAIGPGASALVAGMDEVGRGALAGPVTVGVCAARVPALGV
+VPAVRDSKALTDRRRRALASEIEAWAAGVVLGEASPAEIDRLGITRALALAGCRAWAGLL
+AALGEEPVALILDGSDDWLRHARGGGMDDVVTGPVPPAPHMMVKAEDRCATVAAASIAAK
+VGRDDAMIALSAAHPAYGWAGNKGYGAAAHRSALVELGVTEHHRRSWNLGVPGTGAEPDV
+LF
+>GCF_023573625.1_00860
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000786.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..623114df910d10921306172d894b8d481baeb391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000786.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00913
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>GCF_003691675.1_00632
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>GCF_005280335.1_02029
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD
+>GCF_020097155.1_01927
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT
+LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR
+>GCF_023573625.1_00861
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b957dc8716a8005cd1dec76e001054af276a5ecc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000788.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00915
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>GCF_003691675.1_00634
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>GCF_005280335.1_02027
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET
+>GCF_020097155.1_01925
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR
+>GCF_023573625.1_00863
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8526bf3b33519835c74b709ffb4e88dd56f321df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000791.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00918
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>GCF_003691675.1_00637
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>GCF_005280335.1_02023
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG
+>GCF_020097155.1_01922
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG
+>GCF_023573625.1_00866
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43832429dfe92a33ef69d3a072cd60709542906d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000792.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00919
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_003691675.1_00638
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_005280335.1_02022
+MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA
+DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD
+ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS
+GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH
+VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV
+>GCF_020097155.1_01921
+MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS
+EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD
+ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT
+GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV
+VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH
+VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH
+GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV
+>GCF_023573625.1_00867
+MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS
+EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD
+TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS
+GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV
+IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH
+VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH
+GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74b905d8acd1f3f8ca2590d7bb29bf610cdaa0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000793.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00920
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>GCF_003691675.1_00639
+MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
+>GCF_005280335.1_02021
+MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDNAQA
+>GCF_020097155.1_01920
+MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDQAQA
+>GCF_023573625.1_00868
+MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD
+EEVKNLKTVQDAVDFIDGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67c392bc90f69483ca26f04b160eb883bc9e88ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000794.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00921
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_003691675.1_00640
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_005280335.1_02020
+MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE
+TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS
+AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD
+IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_020097155.1_01919
+MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE
+TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS
+AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS
+DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG
+PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP
+>GCF_023573625.1_00869
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..772859f69f37f2d67a38e9286204a69f7042a8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000798.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00925
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>GCF_003691675.1_00644
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
+>GCF_005280335.1_02016
+MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA
+DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL
+HATTGAGVSEDWAAQRLVQKRGG
+>GCF_020097155.1_01915
+METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA
+DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL
+HVTTGAGGSADWAAVRLEKRGG
+>GCF_023573625.1_00873
+MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA
+DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL
+HATTGAGASEDWAAQKLVQKRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a61fd8f847e4235dc8bf3e31af2d5468141fe6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000799.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00926
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
+>GCF_003691675.1_00645
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR
+>GCF_005280335.1_02015
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR
+>GCF_020097155.1_01914
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR
+>GCF_023573625.1_00874
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000800.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..543225852474bc88fb25be5d29c1d182af0f9a71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000800.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_00928
+MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
+>GCF_003691675.1_00647
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR
+>GCF_005280335.1_02012
+MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF
+SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG
+ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA
+LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV
+DLPLPAPTPATGPVPVVAGPAPGEEPR
+>GCF_020097155.1_01911
+MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA
+PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY
+SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA
+LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE
+RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR
+>GCF_023573625.1_00876
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba853a09515550a445d82ba6557066ece743d09b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000804.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00932
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_003691675.1_00651
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_005280335.1_02008
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDEQYRRFMNQVP
+LFEKMLADDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>GCF_020097155.1_01904
+MELLQPDAPRENLREFIDNLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYEERLSR
+EEYEIEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARTVA
+LSKPTERELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDHQYDLFMRQVP
+VFEKMLVEDGVHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIKSNDKKRARLNAMRYFLSRFEYEGKDHDVVGVPDPLIVQRGRD
+AVGD
+>GCF_023573625.1_00881
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000806.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78c07d024d8ad4c8e11afb386434d0ca785bc55f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000806.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00934
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK
+PLVDPAEYVDPALWI
+>GCF_003691675.1_00653
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
+>GCF_005280335.1_02005
+MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS
+QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK
+PLVDPAEYVDPAMWI
+>GCF_020097155.1_01902
+MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS
+QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK
+PLVDPAEYVDPAMWI
+>GCF_023573625.1_00883
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000807.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5663761437e0128af80ca4e2e896fcb660eeb7c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000807.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00935
+MARILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELSPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANVQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>GCF_003691675.1_00654
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>GCF_005280335.1_02004
+MAHILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEASG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQQIVASTPNSIWAQQFANQANVQAHYTGTGPEIWDATEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTELYDD
+VYAASLEESIETSRTLATQEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>GCF_020097155.1_01901
+MAKILDNITQAVGGTPLVRLNSLTEGLPGDVAVKVEFYNPANSVKDRIGVAIVDAAEKSG
+QLTPGGTIVEGTSGNTGIALAMVGAARGYKVILTMPETMSAERRVMLRAFGAEIVLTPGA
+DGMRGAVERAQQIVRDTPNSIWAQQFANEANVRAHYTTTGPEIWDATGGAVDTFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPSDSPILSGGQAGPHKIQGIGANFVPEILDTELYDE
+VYAATFEESIATSRALGAREGILGGISTGAIVSAALKEAAKPESEGKLIVAVVCDFGERY
+ISTALFEDVRG
+>GCF_023573625.1_00884
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000809.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81c6aa0929c981ffab555d8aa243ec0536be4e65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000809.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00937
+MAGMTVSRPAVPASPEHALAPPTLGQVLEVVEGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAKGRLLHTLIEHRIALL
+AAHTNADAVVGGVSDVLARAVGVTGALSPLTASAAGTGAEGIGRVGDLPEETDLAAFARA
+VHAALPATAGGVRVAGGPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASEA
+RETAASGDGRPALVDVSHWASESLWLEHGARALEAALVERGLGVTTLFSDHRSDPWDFLV
+GGERADEGSRA
+>GCF_003691675.1_00656
+MAGMTVSRPTVPASPEHALAPPTLGQVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRVAL
+LAAHTNADAVVGGVSDVLARAVGVIGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAAPGEGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>GCF_005280335.1_02002
+MDRMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRDLAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+FAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+VVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAVSGDGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>GCF_020097155.1_01899
+MTVPDHPLQGAGEGACGRAVATDAVASDVPRLSDVLAAVERLWPARLAESWDAVGPVVGR
+AGRPVRHVLWAVDPVQDVVDEAVRIGADLVVTHHPLMLRGTTSVAAVGHGGAFKGEVVHT
+LIEHGIALVAAHTNADSAVGGVSDAIAWRLGLTDVSPLQPSAGGSGAEGIGRVGELPAPV
+PLVEFARTVAALLPATAGGVRVAGDADLPVRRVAVCGGAGDSLFDAVRAADADVYVTSDL
+RHHPASEAREAARHAGGRPALVDTAHFAGEWLWLADGAAALAEELARGGHRARMTVSELV
+TDPWDLHLPSGLAERTTS
+>GCF_023573625.1_00886
+MAGMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+LAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGVEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+AQETAVSGGGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..302286f0865712e5ec6f6aa89288330e1b8d8052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000815.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00943
+MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>GCF_003691675.1_00662
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>GCF_005280335.1_01995
+MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF
+TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA
+GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT
+WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA
+>GCF_020097155.1_01892
+MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF
+TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT
+GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT
+WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR
+>GCF_023573625.1_00893
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHEEIEDHEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000816.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1116464ee81cc785f27b588423aae4345feac52b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000816.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00947
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFRRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>GCF_003691675.1_00666
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>GCF_005280335.1_01990
+MSVVKINAITVPEGAGPELEKRFAVRKHAVDAEPGFEGFQLLRPTAGEDRYFVVTTWATE
+EDFQNWKGGRMPAAHAAESEGRPAPVATGAELLEFEVVDLD
+>GCF_020097155.1_01891
+MSVVKINAISVPEGAGPELEKRFAVRKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHADEQGGRPTPVATGADLLELEVVDLG
+>GCF_023573625.1_00895
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFKGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000820.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c8d3514a4c947da01c3f39f44b846a2903529f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000820.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_00960
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY
+PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>GCF_003691675.1_00673
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>GCF_005280335.1_01928
+MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV
+AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV
+TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS
+SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN
+VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA
+STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL
+TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV
+LRHPDRAVSPTCTQYLQHR
+>GCF_020097155.1_01879
+MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA
+KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII
+MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV
+WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT
+SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL
+LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR
+VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE
+AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER
+VWSQGDVVVLHHPTRPVSATCTDYLRHR
+>GCF_023573625.1_00906
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3944ef74422c0ffc316463f56d13195b3000bca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000821.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00962
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA
+GVA
+>GCF_003691675.1_00675
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG
+VA
+>GCF_005280335.1_01926
+MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ
+LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA
+ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS
+SEEGDEADEADDDAHGVRALCGGVSAA
+>GCF_020097155.1_01877
+MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR
+ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA
+>GCF_023573625.1_00908
+MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ
+LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA
+AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG
+VA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000823.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdb1d6fbdf1ee25ea9d0401485effb007d96a759
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000823.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_00964
+MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQALAAASRTVPAARPAHSL
+HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV
+AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVTPAIYVDPAAETENRNMVW
+MKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPGMSAASLDHAMWFHRPARV
+DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMVRLPEGAAARRARVRGAAQR
+MAMRTVLRRSWRR
+>GCF_003691675.1_00677
+MPQRHPRPRPGRAPARPASAPKDPTDVLRGILELTPAAPDPVTGQVRFTGTTPRQTHGRV
+FGGQVLAQALAAASRTVPAARPAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA
+SQNEKAILALTCSFQEPAGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSR
+PFDIRHVTPAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQH
+GVAWIQPGMSAASLDHAMWFHRPARVDQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVAT
+VAQEGMVRLPEGAAARRARVRGAAQRMAMRTVLRRSWRR
+>GCF_005280335.1_01923
+MPQRHPAPRPGRAPARPASAPKDPTDMLRGILELNRADADPLTGQPRFTGTTPRQAHGRV
+FGGQVLAQALAAASRTISADRPVHSIHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA
+TQNEKAILALTCSFQEPAEAALDHQVAMPEGVPAPEDLPSTADVLGRINHPIAQEWAWAR
+PFDIRHVTPAIYVDPAPEAENRNMVWMKTFTPLADDPALHVAALTYASDYTLLEPVLRQH
+GVAWIQPGMSVASLDHAMWFHRPARADEWLLYVQHSPSAQGARGLGTGSVFTRDGTLVAT
+VAQEGMIRMPEGAAARRARLQGAAQRFALRTVLRRSWRR
+>GCF_020097155.1_01872
+MSPKPPARPATAPQDPTEALRGLLDLTDAGPDPVTGEPRFEGRTPAQVGPRVFGGQVLGQ
+ALAAASRTVPTARSAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAIL
+ALTCSFQEPTGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVT
+PAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPG
+MSVASLDHAMWFHRPARVDEWLLYVQDSPTAQGARGLGRGHVFTRDGELVATVAQEGMIR
+LPEGHAATAAKAKNVVQRAAMKTVLRRTWRG
+>GCF_023573625.1_00910
+MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQSLAAASRTVPGARPAHSL
+HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV
+AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWARPFDIRHVTPALYVDPAPETENRNMVW
+MKTFTPLADDPALHRAALTYASDYTLLEPILRQHGVAWIQPGMSVASLDHAMWFHRPARV
+DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMIRLPEGAAARRARVRGAAQR
+MALRTVLRRSWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a24b61d54ac312ee63671c65353551286ec1b0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000825.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_00967
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA
+>GCF_003691675.1_00680
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
+>GCF_005280335.1_01920
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA
+>GCF_020097155.1_01868
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA
+>GCF_023573625.1_00913
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000828.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..396495ed7edcd453289240accea5fa665012e132
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000828.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_00976
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA
+AEQA
+>GCF_003691675.1_00690
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGADEAAEQA
+>GCF_005280335.1_01914
+MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG
+REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV
+KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP
+VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK
+AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE
+ASEQA
+>GCF_020097155.1_01861
+MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG
+REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE
+LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ
+VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE
+RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP
+ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG
+ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV
+DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA
+>GCF_023573625.1_00919
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000829.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..feda3c6c52ab801e22705e0c34acce6d9c3cf777
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000829.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00977
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
+>GCF_003691675.1_00691
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
+>GCF_005280335.1_01913
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAKEA
+LEYGFIDHIADRAASVTGGGGVQG
+>GCF_020097155.1_01860
+MTDLTPRMTSVEPTQREDYLYNQLLKNRIIWLGSDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGAPGKRYATPHARI
+LMHQPSGGIGGTESDIRIQAQLILHMKQIMAELTAAQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDRIAQSAASVTGGGGVEG
+>GCF_023573625.1_00920
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07f84bcbae4f8670b683c00a68276457a6101cb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000830.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00978
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>GCF_003691675.1_00692
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>GCF_005280335.1_01912
+MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN
+RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG
+>GCF_020097155.1_01859
+MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN
+RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA
+>GCF_023573625.1_00921
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5852ded3ea96fd98609d566cdd1f61d9312f7760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000831.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_00979
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>GCF_003691675.1_00693
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>GCF_005280335.1_01911
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV
+LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE
+ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP
+AEVERRRRGRSA
+>GCF_020097155.1_01858
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE
+LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE
+ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP
+AEVERKRRRRTA
+>GCF_023573625.1_00922
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd019530698c1463fc4755ff66314aee73aa62bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000832.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_00980
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>GCF_003691675.1_00694
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
+>GCF_005280335.1_01910
+MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR
+STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI
+LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG
+AVALAEYPYFYEIKRARTTDPQFD
+>GCF_020097155.1_01857
+MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR
+HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI
+LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA
+AVRLAQFPYFYEIKRARTTDPQFD
+>GCF_023573625.1_00923
+MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL
+ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD
+ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD
+GAVALADFPYFYEIKRARTTDPQFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000846.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8efff801871a92751e7b114d3d5e333e09820689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000846.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00997
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>GCF_003691675.1_00711
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>GCF_005280335.1_01893
+MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP
+FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN
+LVHGSDSSLSAERELGIWFG
+>GCF_020097155.1_01839
+MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP
+FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN
+LVHGSDSTLSAERELAIWFA
+>GCF_023573625.1_00940
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892b7b1e75ca2685e277bc548793b2c82fe26c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000850.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01001
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_003691675.1_00715
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_005280335.1_01889
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>GCF_020097155.1_01817
+MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF
+ALSAGTVSFGQRRGRKVVDIVAAGE
+>GCF_023573625.1_00944
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000851.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9d511acaa54a24c6219cdd94998f8305fca1ae8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000851.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01002
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>GCF_003691675.1_00716
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>GCF_005280335.1_01888
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGNGGNGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHRAGKHGESLVIPVPDGTVVKDEQGNIVADLVGEGASYTAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAAIS
+AARPKIADYPFTTLVPNLGVVQAGEVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGTLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLVALNKTDLP
+DGAAMAEMVRAELEGRGLRVFDISALARDGLEALKYAMAGLVTEARERVPEPEPAAPVEV
+PRRHRRKGEHAEFTVRREERNLEPLFRIRGEKPERWVAQTDFQNDEAVGYLADRLQRVGV
+EDALFKAGATPGDAVVIGDDASGVLFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDQRRAARAATRAEMEAERRSGLWTETYDRED
+>GCF_020097155.1_01816
+MAAFVDRVVLHLTAGNGGHGCVSVKREKFKPLGGPDGGNGGNGGDITLVVDHQTTTLLNY
+HHAPHRSADNGQPGMGDHRAGRHGEDVVLPVPAGTVVKDADGNILADLVGEGASFVAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGEERELILEVKSVADIALVGYPSAGKSSLIAAIS
+AARPKVADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGKGLGLEFLRHVERCAAL
+VHVLDCATLDPERDPLSDFEAIEAELEAYAVEPVFSQGGAGVVPLNERPRLVALNKTDLP
+DGREMADLVRAQLEERGLRVFDISALAHDGLESLKFAMAGLVEEARAREPEPEEAPVVEV
+PRRRRRGDQADFTVRREERNLEPLFRIRGDKPEKWVAQTDFQNDEAIGYLADRLQRAGVE
+DALFKAGARPGDAVVIGDDATGVVFDWEPTLSAGAELLAGPRGSDLRLEERTRATRAEKR
+AEQDQRRAARAATRAEMEAERRSGLWTGDPVEEEELD
+>GCF_023573625.1_00945
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000855.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba04bc9f12a9123f66edf44ba6ee6991f264eb77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000855.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01006
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>GCF_003691675.1_00720
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>GCF_005280335.1_01884
+MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC
+RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP
+>GCF_020097155.1_01812
+MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK
+SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT
+GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR
+VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP
+>GCF_023573625.1_00949
+MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000856.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33f92713b47f9ce5af5a882adaf248b9bfa934d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000856.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01007
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>GCF_003691675.1_00721
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>GCF_005280335.1_01883
+MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA
+EEHTRPDAAGEGAADDAAPHAS
+>GCF_020097155.1_01810
+MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE
+EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP
+EEATRPDDALDAAAQD
+>GCF_023573625.1_00950
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAAAQDDDASASHAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0614f8b925927f4c9c8e52bda5843c410fbcfa12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000861.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01019
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA
+>GCF_003691675.1_00733
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR
+>GCF_005280335.1_01868
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ
+>GCF_020097155.1_01760
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD
+>GCF_023573625.1_00963
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d10d77b55247b1a9d7b87d57b5b4487a9b81bcd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000866.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01024
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>GCF_003691675.1_00739
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>GCF_005280335.1_01861
+MTVTVYTKPACVQCNATYRALDKKGIAYEIVDMSQDPAALERVRGLGFMQAPVVVTETDS
+WSGFRPDKIAELAEAAAASVA
+>GCF_020097155.1_01751
+MTVTVYTKPACVQCNATYRALDKKGIAYETVDMSQDPEALDRVRALGFMQAPVVITDTDS
+WSGFRPDKIAELAESAATQVA
+>GCF_023573625.1_00968
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000868.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40f66f896e605ee8c13406f9238e54ae3f64fd84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000868.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_01026
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>GCF_003691675.1_00741
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>GCF_005280335.1_01859
+MTLTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVQRVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLTYSHI
+GQDISCNLGSMNIAKTMDSPDFGQSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGL
+GQMNLHGYLARERVHYGSEEGVDFTNMYFYAVLFHALRASNKIAIETGERFGGFEDSKYA
+SGEFFDKYTDQEWTPATERVAGLFSDAGITLPTQEDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>GCF_020097155.1_01749
+MTVTEADLIQQAKHMPEAWQDLGYHELNAMLNLYGSDGKIQFEADHAAARQYFLQHVNTN
+TVFFHDLEEKLEYLQEKHYYEPETFAQYAPEFVKATFDRAYKAKFRFPTFLGAFKFYTSY
+ALKTFDGKRYLERYEDRVAVVALHLAAGDEALATHLVDEMISGRFQPATPTFLNAGKAQR
+GELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNVREQGAPIKHIQNQSSGVL
+PVMKLLEDSFSYANQLGARQGAGAVYLHAHHPDIHRFLDTKRENADEKIRIKTLSLGVVI
+PDITFELAKRNEDMYLFSPYDVERVYGKAFSEISVTEKYYEMVDDARIKKTKINAREFFQ
+TLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHVGQD
+ISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGLGQM
+NLHGYLAREHVHYGSEEGVDFTNIYFYTVLFHALRASNLIAQETGQKFGGFEDSTYASGE
+FFAKYTEQEWTPATARVAELFETAGIDIPTQDDWRELQAKVMEHGLFNRNLQAVPPTGSI
+SYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDTYAA
+ATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGCVSC
+ML
+>GCF_023573625.1_00970
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKISARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEYGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..522ba948ddfb2f984e6a8e6e76cccf19fb15b465
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000870.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01031
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_003691675.1_00746
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL
+>GCF_005280335.1_01851
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_020097155.1_01741
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>GCF_023573625.1_00975
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000874.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62f42a3e4b3ff28bf3be252f02335402aa29934a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000874.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01037
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>GCF_003691675.1_00750
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLPEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>GCF_005280335.1_01847
+MPQKVRGVVARAKDAPVTLETIVIPDPGPGEAVVDVKTCGVCHTDLHYVQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAQELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETVALDEVNEAFETMKAGDVLRS
+VVVL
+>GCF_020097155.1_01737
+MSQKVRGVVAMAKDAPVSIETIVIPDPGPGEAVVDIKTCGVCHTDLHYVQGGIGDDYPYL
+LGHEATGVVSAIGEGVTHVEVGDTVILNWRAVCGECRACKKGEPKYCFNTHNASQKMTLE
+DGTELSPALGIGAFAEKTLVHAKQCTKVDGVDSTEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRALTGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>GCF_023573625.1_00979
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d648df4cdb73858cdf2d217a1cd986b25ce66271
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000878.fa
@@ -0,0 +1,109 @@
+>GCF_002008305.4_01045
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>GCF_003691675.1_00758
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>GCF_005280335.1_01844
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER
+>GCF_020097155.1_01731
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES
+>GCF_023573625.1_00986
+MSQAAAAGRTAAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDENAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALRRWEAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000880.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c04fb9eeefe7052f654cec52e6c90a17e2f092f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000880.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01047
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA
+>GCF_003691675.1_00760
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA
+>GCF_005280335.1_01841
+MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT
+CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA
+ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP
+>GCF_020097155.1_01729
+MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK
+GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD
+ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN
+FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA
+>GCF_023573625.1_00988
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000898.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77fdbdd77fe42a9c46de5b1a469fe63170f7397c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000898.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01082
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>GCF_003691675.1_00801
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>GCF_005280335.1_01815
+MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV
+WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA
+LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG
+AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA
+>GCF_020097155.1_01703
+MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW
+SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL
+PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI
+NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA
+AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP
+DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM
+LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG
+TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA
+GIVADSDADAETAETVTKATAPLRAVLTAAELRGA
+>GCF_023573625.1_01031
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70a919b2c4b28f836a50dd386ebb2ab72b09ff6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000900.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01084
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH
+>GCF_003691675.1_00803
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
+>GCF_005280335.1_01813
+MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF
+VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH
+>GCF_020097155.1_01701
+MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM
+AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH
+>GCF_023573625.1_01033
+MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL
+VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14a610ce264812154218d367c84b636aa6c0b694
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000903.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01087
+MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP
+VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGALARELAAGAVREG
+>GCF_003691675.1_00806
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
+>GCF_005280335.1_01810
+MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS
+VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALGEGGPQAVGALARELAAGAVREG
+>GCF_020097155.1_01698
+MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD
+VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD
+RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV
+ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA
+DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES
+>GCF_023573625.1_01036
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a3d972b8c42ca1812ff1fc778634cfc56651b48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000905.fa
@@ -0,0 +1,135 @@
+>GCF_002008305.4_01089
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>GCF_003691675.1_00808
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
+>GCF_005280335.1_01807
+MQHPSKTPHADPFRAFAAQPEAAGLYDPEQEKDACGLAAVATLRGPATHKIVQDALTALR
+ALEHRGAVGADEGTGDGAGIITQVPDALLRATVSFELPAAGEYAVGTAFLPQDEAARTAA
+QEAIAEAAVVEGLDLLGWRPVPTDESVLGPGSRAVVPVFEQLFLAVSAGEDVEAPGQSLD
+ARAWRLRRRAQRSGVYFPSLSSRTLVYKGMLSTAQVEPFYPDLSDERYVTRLAVVHSRFS
+TNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGELRHPLLGEVPEEMFPIVSASGS
+DSASFDEVAELIHLAGRPLSHAIMMMVPEAWENHTTMDEDRRAFYQYHSMLMEPWDGPAA
+IAFTDGVQLGSVLDRNGLRPARYWETRDGLVVLASEVGVLDIDPATVVRKGRVKPGRMFL
+LDTEQGRIIEDEEVKAEIAASAPWKDWVADSLRRIEDLPEREPVRYHGDSVRLRQRLFGY
+TDEEVRTIIEPMARHGAEPLGAMGTDTPIAALSPRPRLLFDYFTQNFAQVTNPPLDSIRE
+EQVTSMRTCIGPQASLLAAGKVTTDAVEIPFPVLDNEQLARIAAVRAEDGTRRALKVKGL
+YLVAGGAEEMRSRLKEICEQVSAAVQRGVQYVVLSDRDANAQWAPIPSLLLTSAVHHHLL
+ASASRTRTSLLVEAGDVREVHHVAVLIGYGASAVNPYLSMETAEELVRTGTLTGVTEQEA
+TRNLIHGLGKGVQKIMSKMGISTVASYCGAQTFEALGLSRSFVDRYFTGTRSPMDGVGLD
+VIAAESAARHATAFPVDGSSASTVGPRGTSGLPVGGEYKWRREGPPHLFNPETVFRLQHA
+TRERRYDIFKDYTRRVDEQSADLMTLRGLLGLATKGRERVPVSEVESVESIVKRFSTGAM
+SYGSISQEAHETLAVAMNRLGARSNSGEGGEDPERLLDPERNSRVKQIASGRFGVTSLYL
+STATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIEDLAQ
+LIHDLKRANPQARVHVKLVSETGVGTVAAGVTKAKADVVLISGHDGGTGASPLNSLKHAG
+TPWELGLSEAQQTLRLNGLRDRVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVVSGC
+IMMRVCHLDTCPVGVATQNPELRARFTGRPEFVVTFFEYIAQEVRELLAELGLRSLDEAI
+GRQDLLHKDAAIGHFKTEGLDLSGVLSDAGVPEEAPRRRLTEQDHRLQDQADQRWLDQVA
+DAVVTETPVTVTDRLVNTDRSVGTLLGHRVTAARLDDELPRDTIRIELTGEAGQSLGAFL
+PAGVSITLSGDANDYVGKGLSGGTVALRPAPEAPFAAEENMIAGNVVGYGATSGRLFLNG
+RVGERFLVRNSGAVAVVEGIGDHGLEYMTGGTALVLGNTGRNLAAGMSGGVGFFLDLDPA
+QLNPLAVKDDELLLGRPEGADRALIRELLEEHRAATGSDLAARLLAELDGPAESAEALWE
+RFTTVLPRRYAAVQEIRTDSRDAGTDPDGDAAWARILEVTRG
+>GCF_020097155.1_01696
+MTVAPLSAPTPRSGRSDDPFVRYAAFPEPQGLYDPARETENCGLAVIATLRGTPGHDIVE
+HALTALRALEHRGAVGADEGTGDGAGLLTQLPDELFRAVLDVELPPVGEYAAGIAFLPPL
+EGERAEAKAAVEELAQAEGLDVLAWRVVPTDPSALGTGSRAAMPSFEQVFLALAEGEDGT
+EPGQSLDVRAWRLRRRTQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDPRFTTRL
+GIVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEELF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAVMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARYWETRDGLVVLASEVGVVSIDPADVVRKGR
+VAPGRMFLVDTEQGRIVEDEEIKAEVAAAAPWEEWVSQNLLDLDALPEREHLRPSSESIQ
+QRQRIFGYTAEELRVLVGPMARDGAEPLGAMGTDTPIAVLSKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTGIGPQGNVLSAERVHTRQVDVPFPVIDNDQLARIQHLRDGDGGR
+LALKVTGTYRVAGGAEELRTRLKEICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTRTSLVVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEI
+EGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFAGTTS
+PLDGVGLEVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDGQAEELMTLRGLMRLRSEDRTPVPISEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLTTATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRSNPAARVHVKLVSESGVGTVAAGVAKAKADVVLISGHDGGTGASPLNSLK
+HAGTPWELGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVVAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRSRFTGKPEFVVNFFEFVAQEVRELLAELGFRTLD
+EAIGHRELLDVDAALHHWKTEGLDLSGILADPSVGRRAGAADAPMRRMVDQDHDLAAHID
+NRLIARLGDTLATGAPVVMDESVVNTDRSIGTMLGHHVTSTRLADELPADTITVRLTGEA
+GQSLGAFLPAGVTLRLDGDANDYVGKGLSGGRVVVRPDATAPFAAEDNTVAGNVIGYGAT
+SGELFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALVLGETGRNLAAGMSGGRA
+WILDLDRADLNPLAVREGDLLLSTPSAADRERIAALLRTHRAETGSAVAERLLADLDAGG
+DAAQGVWDRFTTILPRRYDLVLRTRAEAVAEGLDPDGEAVWDRLLEVTRG
+>GCF_023573625.1_01038
+MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ
+HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV
+DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT
+EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL
+GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF
+PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM
+EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR
+VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL
+QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN
+PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR
+LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT
+SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV
+SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS
+PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL
+QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST
+GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS
+LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED
+LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK
+HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV
+SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD
+EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID
+HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA
+GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT
+SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA
+WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG
+DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000907.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d48e8787b08fefa4020367fa4fceb36e09eab3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000907.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01091
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEESRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGTVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPLGFWPARSPL
+>GCF_003691675.1_00810
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAIMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGGDAAGGSSAASP
+QTREPVGFWPARSPL
+>GCF_005280335.1_01805
+MRHAKIIATFGPATASDETTRSIIRAGADVVRLNMSHGDHEVHAASFERVRRLSVEERRP
+VAIFADLQGPKIRLGRFADGPHHLETGDRFTITTRDVEGTAELVGTTHAGLPGDVRPGDT
+LLVDDGKVRLRAVEVTDTDVVTEVEVGGDVSDSKGINLPGVAVDVPALSEKDEEDLRWAL
+RTGVDMVALSFVRDAADIERVHAIMDEEERRIPVIAKIEKPQAVDNLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGRYPVETVQTMARIIESTETHGLEMIHPLGSRPRTRGGAITRAAVE
+VADQLDIPFLATFTESGDSARRLSRLRPRQPIYAFTHREHTHNILCLTWGVYPKMVSFQD
+STDKMTLQVEESLTSEGIAERGDLVVIAAGSPPGMVGSTNTLRVHRVGDDAGGGSSPARP
+VQKEPVGFWPARSPL
+>GCF_020097155.1_01694
+MRHAKIIATFGPATQTDETTRALIRAGADVVRLNMSHGDHEVHASSYERVRRLSVEEKRP
+VAIFADLQGPKIRLARFSDGPHELAVGDRFTITTREVTGSREIVGTTHKGLPGDVSVGDP
+LLVDDGKVRLRAVEVTDTDVVTEVVVPGKVSDNKGINLPGVAVNVPALSEKDEEDLRWAL
+ETGVDMVALSFVRDAADVTRVHEVMDEVGRRIPVIAKIEKPQAVDNLEAIVDAFDAIMVA
+RGDLGVELPLEDVPIVQKRAIELARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVQTVETMARIIESTETHGLDMIHPLGSRPRTRGGAITRAAVE
+VAGQLDIPFLATFTESGDTARRLSRLRPSQPIYAFTHEEHTHNILCLTWGVYPKMVPFAD
+STDKMTMQVEESLTSEGIAEQGDLVVIAAGSPPGKVGSTNTLRVHRVGDGVAADSSPVAP
+EDREPVGFWAAHSPM
+>GCF_023573625.1_01040
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSNNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPVGFWPARSPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000910.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86546ea76b24e1c64db4d6824679b0d389e425a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000910.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01095
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>GCF_003691675.1_00814
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>GCF_005280335.1_01800
+MTIAITVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGRGDV
+ETQADALPQAFVLTAIVIAFAITVLLLTLAVTGRDDDAVADGHEAPDPLEQSAADARFPR
+EELRAAAARLGREAEARDGGRA
+>GCF_020097155.1_01690
+MTVALTVGLLMAGAVYLFSKRELLRVILGMVLLGHAANLAILATGGTDRRALPFVDGGPA
+PAGAADPLPQAFVLTAIVISFAVTVLLLVLAVTGRADDAVAAPGERPDVREAAAADARFP
+LAERHAAARTLTGSLPAAPEAGATPEREERA
+>GCF_023573625.1_01044
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000912.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cbdbb78d07c76d9733058c03c1f330db86093ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000912.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01097
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>GCF_003691675.1_00816
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>GCF_005280335.1_01798
+MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD
+QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG
+LYADDADALRGEIHDMERRLLHAMRKQGVA
+>GCF_020097155.1_01688
+MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA
+RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD
+ALRAEIHDMEARMLHAMRRTGVAR
+>GCF_023573625.1_01046
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000913.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..283712fad20b0bed06b3d46cb41cd178dbaf757e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000913.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01098
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
+>GCF_003691675.1_00817
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
+>GCF_005280335.1_01797
+MPVDYDWSHLGIDVAVALLAVAALVSAYRIVKGPLDADRAVSGDLLTFSILGMLVLFGVR
+MDNPFTFDLVLVAAIVAFLSGMSLARALTRGKR
+>GCF_020097155.1_01687
+MSGLLQDYDWSLAGIDLAIALLLVAALVSAVRILRGPLDADRAVSGDLLTFSVLGMVVMF
+GVRAQNPFTFDLVLVAAIVAFLSGMSLARALTRGKR
+>GCF_023573625.1_01047
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ba783b38fa6f92827496d023d612ae88f02180f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000915.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01100
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>GCF_003691675.1_00819
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>GCF_005280335.1_01795
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG
+>GCF_020097155.1_01685
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR
+>GCF_023573625.1_01049
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000919.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bfbe7a5d8cffb8bfe1a6a5f45a07dfda976cc2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000919.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01105
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>GCF_003691675.1_00824
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>GCF_005280335.1_01789
+MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA
+RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG
+GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD
+AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD
+>GCF_020097155.1_01680
+MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR
+RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV
+VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT
+GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA
+>GCF_023573625.1_01054
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000920.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7714943e57810f448b55d042bac8393bb362f8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000920.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01107
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>GCF_003691675.1_00826
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>GCF_005280335.1_01786
+MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV
+QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA
+DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD
+>GCF_020097155.1_01678
+MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA
+VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV
+VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV
+ADVVIVNDGDLDRLREITRRVWEGMAA
+>GCF_023573625.1_01056
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000923.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3764bb03258168d6aad9e53513a35370dc1f5630
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000923.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01110
+MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG
+GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA
+LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>GCF_003691675.1_00829
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>GCF_005280335.1_01782
+MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG
+GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA
+LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME
+RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA
+LVWVGLGAPALS
+>GCF_020097155.1_01675
+MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL
+ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET
+ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ
+AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL
+AGG
+>GCF_023573625.1_01059
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000930.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bafaa6423bd50a35513e44d72273c9f5e20db74f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000930.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01121
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFHSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIEMADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVSIGEAMTH
+>GCF_003691675.1_00840
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAVV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPEVRSALAATAARRLMVLNLRTGDQETTGLAHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
+>GCF_005280335.1_01772
+MTSPLTGQLPLPPGVGTAVRGPAGGMARPAIRVTALGGGHGLSASLTALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVDAEEAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGG
+LRTRRVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALAAIELADWVVLGPGSLYTSVLP
+HLLMPEVCQALDATAARRLMVLNLRTGDQETTGLTHADHLRVLHSHAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTD
+>GCF_020097155.1_01665
+MTGPVTGPSTSSLPLPPAAARGAWATTSGTVRPQVRVTALGGGHGLSASLAALRLVAGHL
+TAVVTVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVPE
+AEATLDGHALGNLLIVALWELIGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDLLAED
+DAGRLVRRHVEGQVALAQAAHDGRVVDVRLSPADAPATPEALAAIELADWVVIGPGSLYT
+SVLPHLLMPEVRGALEVTTARRIFVLNIDTGTQETTGMTHADHLKVLREHAPGLQLDVVI
+ADADAVADRAAVVQEARRLGARVAFSRVAHAANRLAHDPLRLAVAIDEAMSS
+>GCF_023573625.1_01071
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eb314b6a76bcec3f7738715e881f4f808241b85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000932.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01123
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>GCF_003691675.1_00842
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>GCF_005280335.1_01770
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA
+>GCF_020097155.1_01663
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA
+>GCF_023573625.1_01073
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000934.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55d4f32c0ba4862fc4d6625de9242d2e80c8c936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000934.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01125
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
+>GCF_003691675.1_00844
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALADEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
+>GCF_005280335.1_01767
+MPAQTLNDLLEAGVAGRTVLIRSDLNVPLDGETVTDDGRIRASLPAIRQLADAGARVIVM
+AHLGRPKGEPDPKYSLRPVAARMGELLGADVALAEDVTGPSARAAAEALADGDVLLLENV
+RFDARETSKDDAERAELAAEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAGELEVLTRLTQSPERPYAVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVRAYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLPVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAETVFWNGPMGVFEFEAFAEGTRAVAQALTEATAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALSGEGEA
+>GCF_020097155.1_01661
+MTAQTLTDLLEAGVAGRTVLIRSDLNVPLDGQTVTDGGRIRASAPAIKDLADAGARVVVM
+AHLGRPQGEPDPQYSLAPVARRLGEVLGADVQLASDVTGEDARAKAAALQDGQVLLVENV
+RFDARETSKDAAERGELAREMADLAGEDGAYVGDAFGAVHRAHASVADIAGLLPAYQGPL
+VAAELQVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLMEKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLETVRGYLERSGKDGAAEIVLPTDIVMASAFAKDAEHEVLPVDALTTG
+AHGADALGLDIGPGSAAAFGERIRGARTVFWNGPMGVFEFPAFAEGTRAVAQALTEATQA
+GGLSVVGGGDSAAAVRSLGFTDEQFGHISTGGGASLEYLEGKELPGVSALSGTDT
+>GCF_023573625.1_01075
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGADVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000937.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b898c70f95a142c834e2650a7ec6ffb1d2ebb6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000937.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01128
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>GCF_003691675.1_00847
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>GCF_005280335.1_01764
+MKIRMHDTTTSQVAKRITQLREKGGVVALGRVLTLVISTDDAGIEAAVEAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVA
+WWPGVPPAVPSETALGRLAHRRITDTASAARAEPALWTLRQGHRDGDTDLAWTRLTLWRI
+QVAGIFDTLDVAALRSVTVDGAPDSPSTMLLAAWLTLALKVPVTIAHSKAGHGIRAVRLR
+CQDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTDQDCLAEELRRLDPDEVFGAVLHRGL
+PRTDLSPVQASER
+>GCF_020097155.1_01658
+MKIRMHDTTTSQVAKRLTALRESAGVSALGRVLTLVIVTDDAGIEAALGAANAASLEHPC
+RIVVLALGDPLAPTRLDAEIRVGGDAGASDVVVLWCQGEDAVADEPLVSGLLLPDAPIVV
+WWPGEPPAEPATTALGRLAHRRITDSATCRDAKETLQRLAAGLHDGDTDLAWTRLTLWRS
+QVAAILDNLDLADVRSVTVDGAPDSPSTLLLAAWLTWGLDRPVTIAHSKAGHGIRAVRLR
+GPEGDVVLSRSQSEVARLYQQGRPVQRISLPRRSDQDCLAEELRRLDPDEVYGDVLRVGL
+PRTDLAPVDASDR
+>GCF_023573625.1_01078
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5309781ee14b49f117c9a369e9a82e5dbe38491
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000939.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01130
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>GCF_003691675.1_00849
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>GCF_005280335.1_01762
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR
+>GCF_020097155.1_01656
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA
+>GCF_023573625.1_01080
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000942.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..152454a94310d2dbf4f616877e59d358a6a3fb5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000942.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01133
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>GCF_003691675.1_00852
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>GCF_005280335.1_01759
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA
+>GCF_020097155.1_01653
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS
+>GCF_023573625.1_01083
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000946.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edf5f90b523d4268567103f1b32bb6d76e19d9b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000946.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01137
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>GCF_003691675.1_00856
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>GCF_005280335.1_01755
+MVYSDLPSHRAAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDA
+LVEVKRVTSARGAGRPSRRYVVTSHAQEHLPKDHLAVALHSLARLEELGGDEEVRRTARR
+AFRDVEERFAAAVDGRDTELQERTRILASVLDDAGFAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPQFCEEETELFARLLQVDVRRLSTLAAGAHVCTTHVPLGRD
+>GCF_020097155.1_01649
+MYSDSADPAAPAPGTRERVLERVLSHGPVSAAEIGGALGLTAAAVRRHLDALEEEGFVEV
+KVVSAARGAGRPSRRYVVAPQAQRRLGGDHLGIALQAVDRLVEVGGEGEVRRLAADALQP
+VEEAFQAAVAGREMGLEERTRVLADLLDDAGYAASIRHVGAGLAPTLRAEQLCQGHCPLQ
+GLPARHPEFCEEETALFARLLGVDVRRLSTLAAGGHVCTTHIPLGRA
+>GCF_023573625.1_01087
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000947.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d62d87cf92a0e00f7e74e89fa00ed0f0673469a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000947.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01138
+MTDQIVQRDSTETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>GCF_003691675.1_00857
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGSVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>GCF_005280335.1_01754
+MTDQIVQRDPVENADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRNLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYNSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVESGGTMEWVDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PNTSSSIVSKSVARNGGRAAYRGLVQVTEGAKNSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGLSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>GCF_020097155.1_01648
+MTDQIVQQDSRGADPGVISEILEKNPELNAIGAYQYGWADSDAAGSSARRGLNEDVVKDI
+SAKKSEPEWMTKLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWDDLPE
+DIRNTYERLGIPEAERDRLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPEI
+FEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERTL
+IIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKRA
+VVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEGATGETLSVAFAGKDQHQDTGSKMVHMAP
+NTNSSIVSKSVARNGGRAAYRGLVQVNEGARGAANSVVCDALLVDTVSRSDTYPYIDIRE
+DDVTLGHEATVSRVSEEQLFYLMSRGLAEDEAMAMIVRGFIEPIARELPMEYALELNKLI
+ELQMEGSVG
+>GCF_023573625.1_01088
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cebe2ab23512d3d2ee66775191d9ddd4c31c2791
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000948.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01139
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>GCF_003691675.1_00858
+MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL
+>GCF_005280335.1_01753
+MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP
+DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH
+RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV
+RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL
+>GCF_020097155.1_01647
+MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW
+RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA
+AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL
+AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA
+RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL
+IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA
+RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL
+>GCF_023573625.1_01089
+MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT
+GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP
+DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH
+RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV
+RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV
+WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ
+LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..844db32530adc4b84956c5fea261bfff7706a079
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000951.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01142
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI
+>GCF_003691675.1_00861
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
+>GCF_005280335.1_01749
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI
+>GCF_020097155.1_01644
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI
+>GCF_023573625.1_01092
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76e241d03b468de09e1d3cb77a4e4aa9b3a80e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000952.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01143
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>GCF_003691675.1_00862
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>GCF_005280335.1_01748
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA
+>GCF_020097155.1_01643
+MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV
+SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS
+RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM
+NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG
+VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA
+>GCF_023573625.1_01093
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..520eee4ecabeed13b8704d79ade4f4529d824578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000955.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01148
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE
+LVGGAEDFLGQD
+>GCF_003691675.1_00867
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
+>GCF_005280335.1_01744
+MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA
+VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF
+AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE
+LVGGARDFLARGEG
+>GCF_020097155.1_01638
+MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA
+VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF
+VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE
+LVGGAQDFLGQD
+>GCF_023573625.1_01098
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da145b76b98f615c409797d98abc483df248432a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000957.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01150
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA
+GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR
+>GCF_003691675.1_00869
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
+>GCF_005280335.1_01742
+MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL
+LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY
+GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL
+LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA
+GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ
+>GCF_020097155.1_01636
+MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP
+NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ
+DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL
+MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL
+ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA
+>GCF_023573625.1_01100
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..792227fbf7a3e651ca5a27ec6f685f87dcefb5de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000958.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01151
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>GCF_003691675.1_00870
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>GCF_005280335.1_01741
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG
+>GCF_020097155.1_01635
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA
+>GCF_023573625.1_01101
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000967.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bb16d707e2a98793e7a71e54094b8d5c6c4c20b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000967.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01163
+MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA
+VGSANPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETALRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP
+>GCF_003691675.1_00882
+MQTTQLSAPPSLARLYARAARQAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVSAWRGA
+VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETPLRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP
+>GCF_005280335.1_01727
+MRTTELAAPPSLAGLYARAAGQAAKDALTRRSRPAVLPEREVVVTGHRIPRAAVAAWRDA
+VGPADPAALPSVLVHTQVFGAAMELMADPEFPLPLPGMVHLTNTVLHRRPVPAETALRVT
+ARAVGLVPHHAGTAVDVAVTVEGPHPAGGEAVLWEGVSRYLAKGVHLTGLRPERPAREEF
+TAPARTAEWRLGAGAGRRYADVSGDWNPIHLTGVSARLFGMKGAIAHGMLLAARMLQGRE
+PAAGGFRWEIEFDAPVVLPGTVAVRYEPADGQGTRVIGWDGRRCRRHFTGRIAPLAD
+>GCF_020097155.1_01624
+MHTRTESSMPALAGLYRRAAGQALADAARRRTRPAELPDERLVVEGHRIPERALRRWQAE
+IGPVDPASVPSVLVHTQVFGAAMALMAEPDFPLPLPGMVHLTNAVEHRRPVAAGEALDVT
+ARAVGLVPHHAGTAVDLQVAVREAGETDDAPAAWEGVSRYLARGVHLAPLRPERPERPEF
+TPPAPTAQWMFDGGAGRRYAEVSGDWNPIHLSALSARAFGQRRAIAHGMLLAARMLNRRE
+PRAAAFGEGFGWDVEFHAPVVLPARVAVRYEAAADGSTRVSAWDPRRGRPHLDGRIRHAR
+P
+>GCF_023573625.1_01113
+MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA
+VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVPAETALRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGGEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVYGWDARRRRPHFSGEITPLES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cc8e68c0c679799866f2b721f5bd57680cea554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000968.fa
@@ -0,0 +1,101 @@
+>GCF_002008305.4_01164
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>GCF_003691675.1_00883
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>GCF_005280335.1_01726
+MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL
+RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE
+RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD
+VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL
+GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV
+DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH
+SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE
+LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE
+SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL
+APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE
+LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP
+ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG
+EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG
+TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH
+SWEAYADGLLEAAAGLARRQDGA
+>GCF_020097155.1_01623
+MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL
+DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL
+VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV
+AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR
+RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV
+WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR
+RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD
+VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL
+GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA
+DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL
+VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS
+VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV
+TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG
+AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA
+DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD
+ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL
+GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH
+AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV
+AGLPRP
+>GCF_023573625.1_01114
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+AAVPRRSPGLDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000972.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6283ebc9ed005905165354d9c7e15903707dbac0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000972.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01169
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>GCF_003691675.1_00888
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>GCF_005280335.1_01720
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSASDPGAAFTAITQIGTELAVLIYF
+WRDITRIIGRWFQALAGRLPHSDPDVRMGWLIILGSLPIAVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQAKPLERLTVRDGVLYGFAQALALIPGVSRSGGTITAGLAM
+GYTRSAAARYAFLLAVPAVFASGFYKLFQSLAEPGTQGPYGMGETFLATVIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLGLFALLGTGVISA
+>GCF_020097155.1_01618
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSAADPGAAFTAITQLGTETAVLIYF
+WKDISRIISRWFQALAGKVPHSDPDVRMGWLIIIGSIPIGVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRKGRQTKPLEKLTLKDGIVYGFAQALALIPGVSRSGGTITAGLAM
+GYTREAAARYAFLLAVPAVFASGLYKVAKVVTEPGQAGPYGMGETILATAIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLVLFVLLGTGLIAA
+>GCF_023573625.1_01119
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000973.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67f1330da40588cb9451b01a552ff8c97751968e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000973.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01170
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
+>GCF_003691675.1_00889
+MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR
+LR
+>GCF_005280335.1_01719
+MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY
+VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE
+VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG
+QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE
+CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH
+AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL
+RLR
+>GCF_020097155.1_01617
+MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY
+VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN
+VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG
+SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE
+CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS
+KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH
+ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL
+R
+>GCF_023573625.1_01120
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000978.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..098b6e8d410726f3f65bfa6c8b469ea55600017f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000978.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01175
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>GCF_003691675.1_00894
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+TARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPRDPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGGDTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VMEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>GCF_005280335.1_01714
+MDQDAQGGPEQLERRLGEARELLRQSQAEAERLRHQLDSAQRHAARLSERRREAEAQTQT
+AARNNRRMVELLETTRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLVPGAQVLLDESSAIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVELRHGDAVTVDSRVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVATAGSADAARATLIARTVAALYDRGTGTALAE
+LTDVSGTTRALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVVA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>GCF_020097155.1_01612
+MTEDDTQDRAGVLPAGDDARRLAEARELLRQSQAEAERLRHQLASAQRHGAQLSERRRAA
+QAQLDVAARNNRRMVELLEATRTEMTSLKEALDDTTKAPFTFARLEAVHAARAPREGVET
+GAVVRAGADVVQNGRRLRVAVSPLLDAAALTAGAEVLLDESSTIVGEVEHSVSGQLLRVK
+ESLPDGSLVLAGAADEERVVRRAPALAGEVLRHGDAVTVDPRLEWALARVELSEVDDVLL
+EEVPDVTFDDIGGLGPQIERIREAVEVPFLHPDLYREHGLRAPKGIMLYGPPGTGKTMLA
+KAVANALSARSAEGGRSFFLNIKGPELLNKYVGETERQIRIIFQRAREHAAAGSPVVVFF
+DEMESLFRTRGSGVSSDVETTIVPQLLAEIDGVESLDNVIVIGASNREDMIDPAVLRAGR
+LDVKIRVDRPDARGAVDIMARHLDEEVPLHVDEVRDAGSAEQAREELIGAAVTALYERSP
+RTALAELTDITGATSTLHLADLVSGAVVADVVDRAKRAAVRDLLAADLDPAARGLRTRHL
+LDAVDAVLADQADLLGTVAPGEWARTSGWRGPRLAELRMLPGAGGRP
+>GCF_023573625.1_01125
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEIATLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSVRSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVVAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51e200c13544464442fcd64d424af13c3467da9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000985.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01183
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR
+VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
+>GCF_003691675.1_00902
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF
+QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG
+VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR
+>GCF_005280335.1_01705
+MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR
+VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG
+RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD
+HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH
+EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA
+RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF
+QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR
+IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE
+RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG
+EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD
+ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR
+>GCF_020097155.1_01604
+MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR
+AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR
+AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV
+RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA
+ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED
+GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA
+SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF
+DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR
+ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY
+HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV
+PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR
+HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA
+>GCF_023573625.1_01133
+MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR
+VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL
+RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG
+RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD
+HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR
+EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA
+RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF
+QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR
+IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA
+VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET
+FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA
+VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1f67f82de7148c8c7d767f7e213866e0685d9a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000987.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01185
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
+>GCF_003691675.1_00904
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI
+>GCF_005280335.1_01703
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI
+>GCF_020097155.1_01602
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL
+>GCF_023573625.1_01135
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000988.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01a21ce6d7ad1e76d62de03f9bd4965ef5aacb3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000988.fa
@@ -0,0 +1,90 @@
+>GCF_002008305.4_01186
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>GCF_003691675.1_00905
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHIMAGGRLYDLFAE
+DIAFEDAADRDGEALLNPELKRLGEEAERRFQRADWGRPGRQQHRDGRGGGTKGRARGGR
+HTGRDGGRGRTGSSALDRERPVSGRPGGHDGGPRRGPRLSTSRPEMIRVLDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFTAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVARLASRRTYPLRSSFRPTYNM
+SANLLAQVGAEQARGILESSFAQFQADRSVVGLARELRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRSLGRAVVVFPAGNP
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRSTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVHEDAPSPRAALTERGEALRRIYGERDLFTSL
+VLQDPAMDGLTPEEWAAVAALLVYQGKGETEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>GCF_005280335.1_01702
+MSHAPASATPPEEPQLSPAERFARAKAARHHAGSELGRFASRLGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLSRVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGQEAERRSERPDWGRPGRHRGRGGRDGGQRGRGGRGG
+DGRKGGRDADRRGRHGSHAMDREQPATGRVRGQEDGERRGPRLSTSRPEMIRALDREGLL
+PCITFIFSRTGCDAAVEQCLRAGLDLTTAHEKALVAERVEQAARLLPVEDLEILGYWAWR
+DGLSRGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFN
+GENHVDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLKSSFRP
+TYNMSANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEKAMQCHLG
+DFSEYLALRKELASAEKSGSQGRRRAQLAAVKESLADLAVGDVVELDAGRSLGRAVVVFP
+AGNPQNPRVGVVTDKAQLRRITVDDVTGPVEPVAGAALPQVLQVKTPTQRKDVAALMREA
+VRTGRPPAGGGRRTSGFRLREDPAAPRVEELRRALQRHPCHACQDREEHARWGDRWWGMR
+REVSVLRERIAGRTNTIARTFDRVVGLLRSYGYVHEDASSPRQALTARGEALRRIYGERD
+LFTSLVLQDPTVQGLTPEEWAAVAALLVYQGKGEAGHGVVPMPTARLAEVADAAERIEER
+LRADEAQARLEPTPPTDPGLVGPMHRWVRGASLRRTLEGADLAAGDFVRWARQVIDVLDQ
+LANVPGDARRSRACRKAADLVSRGVVATSLPAATAREADED
+>GCF_020097155.1_01601
+MAPHTHHDLPPEEPALSPAERFARSRASASRPGTELSRFAARLGFPLDEFQLEACREVEA
+GHGVLVAAPTGAGKTVVGEFAVHLGLARGRKAFYTTPIKALSNQKYADLAAVHGADRVGL
+LTGDTSVNPDAPVLVMTTEVLRNMLYADSEALTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVVVSEHRPVPLWQHVMAGGRLYDLFAE
+DVAFEAAADADGTPLLNPELQRMAQEASRRVERPDWGRTGHRGRGRGGPGGRGAGRGRGK
+GGPRGGREGASSGWDRERPHRADASPGDGERRALGLSTSRPEMIRALDREGLLPCITFIF
+SRAGCDGAVEQCLRAGLDLTDRREKALIAERVEQAAAALPPEDLEILGFWAWRDGLSRGF
+AAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGVNMPARSVVLEKLVKFNGESHVDV
+TPGEYTQLTGRAGRRGIDVEGHAVVLWRPGLDPSAVAALASRRTYPLRSSFRPTYNMSVN
+LLAQVGAERARGILESSFAQFQADRSVVGLAREVRAKQSSLEKYADAMACDRGDFAEYLS
+LRKELAAAEKSGSRGRRREHLRAVKESLADLAVGDVVELHDGRALGRVVVVAAAGNPQNP
+RVAVVTDKAQLRKVAVEDLVDPVEPVAGAALPQTVQVKTPSQRKDVAAAMREAVRAHRPP
+TGGTRRGTGFRLREEVASPRLEELRRALQAHPCHACPDREDHARWGERWWDMRREVSLLR
+ERIAGRTNTIARTFDRVVELLGRLGYVGDDPDAPSRALTERGQTLRRIYGERDLLTSLVL
+HDPSTRSLTPEEWACVAALLVYQGKGDTQGLPVAMPTARLQALAEAVDRIEGGLREDETA
+ARLEPTPPTDPGLVAPLHRWVRGASLRDSLHGADLAPGDFVRWARQVIDVLGQIAQVPGD
+ARRTRACRKAADLVGRGVVAASLPAAAAGADGVEGEEPDRVDR
+>GCF_023573625.1_01136
+MAHHPASATPHDEPELSPAGRYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000990.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d1348fd5b92bcda282a9232a5356dd7efbfc21d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000990.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01188
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>GCF_003691675.1_00907
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>GCF_005280335.1_01700
+MRVLTIIPTYNEIESLPLTLGRLRDAVPTSDVLVVDDASPDGTGQWADARAAQDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLDAVRTADLVIGSRRV
+PGGKMVNWPASRKMISWAGSLYPRIMLGLRLTDVTAGYRAYRAETLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRSR
+LGL
+>GCF_020097155.1_01599
+MRVLTIIPTYNEIESLPLTLGRLRDAVPDSDVLVVDDASPDGTGAWADARAAEDDHVHVL
+HRAEKNGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPASRKLISAAGSLYPRIMLGLKLTDITAGYRAYRADTLRRIDLGAVQSKGYG
+FQVDMTFRVARLGLRIVEVPITFVERELGESKMSGGIVGEAVVNVTKWGLQARWETLTGR
+GPQRG
+>GCF_023573625.1_01138
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf5fd1c9c512ac235071d6dff7c8ae21de9ab761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000991.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01189
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
+>GCF_003691675.1_00908
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA
+>GCF_005280335.1_01699
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA
+>GCF_020097155.1_01598
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV
+>GCF_023573625.1_01139
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000995.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..babcb004df59284c1dbd60a517d9e408ef300497
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000995.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01193
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR
+LT
+>GCF_003691675.1_00912
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL
+YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
+>GCF_005280335.1_01695
+MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL
+YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH
+DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR
+LA
+>GCF_020097155.1_01594
+MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD
+DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV
+LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL
+VVARLV
+>GCF_023573625.1_01143
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85436f77dd16b08484ccf81f070c710b0328cd15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000996.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01194
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>GCF_003691675.1_00914
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>GCF_005280335.1_01693
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG
+>GCF_020097155.1_01591
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA
+>GCF_023573625.1_01148
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c8d3f548a637e7b11f50e523e80ff1c1f919153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0000997.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01195
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>GCF_003691675.1_00915
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>GCF_005280335.1_01692
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV
+>GCF_020097155.1_01590
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS
+>GCF_023573625.1_01149
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001000.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf9e8a22b802a5020b58d2650f864f22d814e725
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001000.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01198
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>GCF_003691675.1_00918
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>GCF_005280335.1_01689
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>GCF_020097155.1_01586
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT
+AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA
+ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>GCF_023573625.1_01152
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a37948f4eb0628c683ed788ed644b0b8680ddf07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001002.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01200
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>GCF_003691675.1_00920
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>GCF_005280335.1_01687
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>GCF_020097155.1_01584
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>GCF_023573625.1_01154
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10b993fd9ff7ccf1a9802214ac891cb7dfc3ad58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001004.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01203
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF
+GWVYEFSRGKFAH
+>GCF_003691675.1_00922
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV
+GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF
+GWVYEFSRGKYAH
+>GCF_005280335.1_01684
+MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL
+GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF
+GWVYEFSRGKYAH
+>GCF_020097155.1_01582
+MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL
+GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF
+GWVYEFSRGKYAH
+>GCF_023573625.1_01160
+MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV
+GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF
+GWVYEFSRGKFAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001005.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e8587472c35428cc7314fea23b17762827376c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001005.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01204
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWYAYAPLSNTTFSPGVGGDLWVFGLALQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILILMAFPPLAAALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGIVSEIIPVFSRKPIFGYKSIVFA
+TTAIGALSFSVWAHHMYVTGSVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFENPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQLNDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVTGMPRRYADYMVEDSFHAMNAFSSV
+FSFVLGASLIPFFWNVYITARYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ
+>GCF_003691675.1_00923
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFVFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDSFQAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGASLEWTTSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQNTSEAFGEKVAQ
+>GCF_005280335.1_01683
+MTTYEYATDEVRSQAQPRVVPRSLGKIAVSWLTTTDHKVLGYMYLIVSFMFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFILGASLIPFFWNVYVTARYGKKVTVDDPWGFGASLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTPEAFGEKVAQ
+>GCF_020097155.1_01581
+MTTYEYATDEVRTQAQPRVAPRSLGKIVVSWLTTTDHKVLGYMYLIVSFVFFCVGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVAFP
+RLNALAFWFFLFGSFIACAGFLTPQGAASFGWFAYAPLSDTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFLLGASLIPFFWNVYVTTRFGKRVTVDDPWGFGSSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELAAYSPQAEPEVFGEKVASK
+>GCF_023573625.1_01161
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDTFTAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001010.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c04dd4bf86a6cde0ad23a32808d32973e15b5542
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001010.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01209
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPTRPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLAQGYTAFLYEGPF
+WAGRITAGLARSLRG
+>GCF_003691675.1_00928
+MQLPDPKSAVDGILTSRAPRLYPPFFRAVFGGMDAERAHHRGFDAIRLAERTGASAALRA
+AFRPDPMLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADADVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRTTAGLARSLRG
+>GCF_005280335.1_01678
+MQLPDPKAAVDGVLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLAERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKEGRGTAALADLGFGHIEVGTITAQAQPGNPQ
+PRLFRLVEDRALVNRMGFNNDGAAAVAPRLARTRAVLERRFGAVRPVLGVNIGKTKVVAL
+EDAAEDYRASTRLLTPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRVVTGR
+RVPLTVKIAPDLTDEDVRAVAALAERLGLDGVIATNTTISREGLATPRADVDALGAGGLS
+GAPLKERSTEVLRVLRAALPVGTAVISVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRISAGLACALRG
+>GCF_020097155.1_01576
+MQLPDPRFRVQSVLRSSAPRIYPPFFRAVFAGMDPERAHHVGFAGIRAAEASGASRALRS
+TMAPDLGLARTVMGLRFPSPFGLAAGFDKTGVGTTALAELGFGHIEVGTITAQAQPGNPA
+PRLFRLPEDRALINRMGFNNDGAAAVAPRLAATRRTLEERFGAVRPVLGVNIGKTKVVPL
+DGAVEDYRASARLLAPHADYLTVNVSSPNTPGLRQLQEISSLEPILAAVREEADRAVPDR
+RVPLTVKIAPDLADEDVRAVAELAGRIGLDGVIATNTTIGRGGLSTPASEVEAMGAGGLS
+GAPLAARSLEVLRTLRAALPAGVALIAVGGVTDGDDVLQRLDAGADLVQGYTAFLYEGPF
+WAGRINAGLDAAQRAR
+>GCF_023573625.1_01166
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIWLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPDR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLEVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRITAGLARSLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28cbbd79636b71ef7b2ae0dc491926be6512cf67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001012.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01211
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
+>GCF_003691675.1_00930
+MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA
+>GCF_005280335.1_01676
+MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT
+SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER
+IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP
+GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV
+AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV
+PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR
+SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT
+TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV
+DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT
+AQPAPSSGAPDSASDADGGA
+>GCF_020097155.1_01574
+MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL
+DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG
+RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD
+LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP
+DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD
+>GCF_023573625.1_01168
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45cef053cfd9a106767906cf3878efc65a39c3cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001013.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01213
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>GCF_003691675.1_00932
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>GCF_005280335.1_01675
+MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA
+>GCF_020097155.1_01572
+MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP
+ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE
+RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT
+YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR
+NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF
+SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA
+DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR
+AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA
+FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV
+EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA
+>GCF_023573625.1_01170
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001016.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b381c41397637c3331006f2c824457f5af5357a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001016.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01216
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
+>GCF_003691675.1_00935
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
+>GCF_005280335.1_01672
+MAVEILNESGIEVPEDELLRMARHVYASLHVHERTETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGTAEAPAEGMLGDVVLCPEVAAEQAARGGHGRDDELMLLLTHGMLHL
+LGYDHMDDADRLEMFALQDRLVSEVLGRPAPAPTIED
+>GCF_020097155.1_01569
+MAVEIVNESGVEVPEEALLGMARHVYAALHVHPLAETAVTVVDAQRMAELHVEWMDLEGP
+TDVMSLPMDELTPGTEKSPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHMEEDERAEMFALQDRLVSEVLGRPAPAPTVED
+>GCF_023573625.1_01173
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b781b387f7308f875af5eb1f6893a580672905e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001017.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01217
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>GCF_003691675.1_00936
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
+>GCF_005280335.1_01671
+MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV
+TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI
+GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD
+ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF
+GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD
+AARGAEPAPRGGRGHRGR
+>GCF_020097155.1_01568
+MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR
+DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD
+SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI
+ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY
+MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV
+EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR
+>GCF_023573625.1_01174
+MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV
+DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG
+QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK
+EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV
+APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG
+LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001020.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34be7252bc2f67cefed4f19e20d5b1b9c216d15d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001020.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01220
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>GCF_003691675.1_00939
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>GCF_005280335.1_01668
+MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ
+VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL
+LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA
+RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT
+>GCF_020097155.1_01565
+MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ
+VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV
+LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA
+RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>GCF_023573625.1_01178
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001021.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cfaf4e4007582c3a707e8fdf08a0498efd7ed9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001021.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01221
+MDWSSWGPAGHDDLTRRPARTVPDVPAAPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>GCF_003691675.1_00940
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVSGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVFGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>GCF_005280335.1_01667
+MDWSSWGPAGHEEMTRRPGRPARDVPAAPGTVVEDVASGFTGAVIRVERAGGVHTVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPHVASAPRPPARTASGSRRVEGVRARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIAAFDPGPRRRLGILVDHLVPGSKE
+ERIAAEAMRVPGAAGNVLILGHPYVDVWQVIKPAVLGIPTWPVVPKGQDWKTGVLQGLGW
+PHGTKEATGLGWKRLLSHVGSYADLEPSLLGRVEELIDFLTAEPER
+>GCF_020097155.1_01564
+MDWSSWGPGAHEDLARPAGRTAGEAPATPGTVVEDVASGFVGAVVRVERSGGTHVVVLED
+RRGVRRGFPLGPGFWVDGSPVVLVPPRSAAPAAAARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLPGAIRDFAPGPGRRLGILVDHLVAGSKE
+ERLAAEAMAVPGAAGNVLILGHPYVDVWQVIKPAVLGIDAWPVVPRGQDWKTGVLRGLGW
+PAGTKEATGLGWKRLLSHVRTYADLEPALLGRVEELIDFLTAPGA
+>GCF_023573625.1_01179
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPWRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f629c5e53ccc015adaf044a84d14b5a9c8d199e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001023.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01224
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG
+VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>GCF_003691675.1_00943
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>GCF_005280335.1_01664
+MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM
+STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV
+PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADSAAKK
+>GCF_020097155.1_01561
+MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP
+REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA
+CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE
+PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD
+GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV
+TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL
+GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK
+VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF
+FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK
+LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR
+MKMVGRVEVPQEAFIAALSSDGAEPAKK
+>GCF_023573625.1_01182
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e284f2a659789fcab2d8c52f94a83294029b8bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001026.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01227
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_003691675.1_00946
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_005280335.1_01661
+MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH
+SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL
+RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT
+GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH
+AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG
+IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>GCF_020097155.1_01558
+MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET
+HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL
+LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA
+TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR
+HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA
+GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR
+>GCF_023573625.1_01185
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cd1c572dd8d645c7b55c387811e2617704c6ea5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001028.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01229
+MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA
+AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA
+GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV
+PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG
+PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW
+>GCF_003691675.1_00948
+MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP
+VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT
+DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA
+ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV
+DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
+>GCF_005280335.1_01659
+MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV
+TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE
+PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA
+DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA
+GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR
+VTW
+>GCF_020097155.1_01556
+MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP
+AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG
+VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP
+DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS
+GLQDLDAVPGIGPATLDRLKDHVTW
+>GCF_023573625.1_01187
+MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL
+VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG
+PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV
+LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG
+VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a09115497fd7955e2861c0d03c5c987c27baec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001030.fa
@@ -0,0 +1,75 @@
+>GCF_002008305.4_01231
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK
+SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR
+>GCF_003691675.1_00950
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
+>GCF_005280335.1_01657
+MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE
+WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC
+PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA
+MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE
+LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA
+VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR
+AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL
+NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV
+FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG
+GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL
+ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI
+DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT
+VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI
+R
+>GCF_020097155.1_01554
+MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS
+GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV
+LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE
+ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA
+PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV
+KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA
+AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA
+DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV
+KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR
+>GCF_023573625.1_01189
+MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS
+GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI
+ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV
+LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI
+GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE
+DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ
+RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ
+ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA
+PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL
+RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK
+SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA
+TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA
+ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ
+VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001035.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c2483d7ff18eeae94abdc841c16f981d78ceac9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001035.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01236
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRHADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATAANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSGTEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGAIV
+RFIAGSMSVPAPEGVERVVQVESTQDLLEAVLAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDPTSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDQAAAAVVQAIVDDLAGR
+DPAGASGR
+>GCF_003691675.1_00955
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVQAIVDDLAGR
+DPVGASGR
+>GCF_005280335.1_01652
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGTATWEALSGRPVRTGTF
+EAVDEVNHVRLGRQADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVEPAVGRLTGADSGARRLPEPDEIWELAQAAAADPAARR
+PRATTSRPGPAAAGAAPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGVALARAALA
+AGARVRFIAGSMSVPVPEGVERAVHVESTAELLTAVLEQAADADVLVMAAAVADFRPAEA
+SESKMKKGDDGSSPVIVLERTEDVLATAVRTRAAGGPMAPLIVGFAAETGDAESSVLEYG
+RAKLARKGCEMLVVNEVGRDKVFGRDETAVTILFADGSPAVEAAGSKDEAAAAVVGAVVD
+RLAASAPGSASAR
+>GCF_020097155.1_01549
+MEVVLGVGGGIAAYKAALLLRLMKEAGHGVTVVPTDNALRFVGAPTWEALSGRPVRTDTF
+TDVPEVSHVRLGREADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWRHPATVANVALLRERGVHVIEPDSGRLTGADSGPGRLPEPARIWAEAQDAAARAGGRA
+GREAAVTAAEPGAASPLAGRTVVISAGGTREALDPVRFLGNRSSGKQGTALAEAVLAAGA
+RVRFIAGPMSVAPPAGTEVTAVESTQELLEAVLSEAADADVLIMAAAVADFRPAQVATSK
+IKKTDDGGAPTIVLERTPDVLATAVQTRDAGGPMAPVIVGFAAETGDEHTTPLEYGRAKL
+ARKGCDLLVVNEVGDGKVFGQDATEVTVLSADGAEPVTRTGSKAEAAAAVVEALERVLAS
+REAGGAPGR
+>GCF_023573625.1_01194
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVRAIVDDLAGR
+DPVGASGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08256fcfcc39c7bbae409c72c9d40f0dede2baf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001036.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01237
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA
+>GCF_003691675.1_00956
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
+>GCF_005280335.1_01651
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA
+>GCF_020097155.1_01548
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A
+>GCF_023573625.1_01195
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001037.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c197926441e8f5b5a70e9cc316235b3f3fb84b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001037.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01238
+MTDTFDPGPAPAVPVARTVVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>GCF_003691675.1_00957
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>GCF_005280335.1_01650
+MTDAFDHGPAPAVPVARTAAQERRPGPGVTVLAGPTAVGKGTVSAYVREHYPQAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVAADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRESLPEATFVFLAPPSWEELVSRLVGRGTEGPEEQRRRLDTARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPEHSSPEA
+>GCF_020097155.1_01547
+MSDLSDLGPAPSVPGERAPSRPPAPGAGVTVLAGPTAVGKGTVSAYIREHYPQAWLSVSA
+TTRAPRPGEEDGVHYFFTTPEEFDELVAGDQMLEWAVVHGRNRYGTRRDRVAEAVAAGRH
+VLLEIDLQGARQVRRTLPEATFVFLAPPSWDELVSRLVGRGTEGPEEQRRRLETARLELA
+AEPEFDAVVVNDAVERAAAELVKLMGIDPHDAPASA
+>GCF_023573625.1_01196
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001042.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22ea82ca24b3b0708bb684759cf6cb0bbe519aae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001042.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01243
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
+>GCF_003691675.1_00962
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
+>GCF_005280335.1_01645
+MNALALAAATLASRPVAPQTPGKDYSDVWLPITLGTLAVILVLVGLFALGWRARRRSQAD
+LPAPAAVPAALYEQEPAASASGMHVGTVRGEHRLDRVAVHQLGLRSHAVLEVHDAGEHRG
+LLVLRPDVANLYIPAADLLEAGLSAGIAGKFVEPGGLVAWGWRLGDAELTSAFRPDRAED
+RDRLLAALQTLIDPAPARSAGRAGEGDLR
+>GCF_020097155.1_01542
+MSAVLPAALPLAATPVPPASPMKDYSDVWLPIVLTTVGVIALLLALIAWGWRGRRRRQAG
+IPAPATVPPEVLEREPAVSAEGMWVGTVSGTDRLDRVAVHDLGLRSSGVLEVHTAGDRPG
+VLVLRPNIAPLFVPAAHLMEAGRSAGIAGKFVEPGGLVAWGWRLGDVDVTSAFRPRRPED
+RDRVLEALQTVIDRAGRPDAGQENAR
+>GCF_023573625.1_01201
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da509d32a563b9b02a72523e1defbc8cb1879eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001043.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01245
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_003691675.1_00964
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_005280335.1_01643
+MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR
+SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>GCF_020097155.1_01540
+MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV
+DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR
+SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG
+AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV
+LEQVANGVSVRMAVLHLVLNQDPALAPQEARP
+>GCF_023573625.1_01203
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..789dcb11efd3e1bd54d4c9a74f47a22c77b1298d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001045.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01247
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_003691675.1_00966
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_005280335.1_01641
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>GCF_020097155.1_01538
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA
+>GCF_023573625.1_01205
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34c43e7838492096ed79cb2edb8e5a00c1b409bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001046.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01248
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>GCF_003691675.1_00967
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>GCF_005280335.1_01640
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND
+>GCF_020097155.1_01537
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND
+>GCF_023573625.1_01206
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5580ea88f4a484bf066f87686941b7529f49ab55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001049.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01251
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP
+>GCF_003691675.1_00970
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
+>GCF_005280335.1_01637
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ
+>GCF_020097155.1_01534
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ
+>GCF_023573625.1_01209
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a75333999899b1a007fe4e45c3222e6c11ea531b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001050.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01252
+MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY
+DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>GCF_003691675.1_00971
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
+>GCF_005280335.1_01636
+MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED
+EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT
+LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG
+ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA
+HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA
+GMPEPDWAAVTRAAARALGPAAG
+>GCF_020097155.1_01533
+MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS
+AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN
+TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD
+VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD
+PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA
+LGLPGR
+>GCF_023573625.1_01210
+MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA
+DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN
+TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE
+VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY
+DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD
+ALGPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001051.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d65dcc385274378815f2e37cdde7c66865a1053e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001051.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01254
+MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE
+LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS
+TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR
+>GCF_003691675.1_00973
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
+>GCF_005280335.1_01634
+MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE
+LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS
+TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA
+>GCF_020097155.1_01531
+MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD
+AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH
+RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA
+>GCF_023573625.1_01212
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cf85ab052833067bae4ca2b42195826e923703d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001053.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01256
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>GCF_003691675.1_00975
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>GCF_005280335.1_01632
+MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA
+VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI
+PTTTTQKDTHA
+>GCF_020097155.1_01529
+MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA
+AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA
+>GCF_023573625.1_01214
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..217f0cfde212b1e9cc53e088c948ebe2759b44af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001056.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01259
+MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>GCF_003691675.1_00978
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
+>GCF_005280335.1_01628
+MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP
+DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER
+DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT
+LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL
+DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK
+SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI
+GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG
+HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE
+>GCF_020097155.1_01526
+MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE
+PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR
+EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL
+LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV
+ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV
+DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI
+VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY
+SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD
+>GCF_023573625.1_01217
+MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE
+PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE
+RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL
+TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA
+LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM
+HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ
+AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE
+PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a81c94b98428a743350929433de7a2a476ca2177
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001057.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01260
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP
+>GCF_003691675.1_00979
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
+>GCF_005280335.1_00445
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR
+>GCF_020097155.1_01525
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA
+>GCF_023573625.1_01218
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e35f6042d652bd524e901d8d7164d98b0386cafb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001059.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01262
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>GCF_003691675.1_00981
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>GCF_005280335.1_01626
+MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA
+SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV
+FGAQMDVTLVNDGPFTLVVDTADLTGPRRG
+>GCF_020097155.1_01522
+MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER
+SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV
+FRADMDVALTNAGPFTLVVDTADLAGPRRG
+>GCF_023573625.1_01220
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001063.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f13a4a119387fda3d977876134731807a52326f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001063.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_01266
+MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM
+KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ
+RAVKKAQEALDARLKWKQALEASASELR
+>GCF_003691675.1_00985
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
+>GCF_005280335.1_01621
+MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM
+DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS
+TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV
+KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR
+KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR
+RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER
+AVKKAQEALDARLQWKQALEASASELS
+>GCF_020097155.1_01516
+MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE
+APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA
+PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA
+QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA
+ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK
+SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG
+KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL
+ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR
+RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS
+ASELR
+>GCF_023573625.1_01224
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001068.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dce64a503a06f57bebc5c0030797ea0a4d7c7ec1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001068.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01271
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETTAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>GCF_003691675.1_00990
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>GCF_005280335.1_01616
+MPVATAATLPVIAQQAQGGGGSMLMLIAFAMLAVMLFLSFRKGKKVQQQQAEMRSTLAPG
+VEVMTGAGIFGTVVSVDAENQRVTIETAPGTRMDVHLQGVTNVVEPTAAAAATPADDEAR
+LDRAPGAEYGAQQPVVEPRADDAVDPRDRRGDLA
+>GCF_020097155.1_01511
+MPLTPLAPVLADDAAGGGNVLVLAMFAALAVMLFLSFRRGKKAQAEAADMRARLTPGQEV
+MTGAGIFGRVVAVDAAAQRVTLETAPGTRMDVHLQGIVKIEEPDVAPAADTAPAVGGAHA
+AETAPAADDTDRA
+>GCF_023573625.1_01229
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c442472d3942e7f444d0a9a54af494bb759b922
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001072.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01276
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA
+GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>GCF_003691675.1_00995
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
+>GCF_005280335.1_01611
+MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT
+APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR
+LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR
+LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT
+SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL
+KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER
+FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA
+GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT
+TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE
+PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE
+AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF
+AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA
+>GCF_020097155.1_01506
+MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP
+TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS
+ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV
+ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP
+WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR
+AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA
+LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG
+DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG
+HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL
+ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL
+VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR
+GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA
+>GCF_023573625.1_01234
+MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT
+APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR
+LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR
+LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW
+LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA
+APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD
+ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL
+FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH
+EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA
+GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID
+PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL
+LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b66c0b9b31b11e1899458b43653310421433ad82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001074.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01278
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>GCF_003691675.1_00997
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>GCF_005280335.1_01609
+MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA
+YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER
+VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA
+>GCF_020097155.1_01504
+MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY
+ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH
+VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA
+>GCF_023573625.1_01236
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ca4e8264b9f9a4d45b7e5a170bf52c3ef879eae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001076.fa
@@ -0,0 +1,42 @@
+>GCF_002008305.4_01280
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>GCF_003691675.1_00999
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
+>GCF_005280335.1_01606
+MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV
+PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD
+PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE
+PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG
+GRRADAAVGRGPTHR
+>GCF_020097155.1_01501
+MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV
+AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL
+PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW
+LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL
+KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS
+AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA
+RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL
+LDPDPARDR
+>GCF_023573625.1_01238
+MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY
+GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR
+LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV
+PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL
+WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI
+RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN
+LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..635ceed1d94aa48e58a41683324a5e410e2fe8d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001080.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01284
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>GCF_003691675.1_01003
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>GCF_005280335.1_01601
+MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA
+MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG
+VAAPKGLAPRRRYGAERD
+>GCF_020097155.1_01497
+MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY
+PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED
+>GCF_023573625.1_01242
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001087.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ab71bb2369ed80589dd123ab2505faed753099f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001087.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01299
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>GCF_003691675.1_01022
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>GCF_005280335.1_01593
+MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC
+GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV
+RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS
+SPGAGALTDQASQSPRA
+>GCF_020097155.1_01489
+MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA
+GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV
+RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG
+>GCF_023573625.1_01257
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001089.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28cb54cd7da2a42f7c7a828d275a4cb2c39c3701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001089.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01301
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>GCF_003691675.1_01024
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>GCF_005280335.1_01591
+MSPAAGERADAGPGDLIERRGVVASVTLPGADDATVFRAALADRLPEPGSVTPAESLQLV
+WHGRRRVPGVMPGQWLAVRGRLTRPDGVLTLHNPAFDLIDAPEAALRARPPREESP
+>GCF_020097155.1_01487
+MSPRRTPAPAGERPAGERVGVVVAVTFPGADDATVFRAALADDLPAPGRPEPQEVLHLVW
+HGRHRVAGVMPGAWMRVLGHPVAVAGEPTLFNPEFHLIDDEGGPA
+>GCF_023573625.1_01259
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001095.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06c4c117826d5b51381e2e7346a460f57c83739a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001095.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01308
+MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>GCF_003691675.1_01031
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>GCF_005280335.1_01584
+MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA
+VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA
+>GCF_020097155.1_01480
+MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE
+LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE
+MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG
+YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA
+>GCF_023573625.1_01266
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001097.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..effceb0970016ace263b2d3096a3ae570d36e16f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001097.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_01310
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR
+LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC
+WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL
+PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR
+EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA
+ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA
+KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI
+EAVGAGASPELLSAPPVADDPVTVSAD
+>GCF_003691675.1_01033
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
+>GCF_005280335.1_01582
+MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP
+VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV
+DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP
+NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV
+GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK
+LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT
+LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA
+AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL
+REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW
+AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP
+AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE
+VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA
+DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK
+GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE
+AVGAGASPELLSAPPVADDPVTVSAD
+>GCF_020097155.1_01478
+MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY
+PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI
+VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG
+RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR
+TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR
+LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA
+CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE
+LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV
+GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP
+VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR
+VEAVGAGASPELVAAAPVDDSGVEVSAD
+>GCF_023573625.1_01268
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001098.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1298da6376a5be92cb957a479bc1165c4d6ad50a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001098.fa
@@ -0,0 +1,107 @@
+>GCF_002008305.4_01311
+MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>GCF_003691675.1_01034
+MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV
+GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG
+RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL
+VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH
+HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP
+LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG
+RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI
+GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR
+LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH
+DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR
+QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY
+LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL
+VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA
+LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI
+AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE
+GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS
+GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG
+NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR
+ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC
+>GCF_005280335.1_01581
+MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>GCF_020097155.1_01477
+MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM
+TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL
+GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML
+GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV
+LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY
+GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW
+PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG
+SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG
+GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL
+LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR
+PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA
+PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA
+DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV
+PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL
+LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA
+LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE
+AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA
+AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV
+FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER
+QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD
+VRVRLGGDAAGHP
+>GCF_023573625.1_01269
+MSPSRPAAPAVERSASAAGPHPGRTRRARPPMTPAARRALPALLALAVLRALGWILLAES
+LARLITGLAMTLDPEDSARLLELLFHPPAPVGPVPAAQTLSGPVLLGAAGVALRALAEAG
+QRVVGRRAALGAQQQVRAAVVAQRLAAADGGRPRSGADAVLVTHGLKSLDDHYTEALPAL
+AATAVVPAALGVWILTHDLVSAVVAAITLPLVPLFMILVGRHTQERIDAAQDGLDRLAGH
+LLELARGLPVLVGLHRAGVQRRALQEVSQRHHAATMVTLRTAFLSGLALELIASLSVAVM
+AVFIGLRLVNGQMTLLDGLVVLILAAEVYLPLREVGAAYHASEDGREAESRARAAADAPV
+PAPVLETLAPASGPDRDGGVVIRDLSVRLAGRQVLGGLDLSALPGRLTALAGPSGTGKST
+VLRLLAGLLRQDAAEATGRVAGVDTERTLWIGQHPVLTERTVAGELDLAAGGALPGPVRS
+AVLAAVALEGLQERDPADLSPGECRRVAVARLLARLHAADGTGPWLVLLDEPTAHLDGAV
+AAVVVETLAALPSGAVPGLSTPQCTVLAASHDPTLLTAADAIVRLAPGAGPTAGSPATAM
+PVAAAQGRARPEPVTPRQVSLRAGLRLLPWRQPKLWAGIGWAAGTHVSAALLAALSGWLI
+VTASTRPPVLYLLAVIVLVRGFGLSRAVFRYLDRLTTHDAVFGWATELRLRLWDALGRQP
+RLWGRVGRTDGALSLLVSDVDAFRDAVPRVLVPAPAALLAWLATAALTWALAPELAVVAL
+VPGAVALVVIPALVAVLDRRQTAAQVRGQGALVDRVAAVLNAAGDLRGLGLTEPALRGLA
+VLDDRLQRPRRRAAWAAGGGRALAVAASGGIAVAAAAAAAHTGTSAPVAALVVLLALSWA
+EPYGALAAAAQHWGTLADRARATGELLGPEEGGAAAAPPEPAEAAEPEARVCRLRLVEAA
+FAHPGAPPLWTDLELDLAPGDVAVVTGPSGSGKSTLLAVLLGFLPLTAGRYTLETVPPTP
+QPDPVRPDATALARVAWTPQDALIFDSTARGNLALARGVADAPSDAELTAALELVGLGPW
+LAAAPQGLDTRVGPGGQGLSGGQRQRLAVARALVARADVVLLDEPTAHVDADEARALITD
+LRRALADRIVVIVTHDGRLLEDGDVPVRVGC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001106.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfa170d092ce6c7377248426db7d6487b537ca9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001106.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01321
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT
+KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD
+GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_003691675.1_01042
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT
+ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA
+EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA
+EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA
+KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR
+IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL
+GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK
+TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_005280335.1_01570
+MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA
+KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA
+ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD
+GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_020097155.1_01466
+MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT
+ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP
+KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT
+TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM
+RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM
+LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV
+INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF
+GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV
+YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>GCF_023573625.1_01277
+MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG
+ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS
+AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG
+TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD
+LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG
+RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM
+VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD
+SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI
+GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001108.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..160fe35e383b7bf599d9b5f55aa0387d1e38d59a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001108.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01323
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
+>GCF_003691675.1_01044
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTDDGD
+>GCF_005280335.1_01568
+MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM
+FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL
+AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR
+ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE
+RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG
+SAPAQEDGPPRPSTDDER
+>GCF_020097155.1_01464
+MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV
+DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL
+LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL
+ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA
+ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE
+SVQPRPTTPAQDDEGPAPSPDPQV
+>GCF_023573625.1_01279
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33312e3ea4053977cd364ad75d37b97cae70663f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001110.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01325
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_003691675.1_01046
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_005280335.1_01566
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH
+AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI
+YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG
+>GCF_020097155.1_01462
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK
+LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>GCF_023573625.1_01281
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001112.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02d48c565292155aefd37ea296cc82510190f171
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001112.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01327
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>GCF_003691675.1_01048
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>GCF_005280335.1_01564
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>GCF_020097155.1_01460
+MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN
+HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS
+>GCF_023573625.1_01283
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49578f24720d38047ab32de9a6301202a9aef4d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001122.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01339
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS
+>GCF_003691675.1_01059
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
+>GCF_005280335.1_01553
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD
+>GCF_020097155.1_01449
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS
+>GCF_023573625.1_01294
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0d36c83fe62e1902f253e7bf23b5b7e8205f8a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001125.fa
@@ -0,0 +1,105 @@
+>GCF_002008305.4_01343
+MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>GCF_003691675.1_01063
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>GCF_005280335.1_01549
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG
+AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD
+LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD
+TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV
+VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS
+>GCF_020097155.1_01445
+MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG
+AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML
+AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT
+LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA
+KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG
+LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD
+LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF
+ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ
+VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE
+RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG
+>GCF_023573625.1_01298
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKATAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001130.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e486d444fa9f70af565ef2c192b3b958dcde8c1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001130.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01348
+MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
+>GCF_003691675.1_01068
+MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGVADSPFDGD
+>GCF_005280335.1_01544
+MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV
+VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP
+VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR
+ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD
+>GCF_020097155.1_01440
+MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP
+STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP
+RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT
+PSSVEVVGEEPPAGRDGDAPYDND
+>GCF_023573625.1_01303
+MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001134.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15f9f8f22e4a715a126617f526c1e15e4ce05e00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001134.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01352
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLGALGWVVFFSPVLA
+VDRVEVTGTRHVSAAEVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVVVREHETRARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRAQEERAEV
+AEVLAALPEAVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGPVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
+>GCF_003691675.1_01072
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTALGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLAPVYGVPLSRVGAGRVGELAGGLPGVAEVQTVPRLPTGL
+EVVVREHEARARRDGGDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRVQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEAGVAEIDISVPTRPITR
+>GCF_005280335.1_01540
+MTPGRGGRPPRPAGPAQPPAGSTVVPFPGRSVRRRRAVRWAVAGAVAALLGALAWVLLFS
+PVLAVDEVDVTGTRHVSAEAVQERLAPLHGVPLPRVGSSAVRELVGDLPGVAEVRVVAHP
+PTRVEAAVREHEARARRGGEAGVDLLLDDGTVLAGVPAERVEGESLPEFSEELSAGPRRD
+REEVAAVLAGLPAPVAERVESVDSSRAGQVRLGLRDGVVLVWGDAEDAELKGTVATAFLE
+GDQHGSRAGGVREVDVSVPTRPITR
+>GCF_020097155.1_01436
+MVAFPGRSARERRRRRAGMLAAVFAALALAAWAVFASPLLAVDRIDVTGTRLVDRAAVEE
+RVAPLRGVPLPRIGSSSAGDLLSGMPGVASARTVAVPPTALEVRIEELAPVARSAGGDRA
+QVLLEDGSVLGSVPVSALPGEGEEGGALPSAPEALLTAGPDVRASAATVLRALPDGVRDR
+VRGVDAGSPEQVRLDLGGGRTLVWGDASEPERKAAVAQALLDGLEDARGVREVDVSVPDR
+PVTR
+>GCF_023573625.1_01307
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTVLGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVAVREHEARARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELPQRAQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001139.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..022d4ce8bb73f7fc234954d8bf48d967eb1fe22c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001139.fa
@@ -0,0 +1,56 @@
+>GCF_002008305.4_01358
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>GCF_003691675.1_01078
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>GCF_005280335.1_01535
+MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA
+ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA
+YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA
+SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR
+HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA
+ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ
+FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT
+VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS
+FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL
+MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG
+LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK
+GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP
+>GCF_020097155.1_01430
+MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA
+ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS
+AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA
+YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA
+SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR
+HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS
+QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA
+ALGDRLAAADVTPSTASPSDTTKETRP
+>GCF_023573625.1_01313
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5a095bbda83b2c8e29112ceb0fe45d481a66b63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001144.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01363
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>GCF_003691675.1_01083
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>GCF_005280335.1_01530
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF
+>GCF_020097155.1_01425
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL
+>GCF_023573625.1_01318
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001148.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfe22b0621af7f29e9962308bb38c67133760bc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001148.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01367
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>GCF_003691675.1_01087
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>GCF_005280335.1_01526
+MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN
+LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP
+SLPGRPIDALRDGRKTEVRRRAQALAW
+>GCF_020097155.1_01421
+MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP
+SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK
+TEVRRRAQALGW
+>GCF_023573625.1_01322
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96054a22ee4b6668a12a330980f7e1e666364194
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001151.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01371
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
+>GCF_003691675.1_01091
+MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL
+DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD
+>GCF_005280335.1_01521
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV
+HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL
+DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD
+>GCF_020097155.1_01417
+MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL
+DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD
+>GCF_023573625.1_01326
+MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV
+HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP
+EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL
+DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001154.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..576d7d3b55684ced9895836f60d4f6abccae9a70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001154.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01374
+MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD
+SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI
+SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD
+LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV
+STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD
+AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL
+KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV
+KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH
+RLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>GCF_003691675.1_01094
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
+>GCF_005280335.1_01518
+MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL
+AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF
+VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG
+GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE
+PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV
+TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA
+VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV
+AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL
+DVPDSGLL
+>GCF_020097155.1_01413
+MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV
+AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR
+IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV
+PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH
+DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET
+LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN
+AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED
+AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG
+IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>GCF_023573625.1_01329
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001157.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..363f856a9fc309be3b964ced9bf24c7024757339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001157.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01377
+MTEPRPVPADDAGDVPLSVLGVRVELPEQHHVILLVDPPGRTMIPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
+>GCF_003691675.1_01097
+MTEPRPVPADDAGNVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRGEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
+>GCF_005280335.1_01515
+MTEPRPEDAPEAGDVPMSVLGVRVELPEQHHVILLVDPPGRIMVPLWVGAPEAAAAALAL
+EGVSAPRPLTHELLLSTVAALGAEVVRVRLTEVRNDVVHGELELSTGARVDARASDAVVL
+ALRANAPVLASPAVLAEAGMSARSGEEDGQERTVEDFRDFLDSVRPEDFA
+>GCF_020097155.1_01410
+MAEPPEPAGDVPLTVLGVRVELPEQQHVILLLDPPGEIVLPLWVGSPEAAAAALALEGAP
+SPRPGTHALLLAALAAAGSRLRGVRLTRIEDETVHAALLLDGGAEVDARASDAVVLAVRA
+QVPVLCAAEVIAAAGMAARDAAAGDEDEVDDFRAFLDSVDPEDFA
+>GCF_023573625.1_01332
+MTEPRPVPADEVGDVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRTPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001163.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fba505169fbd84b6b6703b7c4f1f5bd640d6e7e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001163.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01404
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLADYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVGEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
+>GCF_003691675.1_01134
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGSRR
+>GCF_005280335.1_01491
+MTEHTRDDVATTPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADADAVAAAAVAMELEQSTDPDVEAVRVGGTDVTEAIRGAEVTDTVSTVAVVIPVREE
+LRRRQRETIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGEPGVD
+AGTLHRQGGRAGRPRRHRVHVRPPRRGRGARGLHRARLRADRGGRPGRRRGPGRHPGREG
+RPTMTDNPQHRSGDDEFVPAGEDQVAERLAAMTEEEAEARAASLRAGLADYELEDDDAAL
+LDAWQLGPDEDLDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDA
+EWNGREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSM
+LRRKDRPVIVAANKVDDMVQEADAASLWSLGFGYPYPVSAVHGRGVADLLDAALEAMPEE
+SAHGGLVPRGGPRRIALVGRPNVGKSSLLNRLAGSDRVVVDDLAGTTRDPVDELVELGGR
+LWRFVDTAGIRRRQHMAHGADYYAALRTASALDRAEVAVVLLEAPSVISEQDVRILQMVL
+DSGRALVIAFNKWDQVDEDRRHQLEKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDT
+ALDSWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDP
+GYRRFIVRRLRETFGFEGTPLEIGMRVREKRGLAPLSAAAADDDGVPRARRGSTDPAPAG
+GRRRPTPSRGSSHGFLMFRA
+>GCF_020097155.1_01403
+MTENTPLTEGEEYQPAGEDHLAERLAAISDEEADARAASLRAGLGDYELEEDDAALLADW
+DGDDEFDLDLPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYEAEWNG
+RVFTVVDTGGWEHDAKGIHKRVADQAELAVDVADAVVFVVDATVGMTATDEAVVTMLRRK
+DRPVIVAANKVDDMVQEADAASLWSLGFGYPWPVSAVHGRGVADLLDAALEELPEESAHG
+GLVPRGGPRRIALVGRPNVGKSSLLNKLAGADRVVVDDYAGTTRDPVDELVELGGRLWRF
+VDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPSVISEQDVRIVQMALESGR
+ALVLAFNKWDQMDEDRRPQLEKEIERDLAHVAWAPRVNISALTGWHKDRLVPALDTALES
+WDRRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQASTRPPTFVLFTTGFLDPGYRR
+FIVRRLRETFGFEGTPIEIGMRIRERRGRKR
+>GCF_023573625.1_01354
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8a4fc4eb0b5e52f6a002d1f9a57c89a336e71bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001165.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01407
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>GCF_003691675.1_01137
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>GCF_005280335.1_01489
+MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR
+GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR
+VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS
+VRALSAQELGHLKALVGL
+>GCF_020097155.1_01400
+MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG
+KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV
+RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV
+GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL
+AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG
+SVRAMTAQEQGHLKALVDL
+>GCF_023573625.1_01357
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001167.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8710b81ae06d63dc7cf35d0d8288e17459cbe29b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001167.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01413
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
+>GCF_003691675.1_01144
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
+>GCF_005280335.1_01486
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPVREALSRLVADGLAEQAPG
+RGTVVADLSLEQADQLFDLRIALESLLARRAAQRATPETAARFTALAARFQEAGEALRAG
+TDPADYYAMTAELDASLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLATSAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRTRADETPTLLSPTEGDRP
+>GCF_020097155.1_01393
+MPPFTPAGVSVYSGAMRVSDRAYAALRGEILDWTLPPGTVLGEVELADRLGISRTPVREA
+LARLVADGLAAQAPGRGVVVADVSLEEAEQLFELRIALESLLARRAAERADADQAAAMGA
+LADRFLAAVPRLEAGDEPAGYYTLTDELDAGLDAAAGNPYLVSTLRTLRLHLARLRRLAA
+HDPARLASSAAEHADIAAAVAAGAADLAEATTRVHLHHAATHLTRRARAAESTTLLTPTP
+FEGAHQ
+>GCF_023573625.1_01363
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEVALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001168.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98991f27be1b070901a8b2b046279d625a5ab0d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001168.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01414
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR
+GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>GCF_003691675.1_01145
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>GCF_005280335.1_01485
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR
+GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL
+TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP
+GELDQLNVTADPAFLSQADLDNAPKGLF
+>GCF_020097155.1_01392
+MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH
+PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV
+ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL
+TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA
+GELDQLNVLANPAFLSEADLAAAPKGLF
+>GCF_023573625.1_01364
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001185.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f31c2c4e902dc61e89118d3413babaf8dee9bd11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001185.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01435
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVKHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>GCF_003691675.1_01167
+MSTDQSALLKRYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>GCF_005280335.1_01463
+MSTTQDALLARYADSLTGVFGRPARVLVRGEGVHVWDADGRRYTDLLAGIAVNSLGHAHP
+AVVRAVREQIAGLGHVSNLFTSEPQIRLAEELLAVADAPAGSTVFFANSGTEANEAAFKL
+ARRHGGQDPSGSRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDVDA
+LRAALAPGASGATVAAVVLEPVQGEAGVHGWPVGYLAQVRALTREAGALMILDEVQSGMG
+RTGTWFGFQNPSVTGSDDPVLPDAFTLAKGLGGGVPIGALVCVGPEVSGLLSAGQHGTTF
+GGNPLATAAGLAVLETIRSEGLLEHVRAAGERAAKLLADLPEVAAVRAHGLWIGVDLAAP
+RGPVPDGGLAPAVVAAGLEAGWILNATGPDTLRLAPPLVIAAEDLERFVELLPALVAAAT
+TEGDPS
+>GCF_020097155.1_01371
+MSTAPGTDPAAPQEELLARYAHALTGVFGAPARALVRGSGTSVWDADGREYTDLVAGIAV
+NSLGHAHPAVVEAVSRQVATLGHVSNLFTSEPQVRLAEALLDRAGLPEGSSVFFCNSGTE
+ANEAALKLARRHGTQDPTGRRTRVLALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEF
+IAGGDAGALAAALAPDAEGRTVAAVVLEPVQGEAGVHGWPAAYLARVRDLTREAGALMIL
+DEVQSGVGRTGTWFAFQNPQVTGSGAPVVPDAFTLAKGLGGGVPIGALVSVGPQVSRLLA
+PGQHGTTFGGNPLATAAGLAVVETLEAEGLLDHVRTVGARVSERLETLAEVTAVRAYGLW
+IGVDLADDAAASPTGGLAPAVVRAGLDAGWILNATGPRTLRLAPPLNVEAADLDRFADAL
+PALVRAARAAAPTPHAPKEETA
+>GCF_023573625.1_01385
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQIATLGHVSNLFTSEPQIRLAERLLELAGVPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSRLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPVPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa900f915174612a215c9e320032a4f757a2338b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001187.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01437
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_003691675.1_01169
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_005280335.1_01461
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS
+DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER
+LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM
+LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA
+ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP
+NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>GCF_020097155.1_01369
+MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT
+DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT
+LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM
+LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG
+AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP
+NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH
+AGDAVVELWTNDLTHDYVHENSAYST
+>GCF_023573625.1_01387
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT
+LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001191.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c2fa5aa0e0ce64c678f4c28eef0586c304dc8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001191.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01442
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>GCF_003691675.1_01174
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>GCF_005280335.1_01456
+MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP
+RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA
+LRRA
+>GCF_020097155.1_01364
+MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP
+ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED
+PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG
+TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS
+>GCF_023573625.1_01392
+MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH
+GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001194.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcc529f471b3b57ef1ae1760180113e3169bd881
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001194.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01446
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRASLALGGYIERPVVRGLRRRR
+>GCF_003691675.1_01178
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
+>GCF_005280335.1_01453
+MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG
+WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST
+WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR
+>GCF_020097155.1_01357
+MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP
+GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP
+ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA
+>GCF_023573625.1_01396
+MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a86c90699f691af6f100508a7ee0d503ec96ad4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001195.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01447
+MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA
+VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL
+QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV
+MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP
+GGTLH
+>GCF_003691675.1_01179
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS
+ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA
+LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH
+>GCF_005280335.1_01452
+MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP
+ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA
+HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH
+RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH
+>GCF_020097155.1_01356
+MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA
+LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL
+PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ
+TPALPAADLARAVAAVARAALVEGPDLDVPGGALH
+>GCF_023573625.1_01397
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP
+ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA
+LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001198.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5c9a2853b2cb950e82d63e5002023817946fe85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001198.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01451
+MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLVFNINVNEKFF
+SLGTWIFAIIGGVIVAAVWQAITRRTGTRA
+>GCF_003691675.1_01183
+MFTIIAWIIIGLIAGAIARLILPGRQGSGWLGALITGLLGAVLGGWISTLLGGEGLGDAF
+SWQTLIWSVIGGVIVAFIWQAITSRRGTRV
+>GCF_005280335.1_01448
+MGFIAWIVLGLIAGAIARAILPGRQGTGWLGALITGVLGALLGGWIGHLMGFSTNDSFFD
+LATWIFAIIGGVIVAFIWQAITGRRGTRV
+>GCF_020097155.1_01352
+MGFLAWIILGLIAGAIARLILPGHQGSGWLGALITGVLGALLGGWLGRTLFGASTNDGFF
+DLATWFWAIIGGVIVAFIWQAIAGRMGRGTRV
+>GCF_023573625.1_01401
+MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLLFDFDVNEKFF
+DLGTWIFAIIGGVIVAAVWQAITRRTGTRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac71a94769ae8bb0df8d4ac6d440e6cd818fcde4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001199.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_01452
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ
+WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA
+PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
+>GCF_003691675.1_01184
+MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ
+WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG
+QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD
+PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA
+RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD
+>GCF_005280335.1_01447
+MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA
+EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH
+VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV
+ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV
+VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF
+GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG
+>GCF_020097155.1_01351
+MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER
+TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV
+TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS
+VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL
+GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA
+>GCF_023573625.1_01402
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ
+WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA
+PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001200.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..488242ceb5eaa176af9cb468f4388b8294669efc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001200.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01454
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
+>GCF_003691675.1_01186
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
+>GCF_005280335.1_01446
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDKLVSKGSLKQIKR
+MLGI
+>GCF_020097155.1_01349
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLAGDKVVSKGSIKQIKR
+MLGI
+>GCF_023573625.1_01404
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001201.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90f6886d658803ae1772b484f95ba74d5bba3e0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001201.fa
@@ -0,0 +1,39 @@
+>GCF_002008305.4_01455
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA
+TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP
+KPGPRA
+>GCF_003691675.1_01187
+MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH
+AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV
+GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA
+FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA
+TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA
+>GCF_005280335.1_01445
+MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP
+TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL
+SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT
+KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL
+KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA
+PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA
+>GCF_020097155.1_01348
+MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR
+PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE
+ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE
+TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN
+MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN
+SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP
+KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG
+>GCF_023573625.1_01405
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS
+PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf4102b2cbe58fdfb607e896a68ee6c0c3fa6b97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001202.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01456
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
+>GCF_003691675.1_01188
+MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG
+LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN
+>GCF_005280335.1_01444
+MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>GCF_020097155.1_01347
+MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>GCF_023573625.1_01406
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f22aa69761b69df4cb8ec47cc8a1a5a315363a7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001206.fa
@@ -0,0 +1,51 @@
+>GCF_002008305.4_01460
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA
+ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA
+GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP
+>GCF_003691675.1_01192
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
+>GCF_005280335.1_01440
+MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA
+VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA
+DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA
+GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA
+GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA
+AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR
+VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA
+PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG
+VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD
+VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP
+>GCF_020097155.1_01343
+MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA
+RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG
+ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV
+DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG
+PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG
+SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG
+FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD
+RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA
+PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP
+>GCF_023573625.1_01410
+MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT
+AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG
+RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA
+ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA
+GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL
+TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA
+TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ
+VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA
+RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001207.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0b897cbd703c9fb63f8f34e8d0687e05ca3cdf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001207.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01461
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>GCF_003691675.1_01193
+MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI
+AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>GCF_005280335.1_01439
+MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP
+GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR
+RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS
+GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR
+>GCF_020097155.1_01342
+MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP
+GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR
+PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA
+TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG
+>GCF_023573625.1_01411
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001209.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81ac0541fa74da95e555cc782d79ed61c3c7b350
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001209.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01463
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAVAAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
+>GCF_003691675.1_01195
+MRWNGLFDDLEAHWVDLGWQETVAEAAELTRAEWMALSLVDRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPLDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
+>GCF_005280335.1_01437
+MRWDGLFDDLEARWADLGWRQSEAEAAELTRAEWMALTLADRLRGERGRPVRLHLAWGEA
+LDGVLHAVGEDWAGLHLSGGRSAVVPLPGVAAVEAGLHRAVPAPTGPATGLGAVLRGIAR
+ERVPVVVTGTRGVTLVEGTVDRVGRDHLDVSRHPRDEARRAAAVRGRLVVPFTALGVVRT
+ASRLA
+>GCF_020097155.1_01340
+MRWDGLFEDLEARWSALEWDATRAEAAELTRGEWAALTLEERLRGARGETVRLHLVWGEH
+RDVRLGTVGDGWVSVNAAAADSLLVPLTSVVAWEGPLGAASTAPEGVRSRPGLPAALRQL
+ARARAAVRVVAGNGVELGEGTIDRVGRDHVDLARHPRDEARRAGQVRGRLVVPLAALGLV
+ATPGPLG
+>GCF_023573625.1_01413
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbca836e9dc92ee96e399b4221e2a36fe9cdb95e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001213.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01467
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>GCF_003691675.1_01199
+MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
+>GCF_005280335.1_01433
+MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL
+TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ
+NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA
+>GCF_020097155.1_01335
+MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL
+TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF
+VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT
+GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE
+>GCF_023573625.1_01417
+MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL
+TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV
+PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN
+AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001214.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab5ed6c686bbd9b8d32477352f472bf6d20dbe2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001214.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01468
+MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ
+DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP
+DLPGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG
+PSHAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG
+AVVLAAVAPPRDPAEPGPRPGPRVG
+>GCF_003691675.1_01200
+MRSPPSSPSPAFGALGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQDA
+PALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEPDL
+PGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGGPS
+HAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVGAV
+VLAAVAPPRDPAEPGPRPGPRVG
+>GCF_005280335.1_01432
+MPHAPAPEPLLESDSGLPAARRAIAALAALGEAFVDLVLPAECAVCAAPGHRLCAPCRLE
+LNAALARPFRAEHGAAALPLGPGGVPLPVVAAGRYADALAAAVLAFKDHHGLHLRAVLGE
+ALCRSAAVARLAPDVPEAAHALLVPVPGGAAGFRRRGYDPLAELVRALPAPWVVSDAVRA
+PRGPGRARRAGPSHAGAGSAQRRRRARRWRPVPGRLPAGAPVLLVDDVLTTGATLGALAE
+AVRRAGGRPVGAVVLAAVAPPADDPGPVTGAGVG
+>GCF_020097155.1_01334
+MHPLLESVVDLVLPADCAVCGAPGHRLCPDCRCLLGRELSAPHRAEEPALALPLGPDGAP
+LPVWAAGDYRDGLAAALLAFKDHHGFGLRPILGDALARTVAAARLDPGLQEAAHALLVPV
+PGSASGFRRRGYDPLAELVRSLPAPWVRDDVVRAAPAWSAWPPGGGPSHGGAGSRERRSR
+RRGWRVREGALRPGTPVLLVDDVLTTGATLAALHRAVRRAGGRPVGGVVVAAVAPPTGDG
+GAGVGGAGSTLAGAEPGE
+>GCF_023573625.1_01418
+MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ
+DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP
+DLPGAPHALLVPVPGGAAGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG
+PSHAGAGAGQRRRRARDWRVVAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG
+AVVLAAVAPPRDPAEPGPRPRPRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..705bae328f0a3ec8db690b2895d1142eb8b9b51f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001216.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01471
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_003691675.1_01203
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_005280335.1_01429
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>GCF_020097155.1_01331
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV
+>GCF_023573625.1_01421
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cce9e712c0b535b6dc9813d7d6e3bda22cda80e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001218.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01473
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>GCF_003691675.1_01205
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GESPGDADD
+>GCF_005280335.1_01427
+MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE
+LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD
+PAADSLPDGTRTDAGDDPRRGGADA
+>GCF_020097155.1_01329
+MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA
+LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE
+ASDAGSADA
+>GCF_023573625.1_01423
+MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD
+LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP
+GAGSGDADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001219.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..319652bb45729c0d1f62bbf4c804ebe020903812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001219.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01474
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPGRPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
+>GCF_003691675.1_01206
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPARPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
+>GCF_005280335.1_01426
+MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVEDFVAEYAAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGGLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADSPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLTPGPIVDADGCAVGEHAGAQAFTV
+GQRKGLAIGRPAPDGRPRFVLEVRPKENTVVVGGRELLDVDRITGIRPTWAGAALPEART
+GEWFDCALQFRAHGEIVDARARQLEDEAGGPRWEIEPARALRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLAAGSDA
+>GCF_020097155.1_01328
+MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDAQDAWRA
+CEVLGIPFYTWDFSERFQADVVDDFVAEYAAGRTPNPCLRCNEKIKFEALLDRALELGFD
+AVATGHYARVEWGEDGRVQLHRAAEDAKDQSYVLGVLREDQLEHCLFPLADTPTKELVRS
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVGADGEVLGEHAGAQAYTV
+GQRKGLAIGRPAPDGRPRFVLEVRPKDNTVVVGGRELLDVDRITAIRPSWAGAPLPEAAA
+GGWFDCELQFRAHGEIVPARARQAADDDGRPRWEIRPERPLRGVAPGQSAVLYRGTRVLG
+QATIDTARNAAVDAAERA
+>GCF_023573625.1_01424
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGRELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADEAGNPGWEIEPARPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001223.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1105d62492fd88207be06a979dc3c07a2566e7a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001223.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01480
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVGRLH
+>GCF_003691675.1_01212
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDERRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
+>GCF_005280335.1_01422
+MSAADEHCTAYEVLGVDRDADDAAVRRAYRAAARRTHPDAGGDPAEFRAVSRAWQVLGDA
+DARRRYDLSLPAPGAGRAPASGGAARPGRAAASRPARGAAGRPARTVRYEPPPGEGESDA
+AVLDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLAGR
+WGRPLDVDHAVLCGHRLALVGSVMVPEGAYTWDGSDLRSRGRPVAPPLLGPAMMAWQQVL
+PQVTVGGFVHVMTDRDALHGPVVRHARGADDPGARADLLTVPPAPGREFVRDLLLFLGTG
+EDPDLVDRRVLGTLVERLH
+>GCF_020097155.1_01322
+MSGTGDRRTAYEVLGVPRDADAERIRRAWRAAARRTHPDAGGDARDFRAVTRAWEQLGDP
+EARRRYDLSLPPEPAGTTGRTASAGRSAAQAWPPAGVRERDRPAPGSVVYDPPPGQGEHD
+SSVLDLVRSSQRLHGAPRPRGILPDEHRVVRQARTLDLLARTLPPVLPAVRILTGLHLGG
+RFGRGLDVDHAVLCGRRLALVGSVQVPDGTYTWDGADLRAGARGRPVAPPLLGPAMQAWQ
+HALPQVTVGGFVLVMTDRDAVHSPVIRQARGADRPEAQADLLTAAPAAGRDLLRELQLFL
+GSGPDPDVVDRRALAVLVRHLH
+>GCF_023573625.1_01430
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRSRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001227.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c53f65cdc6d26a747a7398c407e6f082b0bc05db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001227.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01484
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGDAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGSDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGGENAQTVFSDGARVQQVV
+GGSAADAAGLKEGDVITAVGDRAVIDSESLTAVVREYRVGDSVDVTYLRDGAEQKTEVTF
+TEDTQS
+>GCF_003691675.1_01216
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGTDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTVFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
+>GCF_005280335.1_01418
+MRSEDTVAHTPADQTPTDQTPTDQTPAPARPAAEARHPGRRAPRARAGLGLLAAAVLVTG
+LAGCGVAAEPGADASGSAPDSSTSSGSASADPGQDVADTAVGTAAKTALPSVVTISATSG
+QGSGSGSGTILDEEGHILTNTHVVTLGGQASDAELTVRTADGTVYAATVVGTDPLSDLAV
+IKIDAPDLTPIQMGRSADLKVGDDAIAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPRQ
+QESEQGQGPGQGSSSGPERFRFELPGAQQGPQGEVYINVLQTDAAINPGNSGGPLVDGQG
+RLVGVNVAIASAGQGQGEAGNIGVGFAIPVDYAQRVAQDLIEHGEATHAVLGVSVTPEPA
+EVQGGDAQARTVFSDGARVREVVADSPAAQAGLREGDVITAVGERAVIDTESLTAVVREH
+RVGDSAEITYLRDGAEQKAQVEFQEDTSQ
+>GCF_020097155.1_01318
+MGRAAHRPDCTDGGADQKPAQTRSEATVEHPAPDTVTPEAAPVASSPRPASPRGRRRALG
+GALAATVLAGSLAACGVAGPGAGASASASASGSSSAAAAPAVGSTDQPVADNPVGAAAAK
+ALPSVVTISATSGSSAGSGSGSILDAEGHILTNTHVVTLGGTASDASITVRTSDGKVYAA
+KVVGTDPVSDLAVIKIDAQGLTPITIGSSKDVKVGDDAIAIGAPLGLSNTVTDGIISTLN
+RTIAIQSSAAPEGQTGSSGTERFRFQLPGEQGQSQQQDIYINVLQTDAAINPGNSGGALV
+NGAGELVGVNVAIASAGGSSASGAESGNIGVGFAIPVDYAKRVADDLIADGTASHGLLGV
+TVQPQPAQVQGAAGGSKSTEFSAGALVHTVSSGSPAEKAGLKEGDVITQVGERTVTDTES
+LTAAVREYRDGETTPVRFTRDGREQTADVTLTAMEASR
+>GCF_023573625.1_01434
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGAEQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTMFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001228.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2495a27fab6ca4e21a96106e070778c0ff0bb774
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001228.fa
@@ -0,0 +1,66 @@
+>GCF_002008305.4_01485
+MTVLTRPADVGRLARAVTAAGLGGLGLLVAAPTAQAVAVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEERAYGLDS
+GGDANLQNQVTRTYVGPQLSKIGTDPGSAEWLAVGIAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTTGGGSTAQGASDGGGALTAVLGAGAVAAAVGGGVLVARSRRRTQGGAVER
+GRTEEARRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDI
+DQAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLE
+NQVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETA
+LAKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQ
+DVAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPL
+AGVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSA
+ISLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMGSRYGTRPRAGVGGSFGG
+GLGGALLGGILMNSILNSGHGDSWGGGGFGGFDGGGLGGGDFGDISGGGF
+>GCF_003691675.1_01217
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFREDID
+RAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGAALAAHKKEFDSLRDLEN
+QVPEALERVDARLPEARSRVQESESAIAALHGQYAESALAEVADNATQARERLEFVETAV
+AKARSAWDAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSNPELAGPVAGMKNAVNAVRRALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>GCF_005280335.1_01417
+MTAAGLGGVGLVLAAPGAGAGIAPPGVYVVDEAGVLSSADEQRLTQEITDLRRDTGQGLY
+VVFVDSFETNAQGLADDVARQRGLGTNDSVLAIAVEDRSYGLGSGGDASLQNQITRTYVG
+PQLSRIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEYDPEGALPAGSGAGAGT
+GAGSSQGSDEGSGVLTAVLGAGAVAAAVGGGVLVARNRRKKDGGAVERSGRDARPVERDP
+LDEMSLEDLRTRAGSKLVAADDAIRSSEQELGFAMASYGEDAVRTFREDIDQAKEHMRAS
+FQLQHQLDDHIPDTEEDQRSWLKEIIQRSDAVGAALASHQKDFDSLRDLENNVPEALERI
+DARLPEARARVQQAESSISALHGQYAESALAEVADNAAQARERLDFVETAEAKARQAWET
+QDRSTAALAVRAAEESLSQVDTLTEAVGKAEGSLRTIVGNLQTGLAQSEQDLAEAEALVA
+NGSHPELAGPVAGMKTTLAAVRRSLSGGRPDPLDLLHQLEAAHRQLNTPLSGVRDAREQA
+RQASQMLNSAIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRAAIDLSRTDPVT
+ALQQAQRASQLAERASELARQDVEGFGYGGSMYGPGMGGMYGGRQRSGAGASFGGGLGGA
+LLGGILMNSMFNSGGGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>GCF_020097155.1_01317
+MAESVVRPSAPRLSRAAVLGGLGAITTTALLAPGAHAAVDVPPGTFVVDQAEVLSSAQES
+ELTQDITQLQSKAGQNLYVVYVDKFDSTPQATIDSVVQQRGLGNSDSVLAIAVENRNYGF
+DTGMSSTMQSDIRSAYILPALRKAAAGGDWEAPAVAAVQGLDDAANGTLDGRGRSGETYQ
+PDGTLPQAAEQDSSAQTSTSDSGNGASGALVGAGALAAVAGGAYVVSRRRRKSDGGAEPG
+AVATGPQASRDPLDELSVDELRKRAGATLVAADDAIRSSEQEVGFAMASYGEGAVGTFRQ
+DIEKAKEHMRASFQLQHQLDDEIPDTEADQRSWLKEIIARSEQVGATLAAHKKEFDSLRD
+LENSVPEAISALESRVPQAEGAVQAAERELVDLHGRYAESALTEVNDNATQARERLEFVK
+TAEAKARASLEAGDRSTAAVAVRAAEESLSQVGTLTEAVSKAGAALSTHVANLQMGISQS
+EQDLAEAQALLSAGRNPELAGPVGGMQQTLAAVRAELQSGRPDPLALLQRLESAHRQLNT
+PLSGVRDAREQARQAEQMLSAAISQAQAQIDGTADFIGARRGAVGSEARTRLAEADRSLQ
+TAMSLRSTDPVAALDHAQRASQLADRASERAQQDVADFGYGGMGGYGGLGGGYAGAGYRG
+GYGMPRSGAGGGFAGGLGGALLGGILMNSMFGGHHHDSGFGGGDWGGGGFGGFGGGGLDG
+GDFGGFGDADFGGF
+>GCF_023573625.1_01435
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDID
+QAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLEN
+QVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETAL
+AKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001233.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e1ba89852403a039dfb3e8d0f9f0e354044f65d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001233.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01515
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>GCF_003691675.1_01224
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>GCF_005280335.1_01410
+MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL
+VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS
+QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS
+DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT
+AQDTWVDDEDAMDADAPDDGPTEDERA
+>GCF_020097155.1_01309
+MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD
+RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV
+TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR
+LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG
+>GCF_023573625.1_01442
+MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD
+GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL
+SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL
+ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001235.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1469c2dca8ffe81c98db07b0b5852a2673188eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001235.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01517
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>GCF_003691675.1_01226
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>GCF_005280335.1_01408
+MSTPDEILRGLDPEQRRAATALQGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQGMRMSVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARGREMPAGWDATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPRIAATIRDQYRVFLVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERHPDATVVELVRDYRSSPQVVEAANRLL
+ADRTKAGQRDRTMPRWPDPLELVSQRPNGPDPVFAECTDDEAEAGWVADRIRALIDDGVA
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVPDRVRDVLASLGYSAQPPAATGAARERWESLHALVNLAEQLAGSRGAEFTLTELVA
+ELDERAQHQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRAREHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAPGAAKP
+RRRGATVATCRTCGKPLETGAERKVGRCLDCPATYDEAVLEQLRDWRSRTAAEMKMPAFV
+VFTDATLVAIAEAMPASPKELLAVPGLGRTKLEKHGEALLELLHGTPTA
+>GCF_020097155.1_01307
+MSTPDEILRGLDPEQRKAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVDGVQARTFHSAALRQLQYFWPQAVGGQMPTLVENKVRLLT
+EVAHRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARDREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPKIAATVREQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRQDLCVVGDSSQTIYSFTGATSRFLTGFRERYPEATMVKLVRDYRSSPQIVGAANTLL
+AERTQAGLRDRSLPFWPEPLALSSQRPSGPDVVFAECQDDEAEAGWVAQRIQGLLDDGVP
+AAEIAVLFRTNGQSEAFETALSAAGIGYQLRGGERFFSRREVREGVLQLRAAAREAQDLV
+GADVVQRVKDVLSSLGYSDTPPSASGAARERWESLHALVNLADQLAGTREDFTLVQLVAE
+LDERAQAQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFADTPAEVDEERRLL
+YVGITRARQHLHLTWTLARSGGGRANRRPSRFLRAIDPTLGGTREHAPAAAMPARRPRRG
+ATVAVCRTCGRPLETGAERKTGRCVDCPALYDEGVLDTLKDWRSRVAKTDKVPAFVVFTD
+ATLEAIAETMPATPAELIKVKGVGKSKLDRFGQDVLDLLHGTSAA
+>GCF_023573625.1_01444
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGSCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKTKLEKHGPELLELLHGTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001238.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c9fef83e384a86cc0a8e574d21f068deed437f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001238.fa
@@ -0,0 +1,105 @@
+>GCF_002008305.4_01520
+MAPLTGDPAAPTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG
+KTSTMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAAAGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRAQRAAGGREDPAGAAPDAAPDRDVSPEEDADAAALLEALDSLPGEGTDWVG
+SRGRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAA
+RRHLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHAS
+KGLEWDVVAVPGLQEGTFPSTRADRWTSPGAGALPWPLRGDRASLPQWDGSWAQDQRDWV
+QSAGTKYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKE
+PLPASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAARTLVARWPFDPLDGPEAFVA
+DPEDPEDEERWQPLPHRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDV
+AGTGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGA
+TGMLDIGSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRV
+DAIYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLER
+IGASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>GCF_003691675.1_01229
+MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTQEQAEVVTAPLTPRLVLAGAGSG
+KTATMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANTVAAPLNAHAAATGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR
+GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR
+HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG
+LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS
+AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL
+PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP
+EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLVRRRDVAG
+TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG
+MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA
+IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG
+ASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>GCF_005280335.1_01405
+MAPLTGGPAAPDADRPAGPDAVPADRPGTADAVHAPQDIAARLGLPAPTEEQAEVVTAPL
+APRLVLAGAGSGKTATMADRVVWLVANGVVRPDEVLGVTFTRKAAAELAERINGRVDALL
+RSGLRIPGFDGEPEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLMGGADAHRLMGSV
+VRSHPVVADTLGVAPSRLVSQALHLAGDMAEHLVTPEEVRTHLARVAQQGRDLPLPPRTK
+APTKEIAAFFTGLADRALMADLVARYDEVKREQDVMDFGDLLRHAARIASEVTAAGEQER
+ARFPVVLLDEFQDTSHAQMRIFAGLFGPRGPEDDAAGLGHCVTAVGDPHQSIYGFRGASA
+GQLFAFPHAFPRLETGPDGGRRRVNADVSHLTVAWRNEESILAVANTVAAPLNAHAAASG
+GAPVEVRTLRPRPGAGDGVVRVDRFLTPEEEAHDVVRRLAALAEADGAAPSRAVLCRTRA
+QFGPVLEALEAAGVPYEVLGLSGLLALPEVAEVLAVLHVLADPVRGDQLVRLLTGPRWRI
+GPADLEVLHERARFVARMRARRAAGEDAQDPEGTGGADPEATAAEDVSPEEEADSAALLE
+ALDSLPGEGTEWTGSRGRGFSAEGLARLRAAHAELRRLSARAGEDPADLIAEVVRETGLD
+VEVALRPGLSAAAARRHLNAFQDAARDFGAGTAGADLAAFLAWTESVMEHEDGLGVENAE
+PTPGLVQVLTAHASKGLEWDAVAVPGLQEGTFPSTRADRWTTPGSGALPWPLRGDRGSLP
+QWDGTWAQDQRDWVQSAGTKYSSKAAQEDNPDPYAAAVEAHAEREERRLAYVAVTRARRE
+LWLSTSAYKGTNKDPLPPSAFLEEAAGLAGRVPGVVAGHAPDEDGMPEANPAAGRTLVAW
+WPFDPLDGPEAFLADPEDPEDEGQWRPLPRRARARRDAVEAAAAAVRAAEPSALAAEPEL
+ARQVDWVLLRRRDVAGSGGDVALPDHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARR
+GTAFHAWLEERFGATGMLDIDSAEDAEDLWVDEALDLEPMQAWFRSSRWAERTPAFVEAP
+VETTVGGITLRGRVDAIYRSGGDPRNPVDPEADWELVDWKTGAVPRGRDLELKSLQLAVY
+RLAWSRLHGIPLERIGASFVYVAHGQERSFPDLPGEAELERRLAEALRRR
+>GCF_020097155.1_01304
+MASLSSPVPLRPAPVDAGPRVDVSRAVHSPQDIAARLGVFPPTDEQVEVIAAPLTPRLVV
+AGAGSGKTATMSDRVVWLVANGFVRPDQVLGVTFTRKAAGELAHRINAKVDALLRSGLPI
+PGFEGEPEDLGRASVSTYHSYAGALVRDYGLRIGVEPEARPLGEADAHRLMSAVAASHPI
+VADGLRVSASTLVAAALRLSGDLAEHLVEPAQVRAHLRERIAVGEALELPPRMKEPSDEI
+VEFFAGLETRVLMADLVERYTQAKAERGVMDFGDLLRHAARVAREIPAAGRAERERFPVV
+LLDEFQDTSHAQMEIFRGLFGPESTDLDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFTF
+PSAFPRLGELPGGAPGRVNADVSHLTVAWRNDEAILAAANAVVAELNAHAADAGTPLELK
+PLRPRPGAGTGEVRVDRHVSAQDEAEALVARLAALGEDPATADLSRAVLCRARTQFGPVL
+DALEAAGVPYEVLGLSGLLSLPEIAEVLSVLHVLADPGRSDHLVRVLAGPRYRIGPADLE
+LLHERARFVSRLRRRAAAHEPLDPATAVEAPDVSADEDADAPALLEALDSLPGESTVWTG
+SHGRPFSAEGLRRLRAANAELRRLSAWAGADPADLIGEVVREIGLDVELALRPGPSAASA
+RRHLDAFQDAARGFAAGDGAPADLPAFLAWTEAVEEHEKGLGIASADPAPGVVQVLTAHA
+SKGLEWDVVAVPGLQTGTFPTARPDRWTSGGTGMLPWALRGDAASLPQWDGSWAENRRDW
+VQSAGTGYSSKTAAATNPAPYGDAVADHAAREERRLAYVAFTRARSALWLSTSHWKGTAK
+KPVDPSPFLVEAAALAGEVPGVVLGEEPAPEELGEANPTAERTLVAWWPADPLEGPEAFE
+ADGEDLDDEAAWTPLPRRTRPRRARVENAARQVAAADPAALAEDTDLARALDWVLLRRRR
+VGAAADGVALPEHLSVSLYGELAADPQAVADQLRRPMPRPPAHAARRGTAFHAWLEQRFD
+ATGMLDIDESDDAADAWVEDALDLAPMQEWFLASRWADRVPAFVETAVETTLAGITLRGR
+IDAVFRTGARPGMPFDPEADWELVDWKTGRVPGGAELRRKALQLAVYRLAWSRLHGIPLE
+RIRASFVYVAAGQERVFDDLPGEEELEAIVTAAVAGPGATSSGEVSPPDAAR
+>GCF_023573625.1_01447
+MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG
+KTATMADRVVWLVANGLVRPDEVLGVTFTRKASGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVSADEVREFLARLAEQGSALPLPPRAKTPSKEIQEFLTS
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAATGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGATPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR
+GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR
+HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG
+LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS
+AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL
+PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP
+EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDVAG
+TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG
+MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA
+IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG
+ASFVYVAHGQERSFPDLPGEEELERHITDALARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ec03eda5a074ce823a843d97fc0bafd69ebcf1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001239.fa
@@ -0,0 +1,104 @@
+>GCF_002008305.4_01521
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>GCF_003691675.1_01230
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>GCF_005280335.1_01404
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR
+>GCF_020097155.1_01303
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR
+>GCF_023573625.1_01448
+MTREHGEDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHGAVLVLGAPG
+TGRTTVAVEYAARRIEEGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPKHEVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGMPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001242.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..284776f58d2fcc46449cff243687453bd0b9d965
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001242.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01524
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>GCF_003691675.1_01233
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>GCF_005280335.1_01401
+MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL
+VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW
+DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV
+QRVLDALPAAAKAAAAATPQG
+>GCF_020097155.1_01300
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL
+VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT
+LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV
+ERVLAALPTAAKAAAAATPQG
+>GCF_023573625.1_01451
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001244.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..313e602541fd935afc4aaf3dcaf094e30f3ca937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001244.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01526
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG
+LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
+>GCF_003691675.1_01235
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD
+>GCF_005280335.1_01399
+MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP
+APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD
+>GCF_020097155.1_00047
+MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI
+IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP
+WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA
+GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG
+MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL
+IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG
+LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF
+GWVVPALVGLVVGLVLEAARGRGRSAAVADA
+>GCF_023573625.1_01453
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001245.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58fbeae9b4be42d8a9b1802368b4c275ed2c446b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001245.fa
@@ -0,0 +1,38 @@
+>GCF_002008305.4_01527
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
+>GCF_003691675.1_01237
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA
+AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT
+KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV
+SLVRRRSRRAEG
+>GCF_005280335.1_01398
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS
+GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR
+GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI
+GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG
+>GCF_020097155.1_01289
+MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA
+TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR
+GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW
+ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG
+>GCF_023573625.1_01454
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001248.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b4539fa625f59d8db0dd74d5a119e1ca8895b05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001248.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01530
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLNRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
+>GCF_003691675.1_01240
+MTPLRIGTRGSALATTQTTHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAVQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
+>GCF_005280335.1_01395
+MSTLRIGTRGSALATTQTTHVAQALAERAGLEHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAILDGAVDLAVHSLKDLPAAQPDTLEIAAVPERADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLVLVDIRGNVQTRLARVPGLEQHDDGAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPDVMVPAPGQGALAVEVRAEDESFLGAALLEPDAPVGRLR
+AGLELVDDRATHVAVTAERALLRRLEAGCAAPIGAVARVVDGEAGAPRIEMTAMVAAVDG
+SRVLRRTSSVQLDPVPEDLAADPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPQPDDPA
+>GCF_020097155.1_01286
+MSGPGAPAGDGLRVGTRGSALATTQTTHVAEALTDRSGMPHELVVIRTEGDVTTGSLASL
+GGTGVFASALRSAVLDGRVDLAVHSLKDLPAAQPAGLEIAAVPPRADLRDALCARDGLTL
+ATLPEGARVGTGSPRRVAQLRALRPDLELVDIRGNVQTRLARVAGHEVHDDDAPAAAGAP
+RGDLDAVVLACAGLDRLGLQHVITERIDPEVMLPAPGQGALAVEIREEDGPLLGPSAVDP
+DSHAGRLRAALELVDDRDTHVAVTAERALLLRLEAGCAAPIGAVARVEEGTAVDGSPAPR
+IVMSAMVAAVDGSQVLRRTSSVQLDAVPEDVAGDPAEADEWIEDTLFMAAGALGVHLAEL
+FVAEGADLLPGTVRGVAKPDPEA
+>GCF_023573625.1_01457
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRMH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVSDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPADVAGDPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001251.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1200429e47b84b12de11d04a3db484d47ee55936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001251.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01533
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>GCF_003691675.1_01243
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>GCF_005280335.1_01392
+MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ
+TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG
+DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA
+PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV
+TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA
+TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL
+THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV
+DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG
+TGLAAVVASVDRAFDAPPPAG
+>GCF_020097155.1_01283
+MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ
+TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG
+DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV
+PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV
+TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV
+AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL
+THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA
+DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG
+TGLAAVVAGVERTVAPAAA
+>GCF_023573625.1_01460
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96149d570bfc755ec2247b7f84a2badd9d408fbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001254.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01536
+MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>GCF_003691675.1_01246
+MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>GCF_005280335.1_01389
+MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR
+GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS
+ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT
+DDDAL
+>GCF_020097155.1_01280
+MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL
+ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA
+GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP
+>GCF_023573625.1_01463
+MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a222843a131cc919eca6742a9c84749204f077b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001261.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01544
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>GCF_003691675.1_01254
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
+>GCF_005280335.1_01381
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA
+DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV
+SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP
+AA
+>GCF_020097155.1_01272
+MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM
+TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR
+NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD
+LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD
+AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM
+ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS
+DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG
+QD
+>GCF_023573625.1_01471
+MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM
+TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR
+NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA
+DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD
+DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA
+MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV
+SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP
+AT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98f7d35a08a7cf759760893ba55e0c5f0aada3b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001263.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01546
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>GCF_003691675.1_01256
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ
+IAQRVAVRPRGLAGRRLPVTPR
+>GCF_005280335.1_01379
+MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI
+EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM
+ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL
+DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG
+VAERLAVRPRGLVGRRLPLSPR
+>GCF_020097155.1_01270
+MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI
+AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT
+RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL
+ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL
+DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE
+VAARLAVRPGSLRGRGLPVSPR
+>GCF_023573625.1_01473
+MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI
+AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT
+RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM
+ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD
+IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL
+DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE
+IAQRLAVRPRGLAGRPLPFTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001264.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c2120d5079375ed2d5ea2d44852351fb31db6ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001264.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_01547
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT
+>GCF_003691675.1_01257
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT
+>GCF_005280335.1_01378
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT
+>GCF_020097155.1_01269
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT
+>GCF_023573625.1_01474
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..390bb25ecc6b5aeb47c22863465fc17247ba0c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001274.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01558
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>GCF_003691675.1_01268
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>GCF_005280335.1_01367
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN
+>GCF_020097155.1_01258
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN
+>GCF_023573625.1_01485
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001278.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..203f4391a2d67434f90465cb747d47a9e9833ceb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001278.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01564
+MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>GCF_003691675.1_01274
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>GCF_005280335.1_01362
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI
+TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS
+VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG
+EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG
+FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF
+IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>GCF_020097155.1_01253
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL
+PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS
+VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN
+LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG
+EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>GCF_023573625.1_01491
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001279.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57d39303f1146d72249b0c554dca9c0122c7eb1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001279.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01565
+MSANDKKGRSMFGKKKENDVTDGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVKLAGREVLTMTPGQLRGIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>GCF_003691675.1_01275
+MSANDKKGRSMFGKKNQNDVTAGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADITGSVQLAGREVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>GCF_005280335.1_01361
+MTAHGNDKEGRPMSGKKNQHDAAGTEATAVGTGAGEHGSHSADLDARGAAVPGSSGTGGP
+TPGPATSSMGVVARHDDLDGKPVLAFRDVDVKFGTEFGEVHAVKGVTFDVKPGEVVALVG
+ESGSGKSVTSATAMGLLPSNADITGSVQLAGREVLDMTPGQLRGIRGDEVAMVFQEPMTA
+LNPVLTVGDQLTEALELHGIAYGTEADKRAVELLTMVGIPDAAERLKQYPHQFSGGQRQR
+IVIAMAISCSPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMA
+DRVCVMLHGELVEQGTVHQVLQHAQHPYTQKLLSSVPRLGATYEVAEPEPVTATQTTAKY
+AIEAEDLHLEYDYRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEG
+SLRIQGHDLAAMPKSEQRKLRKNIGVVFQDPAASLDPRFPIGDVITEPMVVHKVGDRRSR
+LARAEELLDAVRLPRSVVNRYPHELSGGQRQRVSIARALTLDPQVLIADEPTSALDVSVQ
+AAVLDMFAELQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTKEVLHNPREEY
+TRRLLAAAPVPDPDQQAERRQERRDFLASLGEGVY
+>GCF_020097155.1_01252
+MSSKAFDPKDSGTTETSAEDLRARAETLPGSSGEAPQGVVTTATGSLKVPGPATTTMGVV
+EHHDDLGGEPVLAFQDVAVRFATEFGSVHAVKGVTFDVKPGEVVALVGESGSGKSVTSST
+AMGLLPPSADITGSVKLGGREVLTMTDSQLRSIRGQDVAMVFQEPMTALNPVLTVGDQLT
+EALQLHGLAFGTEATKRAVELLTMVGIPDAADRLKQYPHQFSGGQRQRIVIAMAISCSPR
+VIIADEPTTALDVTVQAEILELLRSLKDKMNTGILLITHNMGVVADMADRVCVMLHGELV
+ESGTVQQVLQRPQHPYTQRLLAAVPRLGEALETAEPEPVTSTQTAVKYAIEAEDLCIEYD
+HRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKAVLGLLPVASGALRLQGEDLATM
+KAAEQRALRRKIGVVFQDPAASLDPRFPIGDVITEPMVIHGVGDRRSRLARAEELLDAVR
+LPRDVVNRYPHELSGGQRQRVSIARALTLDPEVLIADEPTSALDVSVQAAVLEMFAELQT
+RYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTGRVLHHPQAEYTQRLLAAAPVPD
+PDQQAERRRERRRLLASFGESAY
+>GCF_023573625.1_01492
+MSANDKKGRSMFGKKNENDVTADGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVQLAGRDVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001283.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd04a84a460fc7abfa2ca5510027aab71ed19081
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001283.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01570
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
+>GCF_003691675.1_01280
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR
+GAALGGVLLGVAAMALSLDLLA
+>GCF_005280335.1_01354
+MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV
+EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM
+VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA
+FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR
+AATLAGVLLGVAAMAISLDLLG
+>GCF_020097155.1_01247
+MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA
+RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT
+ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL
+WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT
+ALAGAAAGAAAMLGSLSLLA
+>GCF_023573625.1_01497
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV
+EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001287.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0430e59e8c297d7aea3ddb945185e9048ef2984
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001287.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01574
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>GCF_003691675.1_01284
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGIGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>GCF_005280335.1_01350
+MPRLSAVSEPLTIAPRSDDAPSVPSSSSDAPRGPGGRRALVRRRVFRSPLQRRIVYAVVF
+ELLAILFTTGILAAFGNSGGSSLAVAVVSSTVALLWNIAFNSMFEAVERRAGITGRPWWL
+RALHAVAFEGGLILFLVPAVALILGVGLWQAFLIEAGLLVFFLVYAAVYAYAFDSVFGLP
+DSAAGATR
+>GCF_020097155.1_01243
+MTPPHDDAPRGPGGRRALVGRRVFRSPLRRRIVFAVVFELLAILFTTLILRAVGNEGAAS
+FAVAVVSSTVALIWNVVYNSLFERLERALGVHGRPWWARVGHTVGFEGGLVLFLVPAVAL
+LLGVTLWEAFLIELGLIVFFLVYNAVYTYLFDAVFGLPDSAGVTAPGTP
+>GCF_023573625.1_01501
+MSETRRARPGVDPASTPPFDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ce936b81c862a1b646fe8452af64bcc7ec7cdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001293.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01580
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EVSPRR
+>GCF_003691675.1_01290
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
+>GCF_005280335.1_01343
+MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL
+SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS
+GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD
+NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN
+FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV
+VDAADAPAPGRR
+>GCF_020097155.1_01236
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE
+EVSPRR
+>GCF_023573625.1_01507
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86ddde4a14c710cda9ae8fe093a7cf55312c7390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001298.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01595
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW
+RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA
+GALADGMRIGADARVRPGMLRYAD
+>GCF_003691675.1_01307
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGALRYADGAARLTPPRGR
+>GCF_005280335.1_01301
+MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH
+CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR
+LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG
+FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV
+SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI
+ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE
+EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG
+AIADGIRIDDDGHGAV
+>GCF_020097155.1_01214
+MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR
+MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH
+GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG
+GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF
+QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN
+EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH
+TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA
+DGMRIGADARVRPGALRYAD
+>GCF_023573625.1_01522
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA
+AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV
+IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGMLRYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bc4b970f90ad4dafdadb02c7251a8fa2f165374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001299.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01597
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>GCF_003691675.1_01309
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>GCF_005280335.1_01298
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
+>GCF_020097155.1_01207
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG
+>GCF_023573625.1_01524
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001301.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..889b112acbe7cdb2f09ec3a6810d7691f78968b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001301.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01599
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>GCF_003691675.1_01311
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVIPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>GCF_005280335.1_01294
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGANPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>GCF_020097155.1_01203
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGSNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>GCF_023573625.1_01526
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGVRVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28ec9e4a744c01d67f1c26c3b9a0e378fd7041c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001303.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01602
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>GCF_003691675.1_01314
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>GCF_005280335.1_01292
+MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV
+LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG
+QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG
+GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV
+RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL
+>GCF_020097155.1_01200
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL
+>GCF_023573625.1_01529
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001304.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9830c03ee020f5ed42c84e97754a2528e0dd323
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001304.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01603
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>GCF_003691675.1_01315
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+ALIAAGADYRKGPDGESFVVTDGTLVTGQNPASSGDAARRLLDLLAR
+>GCF_005280335.1_01291
+MRLVGTVTLARDSVVYDHKSSVPTNERAPDMSRILMILTSHDQLGDTGRKTGFWLEEFAS
+PYYVFTDAGHEVTLASPRGGQPPIDPTSSKPEMQTEATRRFDQDDEAKAALAHTTPLAQV
+DVDGFDAVFYPGGHGPLWDLVSDADSTRIILDSDAAGRPLGLVCHAPGILHPITAADGTP
+FVRGRQVAGFTNGEEDAAQLTDVVPFLVEDSLIAAGADYRKGPDGESFVVTDGTLVTGQN
+PASSADAARRLLDLLAR
+>GCF_020097155.1_01199
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+SEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITTADGTPFVRGRQVAGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDQESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>GCF_023573625.1_01530
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df2504670eb87505e422ec484b5460a2e9fa9fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001306.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01611
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS
+>GCF_003691675.1_01322
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS
+>GCF_005280335.1_01287
+MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>GCF_020097155.1_01192
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD
+DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>GCF_023573625.1_01537
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..213f926d5a43fda16d4a40f8358900010074fa1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001307.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01612
+MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL
+DDGIFPAPSGLTPAVPWPLF
+>GCF_003691675.1_01323
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT
+ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL
+DDGRFPAPSGLTPAVPWPLF
+>GCF_005280335.1_01286
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR
+REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL
+DDGVFPAPSGLTPAVPWPLF
+>GCF_020097155.1_01191
+MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT
+ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL
+DDGIFPAPSGRTPAVPWPLF
+>GCF_023573625.1_01538
+MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL
+DDGTFPAPSGLTPAVPWPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e3e2402a989e26c4d6e877ce9b06371352d6b17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001311.fa
@@ -0,0 +1,19 @@
+>GCF_002008305.4_01629
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL
+QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>GCF_003691675.1_01334
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>GCF_005280335.1_01267
+MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG
+EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG
+>GCF_020097155.1_01175
+MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG
+RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE
+GEPHIVANGHNPLFGQIS
+>GCF_023573625.1_01558
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001318.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ecb85e64c1e348c8a20b0fbe502bd807ff1a5e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001318.fa
@@ -0,0 +1,34 @@
+>GCF_002008305.4_01637
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIMRHVIGAMDPLGV
+HVHAFKAPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>GCF_003691675.1_01342
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIIRHVIGAMDPLGV
+HVHAFKAPTAEERAHDFLWRIRPHLPRPGLVSAFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>GCF_005280335.1_01258
+MAENGTAETVRPDDAEGAETGVFSAPARELFAARRGDAVADPADVDASATPGYTGGKAQG
+KQDLADRADVLADLQELLFAQSTREAPSGEVPSLLLVIQGMDTAGKGGIMRHVIGAMDPQ
+GVHLHAFKAPTAEERAHDFLWRIRPHLPRPGRVSVFDRSHYEDVLVHRVRELSPLAEVEE
+RYGAIREFESRVRAAGTRIVKVMLRISAEEQAERLLARLDDPTKHWKFNEGDLDDRAYWD
+DYMDAYRIAIERTDTEDAPWFVVPADRKWFARLAVQQLLIETLQGLDLDWPEADFDVEAA
+RRRLLAG
+>GCF_020097155.1_01167
+MADTPENRFTEPVRTLLRARRADGAPVGPADVDPHGKPGFDGGKSEGRAVLAARSERLGQ
+LQELLYAQSTREADGGLPAPSVLLVVQGMDTAGKGGIMRHVVGQMDPQGVDVHAFKRPTP
+EEARHDFLWRVRPHLPMPGTLSVFDRSHYEDVLIQRVRSLAPAEEIERRYTAIREFEAEA
+VAAGIRVVKVMLHISPEEQKARLSERLERADKHWKFNPGDLDERELWDEYQEAYRVALHR
+TDATDAPWFIVPADRKWYARVAVQELMIETLEAMGLTWPEADFDVAAARRRLLAG
+>GCF_023573625.1_01566
+MADTPATAAGRPARATDAHGVFDAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGK
+KDLAARGRELADLQELLFAQSVRDAPVGEVPSLLVILQGMDTAGKGGIMRHVIGAMDPQG
+VHLHAFKVPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEER
+YGAIREFEAAVRAAGTRIVKVMLRISPEEQAERLLARLDDPTKHWKFSEGDLDDRAYWDQ
+YTDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPEADFDVAAAR
+RRLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0406ca75ee05ef7376935e60d5e58c983e49fd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001322.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01641
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>GCF_003691675.1_01346
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>GCF_005280335.1_01254
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD
+>GCF_020097155.1_01163
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD
+>GCF_023573625.1_01571
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001323.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff4c4436e29b6f16cca5519608782104dd8d560f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001323.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01642
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVAARTFLKVLPPARAARVARRQAAAGAAGVPVPA
+VLATPEHGVLPLASVPGLPWRALLAGPEAAGLDPARVAALLDRLPPVPEEPPGPAGPTAG
+AAGCADTDDGGPAILLEHATWAAVVLDPEAQDEVAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL
+>GCF_003691675.1_01347
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGFLEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVGRTFLKVLPPARAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGPEAAALDPARVAALLDRLPPVPEEPPGPAGPPAV
+AAGGADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRIRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRAARRAAADAALARVGL
+>GCF_005280335.1_01251
+MSIGRASAPLAVRASGLRWLRTRADALHLQRGRRLARVLDVDVMEGRAGDARVRTRTLVL
+ARDPRTGPDAAPPGSARTSERGVLEDGTLWWWAAADPALPGLALTENDAGLAALLGTAPG
+RVRLTWRGYRPRERAVIALDAADAGLAGSRAYLKVLAPAAAEAVAARLSAARAAGVPVPD
+LLAAPERGTLLLGNVPGLPWGALLGDARADALDPARVAEVLDRMPAPPGEAGPAPDAAAA
+LLEHAAWAAVVLDPERQAESAARADRLRAALAAGDPGPPVPVHGDLHPGNLHVDASGGRV
+TGLVDCDGLGLGHRVDDWATLLAHLEAAAADLGPGGGAVRAVAERVRAHARTETDEVALA
+ARAAVVLAALGADPSVPRAARTARRAAADAALARVSR
+>GCF_020097155.1_01162
+MVLLEGPPGAGVARERVLVLRGPVEPAVAVPGPPGPPVPASGPAPRRRGRGRLPDGTRWW
+LLPHDPALPGLDLALDHERLDAWLPGLGRAGEPAWVAYRPGERAVLRVPLDAVPARPDEP
+GSSLHLKVLPPARLHGMHGRLLAARAAGLPVPPPLAPPDLGVLALGTLPGEPWRARLGAD
+APQPAPAAVAALLDALPDALAAHDDGPSRTPAWSALLAHAVRAGTLLDPGAAEELRERAR
+RLEESLAAADPGPRVPVHGDLHPDNLLLAPGTDRIVGVLDPDSLGPGHRVDDWAVLVGHL
+AVAAADAAVPGPSHDPERARRTAALAAEFTGHACGVVDEEALRARADVTALALAAAPDLP
+AAVRAARRSAR
+>GCF_023573625.1_01572
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRWLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPAAPGAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALVALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVARTFLKVLPPSRAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGSEAAALDPARVAALLDRLPPVPEEPPGPAGPTAG
+VAADADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGTGHRVDDWAVLIAHLEAGAADLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d36463e8af93646443aeaccfd61bea500206ed13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001327.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01646
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD
+>GCF_003691675.1_01351
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD
+>GCF_005280335.1_01247
+MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA
+GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD
+>GCF_020097155.1_01158
+MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG
+APSSTPAAPSSGAASSTGTSSGSSD
+>GCF_023573625.1_01576
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGSAGGSTSDSAAGSSTSSTSSSSSAAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001329.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f10e78f8c1f1ddee2cbf8a4c9dfaec2fd307f01e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001329.fa
@@ -0,0 +1,110 @@
+>GCF_002008305.4_01648
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR
+>GCF_003691675.1_01353
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR
+>GCF_005280335.1_01245
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR
+>GCF_020097155.1_01156
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES
+>GCF_023573625.1_01578
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD
+EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba4b00beb393467c169bbd9eb53516526b651a6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001331.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01650
+MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
+>GCF_003691675.1_01355
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR
+RY
+>GCF_005280335.1_01243
+MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV
+MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV
+VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY
+>GCF_020097155.1_01154
+MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA
+DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL
+SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE
+LAQFPDAARRY
+>GCF_023573625.1_01580
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac5040ccbe21c980409268c56f280382c97f4303
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001332.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01651
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
+>GCF_003691675.1_01356
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEHRR
+>GCF_005280335.1_01242
+MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE
+PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS
+AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA
+AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL
+WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE
+NRP
+>GCF_020097155.1_01153
+MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE
+PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS
+EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA
+AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL
+WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD
+AAHQEPQDGPAGPRKEGQA
+>GCF_023573625.1_01581
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001335.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dafd0b394c0cab63d681536db58cd50cc708f14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001335.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_01654
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTAEHPTWLGETLAT
+VGSIYISLLKAAVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAVYVGLALVMLVVYPLLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIEMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAELVGTPEPRA
+>GCF_003691675.1_01359
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTSEPRA
+>GCF_005280335.1_01239
+MSTTQSSPEPAPRRRLPAWTGNFGWQIVAALVLGLVLGLVARSMGHTPDSPTWLGETLAT
+IGSVYISILKATVIPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVMQPGVGTGQSAPESYQARDVGWLDFLTSMVPANFLGLTVKSTVGEDGAVASSPTFNVL
+QILVIAIVVGIAALKVGEKAAPFLTFSRSVLAVIQKLLWWIIRLAPIGTVGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLAIVMFVVYPVLARLHGLCVKQFFTGVWPAVQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYAAFAVPLGSTTKMDGCAAIYPAIAAVFVAQFYGIEMSLGQY
+ALVVLVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGLALLLAVDPIVDMGRTATNVAGQ
+ALVPALVAKQEGILDQARYDAERVDIMGEDEEEIVEARAQDRDDDQDQMVGAAARPARD
+>GCF_020097155.1_01150
+MTSHPSSPASGASTPARRRRLPAWTGNFGWQIAAALVLGLLLGLAARAMGHTPDSPTWLG
+ETLALIGSIYVQLLKATVVPLVFFAVVASVANLAQVTNAARLAAKTLLWFAITSFIAVLI
+GLAVGVVMQPGVGTGQSAPEGYQARTVTWLDFLTSMVPVNMLGLTVKTTAGDDGALTSTP
+SFQVLQILVIAIAVGVAALKVGEKAEPFLAFSRSVLAVIQKVLWWIIRLAPLGTVGLLGN
+AVASYGWSTMGTLVKFVVAVYVGLALVMLVVYPLLARVHGLSVKQFFTGVWPAFQMGFVS
+RSSLGTLPVTQRVAERSFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFVAQFYGIDM
+TLGQYALVVLVSVLGSAATAGTTGATVMLTLTLSTTGLPLEGMALLLAVDPIVDMGRTAV
+NVSGQALIPALVAQQEGILDRTRYDAERGDVMADEDETIVEARHDDARGASRADLTEAGS
+AR
+>GCF_023573625.1_01584
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTPEPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001337.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f634dd9b9a884259dc004fff811e6a47569e8c3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001337.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01659
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>GCF_003691675.1_01364
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>GCF_005280335.1_01235
+MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV
+GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV
+DGPHGPLAVYY
+>GCF_020097155.1_01146
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYW
+>GCF_023573625.1_01589
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7658c0659160f77873f411a9988c13e1420e229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001347.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01670
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>GCF_003691675.1_01375
+MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA
+LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA
+HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD
+KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT
+AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR
+LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV
+VSV
+>GCF_005280335.1_01208
+MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
+>GCF_020097155.1_01136
+MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH
+LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH
+LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE
+AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG
+LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA
+NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP
+VSAVSAA
+>GCF_023573625.1_01600
+MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP
+EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT
+PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST
+IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR
+HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM
+LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF
+GADPGQPVEVVSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001348.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fba6fe8bcb9d95cee3c0e3196e151046cabe5ced
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001348.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01671
+MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKVL
+>GCF_003691675.1_01376
+MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>GCF_005280335.1_01207
+MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>GCF_020097155.1_01135
+MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ
+AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA
+AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA
+L
+>GCF_023573625.1_01601
+MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed58ddb44f699a35611854be012d418f04601aa4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001350.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01673
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP
+>GCF_003691675.1_01378
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP
+>GCF_005280335.1_01205
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP
+>GCF_020097155.1_01133
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP
+>GCF_023573625.1_01603
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b3ada45f208e8625f52ca3b62a5f4ad6b926de5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001351.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01674
+MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>GCF_003691675.1_01379
+MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>GCF_005280335.1_01204
+MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA
+RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD
+AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR
+VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL
+DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT
+LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP
+ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA
+>GCF_020097155.1_01132
+MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH
+GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV
+SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG
+LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV
+RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL
+VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG
+IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA
+>GCF_023573625.1_01604
+MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001354.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec17a93d3c1b146d1fcfa2488c5dbba6e5a672d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001354.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01677
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAA
+>GCF_003691675.1_01382
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAT
+>GCF_005280335.1_01201
+MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA
+LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA
+PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG
+LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG
+AVSAAPAAATPAAPARGEGPA
+>GCF_020097155.1_01129
+MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG
+LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK
+FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL
+LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD
+LVKRTAGMPVGAVAESAAGVGRAGAGVRP
+>GCF_023573625.1_01607
+MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP
+VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fe6eaf07ad94c889370f3708a52675f1b7f0577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001356.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01680
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE
+>GCF_003691675.1_01384
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
+>GCF_005280335.1_01198
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE
+>GCF_020097155.1_01127
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE
+>GCF_023573625.1_01609
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001357.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38b322b3c747737581179ef89604753cf40c0275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001357.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01682
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
+>GCF_003691675.1_01386
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV
+>GCF_005280335.1_01196
+MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE
+HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT
+ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK
+SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD
+FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP
+NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV
+>GCF_020097155.1_01125
+MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA
+GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI
+HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI
+TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP
+ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF
+MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN
+RQHEVTRVLMRKV
+>GCF_023573625.1_01611
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a767ba5c28816b98fd31b7663bcef5300604966
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001361.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01688
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR
+>GCF_003691675.1_01392
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR
+>GCF_005280335.1_01190
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR
+>GCF_020097155.1_01120
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR
+>GCF_023573625.1_01617
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001362.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d322e632da619b3f9c078ae9587b85cc2816d17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001362.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01689
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>GCF_003691675.1_01396
+MSINENDDVELTSYTSESTAAAEAPVASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>GCF_005280335.1_01189
+MSINEHDDVELTSYTSESTSAGTEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQW
+TINGRTLENYFPNKLHQQEVNDPFTLLELAGAYDVIARIHGGGPSGQAGALRLGISRALN
+EIDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>GCF_020097155.1_01119
+MSINQNDDVELTSYTSESTAASETAAVSERPALTVPGSAVGRRKEAVARVRLVPGSGQWS
+VNGRTLENYFPNKLHQQEVNDPFTLLELNGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>GCF_023573625.1_01618
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e802c2c82ffd6bb0beebfe57a98cca663332aa12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001364.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01691
+MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>GCF_003691675.1_01398
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>GCF_005280335.1_01187
+MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP
+VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV
+VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA
+VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV
+GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL
+>GCF_020097155.1_01117
+MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE
+GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ
+GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD
+ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV
+RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE
+GTRARRAPLADLG
+>GCF_023573625.1_01620
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001366.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca95cd1656476a77608f0a2455fd85d06ff6a582
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001366.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01693
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPDV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>GCF_003691675.1_01400
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSFKDSPAGYDPQAHARQMDDDPFSDF
+>GCF_005280335.1_01185
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLARSLNVEAEGVDLGDEPQT
+AEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>GCF_020097155.1_01115
+MLIAQRPTLTEEVVSDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGSGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADQEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLAKGLNVEAEGIDLGEAPAE
+ADGSADLAQPIEDLELTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGFDPQAHASQDDDPFSDF
+>GCF_023573625.1_01622
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50b0a4949c8a06095f9adafad464749cbc416937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001368.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01695
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_003691675.1_01402
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_005280335.1_01183
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_020097155.1_01113
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
+>GCF_023573625.1_01624
+MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI
+EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK
+KK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71201d907e82fdd1c961a81442cc8b985a3bba31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001369.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01696
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_003691675.1_01403
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_005280335.1_01182
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
+>GCF_020097155.1_01112
+MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG
+>GCF_023573625.1_01625
+MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001373.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5208829b0b09bd8073b043d058c8952c1302d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001373.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01700
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>GCF_003691675.1_01407
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>GCF_005280335.1_01178
+MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL
+TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE
+NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW
+IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ
+VNAQMEQRHYEGLLR
+>GCF_020097155.1_01108
+MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE
+NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP
+VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW
+VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ
+ISAQMEQRHYEGLLR
+>GCF_023573625.1_01629
+MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW
+ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001377.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ab05de98416697103c6d81e63983cb32dabfa67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001377.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01704
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_003691675.1_01411
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_005280335.1_01174
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL
+>GCF_020097155.1_01104
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>GCF_023573625.1_01633
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43a072969dd8c42e5770030f78e31932cac32d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001382.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01709
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_003691675.1_01416
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_005280335.1_01169
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_020097155.1_01099
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>GCF_023573625.1_01638
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001386.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be09b44f404a4190c23e1a00a072aed747d46578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001386.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01713
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_003691675.1_01420
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_005280335.1_01165
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE
+RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>GCF_020097155.1_01095
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE
+RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA
+>GCF_023573625.1_01642
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001387.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0afd92642e33f9b0041293782dc3b1442195c1c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001387.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01714
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>GCF_003691675.1_01421
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>GCF_005280335.1_01164
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>GCF_020097155.1_01094
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGVAFNEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASQDEKGG
+N
+>GCF_023573625.1_01643
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef710c9d3718d51e5ffaaa9a8c9061da2fdebbf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001388.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01715
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_003691675.1_01422
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_005280335.1_01163
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>GCF_020097155.1_01093
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR
+>GCF_023573625.1_01644
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001389.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba912e7987bd676c4b0538214bb7261f8aa8f060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001389.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01716
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_003691675.1_01423
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_005280335.1_01162
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_020097155.1_01092
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>GCF_023573625.1_01645
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f42f29e76369002c5ebb4758050e28ab1dbbe18b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001392.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01719
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_003691675.1_01426
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_005280335.1_01159
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_020097155.1_01089
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>GCF_023573625.1_01648
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f0e0323fc9bc295b7f584ea0f7dd1ee12bd754d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001397.fa
@@ -0,0 +1,65 @@
+>GCF_002008305.4_01724
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_003691675.1_01431
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_005280335.1_01154
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG
+EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV
+KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>GCF_020097155.1_01084
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL
+LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG
+EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV
+GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE
+>GCF_023573625.1_01653
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001398.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..141e3db31089a182ba6cb76f6b6390df0535a7e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001398.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01725
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>GCF_003691675.1_01432
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>GCF_005280335.1_01153
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>GCF_020097155.1_01083
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGVRAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>GCF_023573625.1_01654
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001399.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f41658eee1f50491d6433e6b3563b3da57a36855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001399.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01726
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_003691675.1_01433
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_005280335.1_01152
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_020097155.1_01082
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>GCF_023573625.1_01655
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001401.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77c39b5c7e0ce4759831dc4fffd577b7f65c143d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001401.fa
@@ -0,0 +1,105 @@
+>GCF_002008305.4_01728
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>GCF_003691675.1_01435
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>GCF_005280335.1_01150
+MVASSTSNETATVSPRSGASAGRISFAKISEPLDVPDLLALQTESFDRLIGNERWVARVE
+EAQAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFSEPEFADAKMTEEECKDRDATYA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQMLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTVKGVRDGEAVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAYQIAQANA
+PVAEDGTFEEELVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATAAGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVLVSEGDRVEPLSVIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSD
+PVNVATPVFDGAEAYEITGLLGHVNATRDGDRLMGENGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>GCF_020097155.1_01079
+MVASSTSNETAAVSPRSAASAGRISFAKIHEPLDVPDLLALQTESFDRLIGNERWAARVD
+AAVAADDHSVSVTSGLTDIFEEISPIEDFQGTMSLSFSDPEFADAKMTEEECKDRDATFA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSARIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKALGWTESRILE
+EFGQYDSIRATLEKDGTADQNEALLDIYRKLRPGEPAAVDAAQNLLNNLYFTAKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTIKGARDGEPVEVRVE
+VDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLNALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINPFGFIETPYRRVVDGRVTDQLDYLTADDELAFQIAQANA
+PVDEDGRFVEELVLCRQRGGGGEPVLSTVDDIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLQSEAPYVGTGMEKYVAVDAGDSVTAAQPGVVTEVAADLVTVMNDD
+GSTTHYPIMKFSRSNQGNAYNQRVRVSEGDRVERLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDVVLNPLGVPGRMNLGQVMEIHLGWAASRGWDIEGEPEWIKDLPDFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNKTRDGDRLMGTTGKAQLFDGRSGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDETYRAAEELGIDLSHAEPSSVEEV
+>GCF_023573625.1_01657
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbea181f1c33693e10034b55a7c6e1bc28780241
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001404.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01731
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>GCF_003691675.1_01438
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>GCF_005280335.1_01147
+MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL
+>GCF_020097155.1_01076
+MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA
+>GCF_023573625.1_01660
+MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001408.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535d79661df71e873c17481658416f00bd18105e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001408.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_01736
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPASGLPELREAIADKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>GCF_003691675.1_01443
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>GCF_005280335.1_01142
+MIGFGAGEPDFPTPAYIVEAAVAAAKDPKNHRYSPAAGLPELREAIAAKTLRDSGVAIDV
+AQVLVTNGGKQAVYNTFAALLDPQDEVLVPSPYWTTYPEAIRLAGGVPVDVFAGPEAGYK
+VSVEQLEAAVTERTKALLFVSPSNPTGAVYSPEETEAVGRWALDRGLWVITDEIYEHLTY
+DGMPFTSILKAVPELAEQAVILNGVAKTYAMTGWRVGWMAGPLDVIKAATNLQSHATSNV
+SNVSQRAALAAVAGPLDAVDEMKVAFDRRRRAMVEAMNAVPGFHCPTPQGAFYAYVDVRE
+ALGRTYRGGVTPTTSAELATFILDEAEVAVVPGEAFGPSGYLRLSYALGDDDLAEGVERI
+RALLSE
+>GCF_020097155.1_01071
+MTRAPSNRAGTSAPDGGSVGWPHGRRVRVRRPPEQMRKVPMATPAHRVSARLSAIAPSAT
+LAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVEAAVAAARDPKNHRYSPAAGLPELRE
+AIAAKTLRDSGVELDASQVLVTNGGKQAVYNAFAALLDPQDEVLVPSPFWTTYPEAIRLA
+GGVPVDVFAGPDQGYKVTVDQLEAAHTERTKVLLFVSPSNPTGAVYSPEETRAIGEWALA
+KGLWVVTDEIYEHLTYDGVPFTSILKAVSGLAEQGVILNGVAKTYAMTGWRVGWLAGPLD
+VVKAATNLQSHATSNVANVSQRAALAAVAGPLDAVEEMKTAFDRRRRAMVEALNRVPGFH
+CPTPEGAFYAYVDVREALGRTYTGGVTPATSAELADFILDQAEVAVVPGEAFGPSGYLRL
+SYALGDEDLAEGVERIRALLSA
+>GCF_023573625.1_01665
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDEAVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGRWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALGKTYRGDVTPTTSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbea4efaa805c5c1c3e5a1b33987fcf3f37d86ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001411.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01739
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>GCF_003691675.1_01446
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>GCF_005280335.1_01139
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL
+>GCF_020097155.1_01068
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP
+>GCF_023573625.1_01668
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001412.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..060919037ab0cfa9974431b53af67b708553ea81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001412.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01740
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>GCF_003691675.1_01447
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>GCF_005280335.1_01137
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL
+ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED
+SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ
+KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR
+>GCF_020097155.1_01066
+MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL
+ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV
+VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA
+SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ
+HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR
+>GCF_023573625.1_01669
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebd33db42a162465698db779d20ce391d53e07c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001418.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01746
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>GCF_003691675.1_01453
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY
+ASLGFELFAADAQYRRP
+>GCF_005280335.1_01131
+MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW
+WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE
+STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR
+DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV
+EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR
+LYESLGFGLFAADAQHRRP
+>GCF_020097155.1_01059
+MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW
+GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR
+RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD
+EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP
+AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY
+ESLGFALAAADVQLRPAR
+>GCF_023573625.1_01675
+MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW
+WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT
+SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ
+AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD
+AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY
+ASLGFELFAADAQYRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3e0df3d7344504b94b1c98ab9461a1337282e66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001419.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01747
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>GCF_003691675.1_01454
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK
+GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
+>GCF_005280335.1_01130
+MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG
+KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR
+AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR
+SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT
+KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM
+PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD
+>GCF_020097155.1_01058
+MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE
+GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR
+KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD
+ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP
+WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI
+PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD
+>GCF_023573625.1_01676
+MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK
+LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA
+LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS
+SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK
+GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL
+PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001424.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3db088e8250537402213a96c3a1c52ba50ad114b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001424.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01752
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_003691675.1_01459
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_005280335.1_01125
+MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA
+PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL
+RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>GCF_020097155.1_01050
+MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA
+PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL
+RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY
+QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPIRRMLMIATGNL
+>GCF_023573625.1_01681
+MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA
+PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL
+RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL
+GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001426.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a9b7163bf6f6c7f7638113644108a2cfe64ba75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001426.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01754
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>GCF_003691675.1_01461
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>GCF_005280335.1_01123
+MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG
+AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA
+>GCF_020097155.1_01048
+MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI
+AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG
+AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA
+>GCF_023573625.1_01683
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..508e09144b8738bb3e4ea9ae3b95c537c33bc9ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001430.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01760
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>GCF_003691675.1_01467
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>GCF_005280335.1_01117
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR
+>GCF_020097155.1_01042
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR
+>GCF_023573625.1_01689
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..399c34de2a2f7a6d8d13063aa7d3554e3f465f26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001431.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01761
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>GCF_003691675.1_01468
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>GCF_005280335.1_01116
+MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA
+HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF
+GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL
+WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED
+>GCF_020097155.1_01041
+MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG
+NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA
+FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF
+GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL
+WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED
+>GCF_023573625.1_01690
+MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44f0e41bbcfeb556c36a3df6c655ba75e8d3c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001432.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01762
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>GCF_003691675.1_01469
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>GCF_005280335.1_01115
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG
+>GCF_020097155.1_01040
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG
+>GCF_023573625.1_01691
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d35c68a92b5aa96a70e51e114b7bb7a25ab091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001440.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01773
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR
+>GCF_003691675.1_01480
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR
+>GCF_005280335.1_01104
+MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW
+RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER
+>GCF_020097155.1_01029
+MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW
+RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR
+>GCF_023573625.1_01702
+MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL
+REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW
+RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001445.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f347d534875f0c3f600e0637a038169e4d40fdd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001445.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01781
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>GCF_003691675.1_01488
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>GCF_005280335.1_01097
+MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD
+TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP
+RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT
+EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV
+LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA
+>GCF_020097155.1_01020
+MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL
+LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL
+AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV
+VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE
+RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR
+AEQH
+>GCF_023573625.1_01710
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acecfa0ef6a10ea4d2e5444438b358d080dd90fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001450.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_01787
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>GCF_003691675.1_01494
+MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
+>GCF_005280335.1_01089
+MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA
+RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE
+ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL
+TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA
+PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD
+LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI
+HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA
+YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN
+>GCF_020097155.1_01015
+MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV
+LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV
+ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV
+NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA
+TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG
+LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA
+SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC
+SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV
+VAAAFVLYFGMGVFRGILGLA
+>GCF_023573625.1_01716
+MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI
+LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG
+LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV
+RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN
+VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL
+LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI
+FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ
+IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF
+VAYFGLGVVRAALGLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..650fd3a2cc7b3aee760e6377cdb791df9a406a78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001452.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01799
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_003691675.1_01496
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_005280335.1_01074
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF
+>GCF_020097155.1_01010
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF
+>GCF_023573625.1_01720
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001453.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0389c7a449675119a2ff12d32f033b227ddd388e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001453.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_01800
+MLALLDDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITVLAARPWSSSPRDPAP
+VTDGKLRFTAAVATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTGADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMIFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFLL
+>GCF_003691675.1_01497
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLHFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTAMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLTLGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLITAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDVRVTEGYAQLFALIMVVKIATVPFML
+>GCF_005280335.1_01073
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLVLFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLPTPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
+>GCF_020097155.1_01009
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGHRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
+>GCF_023573625.1_01721
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVRDIPGISEGLVRVVALRHGGMARIAGSADRIEPGDEVVLDG
+TEKNIDEAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9424f4e9e01dc6a8ce40bcc95e6bf098098e5946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001455.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01802
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL
+>GCF_003691675.1_01499
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV
+GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL
+LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL
+>GCF_005280335.1_01071
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL
+>GCF_020097155.1_01007
+MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN
+DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV
+GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG
+LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL
+WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL
+>GCF_023573625.1_01723
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f31714f70f31898fba6c43ac0f8fa2ed359068c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001457.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01804
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
+>GCF_003691675.1_01501
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>GCF_005280335.1_01069
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>GCF_020097155.1_01005
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA
+>GCF_023573625.1_01725
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23990ecfa6ce9edd52a3aee092c1f5d5e97c277d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001458.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01807
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_003691675.1_01504
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_005280335.1_01067
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>GCF_020097155.1_01002
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL
+>GCF_023573625.1_01728
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e8a62bc5c408abd86870b25ec386952a155ee4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001460.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01811
+MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>GCF_003691675.1_01508
+MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>GCF_005280335.1_01063
+MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRP
+>GCF_020097155.1_00998
+MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE
+EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA
+>GCF_023573625.1_01732
+MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001466.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7f4f5589356c260409945965fa899fb0fbfe252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001466.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_01817
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
+>GCF_003691675.1_01514
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP
+>GCF_005280335.1_01053
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA
+>GCF_020097155.1_00991
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES
+>GCF_023573625.1_01738
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001475.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb4aae89149fbb036b787e29472ad12b0e130268
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001475.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01826
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD
+>GCF_003691675.1_01523
+MTHRSHSAQPAVTRPSERDRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVTGALQRD
+>GCF_005280335.1_01043
+MTQLSHTVHDALATAAERHHLARVADAAADETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVELVSGALQRD
+>GCF_020097155.1_00982
+MTHNSTALTETLVPLVGPQRAAALATWAEDETGAQTAEYGILTLAAVGFAGVLAVVLTSP
+EVRELLVDLVSQALQRG
+>GCF_023573625.1_01747
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001479.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84217a23cf8e8f09678f8aae02bad4c80c3fd68d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001479.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01831
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>GCF_003691675.1_01528
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>GCF_005280335.1_01037
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA
+>GCF_020097155.1_00977
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA
+>GCF_023573625.1_01752
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8605bbc52ab56a69f6c37a58855e9975886c2ed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001486.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01839
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR
+>GCF_003691675.1_01536
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
+>GCF_005280335.1_01029
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR
+>GCF_020097155.1_00970
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR
+>GCF_023573625.1_01760
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001492.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd5ead8471a3d97421093bf9796aaedbde2a5f0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001492.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01848
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
+>GCF_003691675.1_01544
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRPR
+>GCF_005280335.1_01020
+MGPRMNSAWLFVGVMFTCALIGFWTLRGLGFARGDLSLPAALGVLAVAAVAAAVITRFVR
+RR
+>GCF_020097155.1_00962
+MTLPPLHHGRDDDADRPAASGPGGRGLGGPAGPGAGLRRTYTFVGVLFACALIGFLSLRL
+LGVERGSMTLPAALGVLAVAAVAAAVITRVVGRR
+>GCF_023573625.1_01768
+MPPLHHGQPGDDGDPRDPRHRPGAGLGPGLRSVWMFVGVMFTCALIVFWTLRGFGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001493.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..546e02bfa6ed27e49984615598e8760a2d7bf491
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001493.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01849
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>GCF_003691675.1_01545
+MSARVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIELLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>GCF_005280335.1_01019
+MTVHVMLVDDHPVVRAGVRAVVEAHPDLRVVAEAADGAEALRILEAASGPVDVVLMDLQM
+GEGMDGVSATRAVRERRPDVQVLILTTFDTEADILAAVDAGAAGYLLKDAPSEEIARAVR
+QAAAGQKALAPQVAATLMGRMAGGADVLSAREIELLELIARGATNKAAAKELFISEATVK
+THLVHVFQKLGVDNRTRAVDEARRRRIIR
+>GCF_020097155.1_00961
+MSVRVMLVDDHPVVRAGVRAVLEADPELTVVAEAGDGAAALDVLQARPGEVDAVLMDLQM
+GEGMDGVSATRRLRAAHPGIPVLILTTFDTEADILAALDAGAAGYLLKDAPAEQIADAVH
+RAVAGRPALTPDVAERLLGRTTGATAASALSAREIELLELIARGDTNREAARALFLSEAT
+VKTHLVHIFQKLGVDTRTQAVHEARARRIIR
+>GCF_023573625.1_01769
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLSVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f3149821e286911c902be13115b02cbb7f2cee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001497.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01854
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
+>GCF_003691675.1_01550
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP
+>GCF_005280335.1_01014
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP
+>GCF_020097155.1_00956
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP
+>GCF_023573625.1_01774
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9887193f297249a23b396ba5685f030e48b9e618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001500.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01857
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLNFVQGAKGVDGGAVLMRGQYAA
+>GCF_003691675.1_01553
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVHGAKGVDGGAVLMRGQYAA
+>GCF_005280335.1_01007
+MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA
+DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR
+SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL
+LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG
+AGLDFVQGAKGVDGGAVLMRGAYAA
+>GCF_020097155.1_00951
+MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM
+WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT
+DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA
+DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP
+TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL
+PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV
+TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD
+>GCF_023573625.1_01777
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVQGAKGVDGGAVLMRGQYAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b20df045f484fa628b1df836db7e8f17683da85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001502.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01859
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>GCF_003691675.1_01555
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
+>GCF_005280335.1_01004
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA
+VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE
+AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA
+RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR
+APVADALAWLDSRL
+>GCF_020097155.1_00947
+MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS
+GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV
+RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA
+AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA
+RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR
+TRVAEALAWLDARL
+>GCF_023573625.1_01779
+MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS
+GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA
+AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE
+AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA
+RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR
+APVADALAWLDARL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001503.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d46d452a9494b4c7b36a6adfa6a36431e2f3dbc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001503.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01860
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR
+>GCF_003691675.1_01556
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR
+>GCF_005280335.1_01003
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRAPEPELDQKPEYEDPYADLYT
+DDDEDDDARAR
+>GCF_020097155.1_00946
+MGRGRQKAKATKQAREMKYMSLGTDLSALERELTGGRTDAPAVEPEVDYEDPYADLYADD
+DEDDDSRVR
+>GCF_023573625.1_01780
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRSPEPDQEPEYEDPYEDLYAED
+EDDDARAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001504.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..634036ea9ce6ee812864616b380d2d305384d64e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001504.fa
@@ -0,0 +1,46 @@
+>GCF_002008305.4_01861
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKAPMGTTQTADRGLGPGQNRAGGNPN
+SPKKLVRSISSDHLRQDITAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHGHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
+>GCF_003691675.1_01557
+MGYVAYVTSTPTMRMPMRRTPTLLAAATLAATLTAAPVSLAAPAAPAKAPVATTQTADRG
+LGPGQNRAGGSTNSPKKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVG
+ELEEAGYDVELQEFEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLTAPAGA
+ATGCADADWAGADLTGSVALVSRGDCTFGQKSQVAAASGAEAVIIYNNAEGALNGTLGTE
+PGDVVGTVGVTRELGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVML
+GAHLDGVPAGPGIHDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVD
+TLTAAEREDIILYTNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHAHQPEGSN
+GRSDYAPFVDAGIASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDAD
+ALGTR
+>GCF_005280335.1_00999
+MSMRRRPALLAASVLAASLAVAPAAAAIPGHAAGGPAPAASAADRAGGNPNSPEKLVAAI
+SAANLERDIRAFADIAEEHGNRAAGTPGYDASVDYAVAELEKAGYDVELEEFEITYTETL
+RNEFTQEGPVQRELPHEVLTYSPSATAESAQLAVPTGALGCTTADWGGADLTGRIALVSR
+GECPFAQKSTTAAELGAEAVVIYNNADGPLNGTLGAPSDDYVGTVGITRDLGQELVAQAA
+AGPVTVSLDLEQLVEQRPTVNILAETRTGRDDNVVMVGAHLDGVPAGPGIHDNASGSAVT
+LEVARQMAKVNKTGNTVRFALWGAEEIGLLGAAHHVAELSQSERDAIAMYVNLDMVAPLD
+HQNTLGVLTGDFSLGAESFLQEQLERDGHEHGPAGNGGNSDYAPFVAAGIPATGLLSYRD
+DNYHTAQDDIENVSITSLTHSARAVANLVGTFMHDTSSVNDKCNAGKSGKPKQC
+>GCF_005280335.1_01510
+MSTSSLSRRSFLALAGAAGAAGAFAMPAWGLDDVRPGAARAPRLTGQDRQIINQIRPARA
+VDHLTLLTEEIGQRYTGTPAEHRAADYIAAQLEGYGYDVELEWFDVPDRRVGLLEAPELD
+GRWSWGVGSAAAAAQDVTVAGRVVLAPSGSVADLTGMVLMRVVTASEDITPLAVAAQARG
+AVAVIATRRDSNPPGQASAFAPALTTARLDIPVVGVSQVQKHALLGVLAAGPLRLTVSTV
+EHRGTRSANVVGTRAGRKGPGKGGRERVMLGAHYDSVIGSRGANDNASGTAACLELARVM
+RNAPTAADLSFGFWGSEEVGLVGSRIHAQAMPADERSRLRGVFNNDMIATSWDPAEKYWL
+LDLRGEANDVNRAVYAAGERLGYRTSMSDLFTMGRSDHQSFSEIGVPSGNFGWLHRDGFI
+LEPEYHSSDDTVKENISVERLMAAMEIQGCAAYALASR
+>GCF_023573625.1_01781
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKASAATAQTADRGLGPGQNRAGGNPN
+SPEKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHTHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a55f3f0a8d213d3a23a54bfb319fa81c700e5b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001508.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01865
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>GCF_003691675.1_01561
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>GCF_005280335.1_00995
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR
+>GCF_020097155.1_00933
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ
+>GCF_023573625.1_01785
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c59f99b190d7f6afde68a717923fa5f2ce179684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001511.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01868
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>GCF_003691675.1_01564
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>GCF_005280335.1_00992
+MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT
+EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL
+VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV
+AALREAREELKKLRQKA
+>GCF_020097155.1_00930
+MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT
+EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL
+LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV
+AALREARQELAKLRKKA
+>GCF_023573625.1_01788
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001514.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4cf05c82d2d3f94eef8cc380a913a548389cbf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001514.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01871
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>GCF_003691675.1_01567
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>GCF_005280335.1_00989
+MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN
+SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA
+AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF
+FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL
+HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV
+DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR
+>GCF_020097155.1_00926
+MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA
+ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM
+AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR
+VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE
+VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA
+LRAGRLVFDLAYARR
+>GCF_023573625.1_01791
+MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5fbf7a87178754ad2282bf3033bb874596aabbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001515.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01872
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY
+RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA
+>GCF_003691675.1_01568
+MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA
+AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP
+WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL
+VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR
+ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY
+RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV
+>GCF_005280335.1_00988
+MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT
+HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP
+GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV
+AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF
+AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR
+TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA
+>GCF_020097155.1_00925
+MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL
+DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV
+VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA
+THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR
+TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA
+RVTAGLPVAGGGPRSGQRRA
+>GCF_023573625.1_01792
+MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG
+PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG
+YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA
+HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR
+SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG
+DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001516.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54e7027f0c3248fae7a0ae2637deac94780f5c9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001516.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01873
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>GCF_003691675.1_01569
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>GCF_005280335.1_00987
+MSARDGAARADRGRERGLDRNAPVFVVSVAAEMADMHPQTLRQYDRLGLVVPARQGGRHR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
+>GCF_020097155.1_00924
+MVSGVAGEHPTGAGRLRGTAGRPGRHDPVFVISVAAEMAGMHPQTLRQYDRLGLVVPQRQ
+GGRHRRYSAADVEHLRAVQRLSREGVSLEGIRRILDLQREVERLQDTVVELASQVDRLHS
+ASALARVFSVGLAGDVSARYAAPAAHRAAEAVQGQRRPGEGATRSAARGGLLRALPAGRA
+AAPRGLTRLPAPRD
+>GCF_023573625.1_01793
+MSARDGAARADRGREPGLDRNAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQGGRQR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..001c1b0abb3c7e6527b62763446444959bcafadf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001517.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_01874
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW
+>GCF_003691675.1_01570
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW
+>GCF_005280335.1_00986
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW
+>GCF_020097155.1_00923
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW
+>GCF_023573625.1_01794
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e981da0294bc5eaa3e5f5ea528e1680bb1bdc6d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001519.fa
@@ -0,0 +1,60 @@
+>GCF_002008305.4_01876
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_003691675.1_01572
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_005280335.1_00983
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>GCF_020097155.1_00921
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN
+NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT
+EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA
+DEDIVDAEVVEDEDEKKN
+>GCF_023573625.1_01796
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001520.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ee278f103042ef6e85bd177dbfec95e63ac23c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001520.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01880
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA
+>GCF_003691675.1_01576
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA
+>GCF_005280335.1_00979
+MSGPGPGRPVLIGVDGRSGAGKTVLADALAARLAPFARVAVLRIESMYPGWDGLAAAVDE
+GGPYPAALRALHADGTAAWRAWDWHRGAPGEPTAIGPADVVVCEGVGALSVAARPLLDLA
+VWLELETPARRSRALARDGETYAPHWERWAAHEEAYLARHGPRAAADLVVRLPSA
+>GCF_020097155.1_00919
+MNASTEPGTARPGGPVSAPRPALIGLDGRSGAGKTTLAAALAARLAPHARVDVLHIEEMY
+PGWDGLAAATADDGPYVRAVAALAAGRPAGWRAWDWHAGAPGEARALDPDALDVVVCEGV
+GALCPGARPLLDLAVWVDAPEDVRRTAALARDGDAYAPHWERWARQEEAYLAAADPAGAA
+DLRLST
+>GCF_023573625.1_01800
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYQGWDGLAAAVGDDGPYP
+AVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLVLRLPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001523.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6b826f6aba8d6c367c11422fc0127723dfb2efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001523.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01883
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>GCF_003691675.1_01579
+MNTLVQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPDDAADETLPLVEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>GCF_005280335.1_00975
+MNTLAQKALSTGITLVGGIIGSRVVAGGWKLVTGHDAPDDAADETLPIVEALSFAFISAG
+VAAILKVAGQRGAGAALRKVTESTAHRVDNEV
+>GCF_020097155.1_00913
+MDKVIQKVLATGITVVGGIVASRLVAGGWKLVTGHDAPSDATDETVPLVEALAFTFASAG
+IASVLKVAGQRAAAEGVRKVAQKTSSDVDNEV
+>GCF_023573625.1_01803
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54edf9e694ac21af415bb575047355fb863d8b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001524.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01884
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
+>GCF_003691675.1_01580
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI
+VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA
+DPGPRRAGARPRGRR
+>GCF_005280335.1_00974
+MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI
+AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP
+ELDPRSPESRRRRRR
+>GCF_020097155.1_00912
+MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW
+QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD
+AR
+>GCF_023573625.1_01804
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfbee05011298bc96235a038c3df4892e5060c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001527.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01887
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>GCF_003691675.1_01583
+MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>GCF_005280335.1_00971
+MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE
+GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF
+HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS
+SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG
+VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT
+AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD
+ARH
+>GCF_020097155.1_00909
+MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG
+GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH
+PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS
+VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD
+SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ
+SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT
+ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV
+SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA
+GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA
+GR
+>GCF_023573625.1_01807
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001529.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14d3a589f5cad474eb2c4278a366903dd2b0e753
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001529.fa
@@ -0,0 +1,95 @@
+>GCF_002008305.4_01889
+MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAARLDRAVPWVPYLETELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLEAAPALMADAGLRGLLEVAVALVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHGLAMWQVLVIGVGLWTLL
+LGGWRALRQTDIKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMVV
+GIIDHEAGTRDLRQLSGIGRRHPALAAVAVVAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPSTQEAAR
+>GCF_003691675.1_01585
+MLVILTALFVVALAAPVIFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAAHLDRAVPWVPYLEIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLAAAPGLLADDGGRVLLEVAVGLVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPAFHELATWQVLVLGLGLWTLL
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGVRDAALAGLAMLLAHALFKAPLFMVV
+GIIDHEAGTRDLRELSGIGRRHPALAAVAVAAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRI
+ARMAVAGGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPDAPEAAR
+>GCF_005280335.1_00969
+MLVTLSALFVVALAAPAVFRWTGRQGFYLLAAVPAAGFVWLLTQLPHVFALQEALDAGRP
+IPASAAHLDRSVPWVPYLDIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ
+APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV
+GIIDHEAGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLASLAAHGA
+AHGGVWAWTPLVVMALGSVLTFAYTWRFLWGSFAVKRDEEGAPVPATRFRTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALARRPFEALQERTESPLDAARGYRRLTGYVDETAVWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRAERPLATSFLAADLIWFETPAQLLIVAIIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFALRGAPDLAITQVLVETIILVTLILGLRVLPPDWHDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGANAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGAFGADSALGSRELSVVRSFAVD
+DREGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAGRRRHPRMP
+TPSTPDAPEAAR
+>GCF_020097155.1_00907
+MTVLLTALFAVALLAPVLFRRTGRRGFHLLAAAPAAGFVWVLAQLPQVFVLQDALDRGAP
+VPASAAHLDTTVEWIPYLDIALSFRLDALSAFMSLIVLGVGALVLSYCASYFREHEPRHA
+VFGAELLAFAGAMFGLVTTDDVMVLYTFWEITSVLSFLLIGYSGQRIFARRSAIQALIVT
+TFGGLAMLAGLVMLAVQAGSWRVSGILAAAPELMERAPRGLLEAAVALVLVGALSKSAQV
+PFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPGFASLASWQVLVLGVGLWTLIL
+GGWRALRQTDVKLVIAYGTVSQLGFLMVANGLGTRDAALAGLAMLLAHAVFKAPLFMVVG
+IIDHEAGTRDLRRLSGIGRREPALAAVAIVAAASMAGLPPLFGFVAKESVLESLAGHGEH
+AGTVWGWTPLVGMALGSVLTFAYTWRFLWGAFATKDGRDSPDGEPVPETRFHSRLTAEDL
+LPPGLLALACLVLGLAPGLPEALISAHTAGLAPLDAAEEPAHLALWHGITPILGVSVAIW
+VLGAALAVARRPLQRLQARVAFPVEAAAVYQRITGAVDAAAVWVTGRTQTGSLRRYLFII
+LATATALPALTMLVPAGEEDRVLATAFLEADLVPFTTPAQLGIAALVCVAAVLAVRARRR
+FMAIMLVSVTGYGSAALFALRGAPDLAVTQVLVESIVLITVILGLRVLPPDWHSKTTGRR
+RVPRLLLGVGFALVMMWVAATALGARTAERISLDMPRLAYEHGYGANAVNVTLVDLRAWD
+TWGEITVLAVAATGVASLVFLEHRDKRRRDLDTVVPGSVGNYGAESALGTRELSVVRSFA
+VDDRNDQWLIAGHTMAPERRSIILEVVTRFLFPAMMLLSVYLLLAGHNTPGGGFAGGLLA
+GLALALRYLAGGRYELQEASRIPAGTLLGLGLGIATLTGLAPLLFGGQVLQSYKVEFHDL
+WLFGDSLKIVSATAFDVGVYLVVVGLSIDVLRSLGAEIDRRGDEWQDARRRAARRRASPR
+PARPRPRPVPEGRAPAARAIPAHAARHRSEEDPR
+>GCF_023573625.1_01809
+MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAARLDRAVPWVPYLEIELAFRMDMLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ
+APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV
+GIIDHETGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLESLAAHGA
+AHGGVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPDAPEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb166c717e025a621b4a8f17ec3c563c7932dcf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001536.fa
@@ -0,0 +1,70 @@
+>GCF_002008305.4_01902
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
+>GCF_003691675.1_01598
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR
+>GCF_005280335.1_00956
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR
+>GCF_020097155.1_00896
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP
+>GCF_023573625.1_01822
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a92ce345f3cdec9b46fc806045308de788532976
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001538.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01904
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH
+>GCF_003691675.1_01600
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH
+>GCF_005280335.1_00954
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH
+>GCF_020097155.1_00894
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH
+>GCF_023573625.1_01824
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001539.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1970a7704fe7115fda61fda8a8115b086790ef10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001539.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_01905
+MHHQTTPVRRAARAATGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGSTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEAAAGQGDAASAEATAQADAS
+DAAQPADTDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>GCF_003691675.1_01601
+MHHQTTPVRRAARAAAGLALLPALVVAGAAPAAAHDELIRTAPAVDETVTTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGSAVAGASIAASPEATASQGDAASAAATAQADAS
+HAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>GCF_005280335.1_00953
+MAAAPAASDASTPASAGSGAGTGEASEAPAEQGSAEAGESAEAGALPAWVWAVGVAGLLV
+LVVALILMGRRARALGHLDDGR
+>GCF_020097155.1_00893
+MNPTPMHPSTPRRAARAAAALTLLPGLAVAAAAPALAHDELLKAVPADGAALAEAPDAVS
+LTFSGDLISGQGIQSIVRVTDAAGNQWQKGDVQVSGPTLTAPLCPDLAQGEYTAAYRVVY
+SDGHSEEQSLDFSVTDPSAPAAGTAPSGCGVAAAGTASSTAAPASSAEQTGAEQSGAAST
+PAAASSTPAESGASAGVPATVWMLGAAGVAVIAVGLAVMGRKARALGRD
+>GCF_023573625.1_01825
+MHHQTTPVRRAARAAAGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEATAGQGDAASAEATAQADAS
+DAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a179623d925a646e8468b48036896e13abb566c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001540.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_01906
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH
+LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
+>GCF_003691675.1_01602
+MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH
+LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA
+>GCF_005280335.1_00952
+MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR
+VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH
+LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL
+QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA
+>GCF_020097155.1_00892
+MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV
+CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL
+LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL
+VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA
+>GCF_023573625.1_01826
+MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG
+VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH
+LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV
+VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7630cda53fe9cea122b179429dbaee6f54747b80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001547.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01919
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLRED
+>GCF_003691675.1_01615
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
+>GCF_005280335.1_00941
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ
+LAPRIYPGLEGTVARVAVQTVAAHLRHLREG
+>GCF_020097155.1_00876
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL
+ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI
+VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS
+LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE
+LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG
+>GCF_023573625.1_01839
+MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c5e8847f2d0f170553b31f15076a02d56adcbaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001549.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_01922
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>GCF_003691675.1_01618
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>GCF_005280335.1_00938
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA
+>GCF_020097155.1_00873
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA
+>GCF_023573625.1_01842
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a061862ffc860b9fd3ef367276dd68f4704d0ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001553.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01927
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>GCF_003691675.1_01623
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>GCF_005280335.1_00934
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ
+AANVTKI
+>GCF_020097155.1_00865
+MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ
+AADVTKL
+>GCF_023573625.1_01846
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001555.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40d3b58a5f68fdca9ebdd025c0127494058aa756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001555.fa
@@ -0,0 +1,62 @@
+>GCF_002008305.4_01929
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT
+PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE
+GRVG
+>GCF_003691675.1_01625
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
+>GCF_005280335.1_00930
+MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG
+YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI
+KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL
+SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR
+MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP
+EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS
+RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG
+RVG
+>GCF_020097155.1_01592
+MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN
+EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK
+ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL
+SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH
+LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD
+LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG
+LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ
+NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL
+REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH
+>GCF_023573625.1_01848
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7891e43d62658570bd8b19ee95abf94cb62cbc26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001561.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01936
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
+>GCF_003691675.1_01632
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA
+>GCF_005280335.1_00923
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR
+>GCF_020097155.1_00857
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG
+>GCF_023573625.1_01855
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001564.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..431fb4e8a09d55931b6024a669bc1bc4954cb749
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001564.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_01941
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
+>GCF_003691675.1_01637
+MATPHTPDPQDARRAREATDETSGVAFDGDTPPAEGAGVGPHNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLVFILGRVAGLG
+>GCF_005280335.1_00918
+MAAPHTRRPHDSDPHDARRAADEHSGHTDRGGTPPAEGSGVGPTNPQMDVEQPGERSTGR
+IVLFAIIALLVIGILLFVLGRVFDLFG
+>GCF_020097155.1_00853
+MATPHHPDQPADAHRSDHLARATDENSGHAVAGDTPPAEGLGVGPTNPGMEADKSGEGGM
+GRILLGLLIALVVIGVLLFVIGRISSIG
+>GCF_023573625.1_01860
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..724735d5be7b016bcacaf4dffdc17dfa35568f92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001565.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01942
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_003691675.1_01638
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_005280335.1_00914
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_020097155.1_00852
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>GCF_023573625.1_01861
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001567.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c61049ef12b079f1e90133c7cf1618ea888ba9c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001567.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01944
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_003691675.1_01640
+MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_005280335.1_00912
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL
+LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_020097155.1_00850
+MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL
+VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA
+SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA
+AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR
+LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL
+AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL
+EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>GCF_023573625.1_01863
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001582.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dffc60351a57bbad8e544786927414a8ccc19798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001582.fa
@@ -0,0 +1,55 @@
+>GCF_002008305.4_01981
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>GCF_003691675.1_01675
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>GCF_005280335.1_00877
+MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA
+AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT
+VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV
+AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL
+TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP
+AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG
+EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW
+SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF
+ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW
+SVALLLMVCTIVFLQSNVLSWMLP
+>GCF_020097155.1_00812
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWLLPAAG
+>GCF_023573625.1_01907
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f47556548e4e8d7ad5834a0e94b35321639be49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001584.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_01984
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
+>GCF_003691675.1_01678
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>GCF_005280335.1_00873
+MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD
+PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI
+PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG
+PLGLDPRKDARTTADVLASA
+>GCF_020097155.1_00809
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>GCF_023573625.1_01910
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab1ff14caaa3fc7c069f5bc4468a724a780b0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001586.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_01988
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_003691675.1_01682
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_005280335.1_00869
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>GCF_020097155.1_00806
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA
+>GCF_023573625.1_01914
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001587.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35b8f53aff2b0e91e9c7558c9e53c0b34eb087e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001587.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_01989
+MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR
+ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP
+AEESSWGPAEPTQGTWSPGPEPSAP
+>GCF_003691675.1_01683
+MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE
+ESSWGPAEPTQGTWSPGQEPSAP
+>GCF_005280335.1_00868
+MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV
+PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE
+TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR
+PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED
+PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE
+PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP
+>GCF_020097155.1_00805
+MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG
+CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS
+TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD
+PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS
+TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA
+GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG
+>GCF_023573625.1_01915
+MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE
+PSTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001594.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e4ee95bf19ddad0a0fabf34fad57e8c3bd9c1b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001594.fa
@@ -0,0 +1,56 @@
+>GCF_002008305.4_01998
+MTTSAPTLSSHFADTFPELALPWQAQVTDGPQLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQPGPHARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEGGDLAPVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>GCF_003691675.1_01692
+MTTSVPALSSHFADTFPELALPWQAQATDGPRLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQSGPDARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDESIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVPLAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+EWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>GCF_005280335.1_00859
+MPVRHNTQPLVRDLFTTEAKAARGGRPAAGMFLSSGDCTAAEICAGAGLDYLLIDGEHAP
+LSLENVQAQLRTIAGYGVPVMTRVPFLDWISIKQYLDLGAQTLLVPMIDTPEQAAEAVRA
+LRYPPHGDRGVGSALARSGRWNRIEGYLQHDEEHVSLFVQIETVRGVENAAAIAAVPGVD
+GVFVGPSDLSASMGLIGQQSHADVVAAVRRVIEACNAAGTTVGVNAFATDQAQAYADAGA
+DFVNVGADVALMARGAEALADRWCPTPGTGADEGAGEGAGAGAGARANARPARRTDGGRP
+TRPPAPHAWECGVMDDVAPAHPALAPQPGRPALRHRFADLFPELAVPWQAQETDGPELVL
+LNTGLVTELGLDADWLASDDGVRLLTGEQLGPDARPVAQAYAGHQFGHYSPRLGDGRALL
+LGELVPPRRTRDANDAPQALPTWRELHLKGSGRTPFARGDADGQAVLGPMLREYAVSEAM
+HALGVPTTRALAVVATGRPVRRAGWQPGALLARTAASHLRVGSFQYAAALPERADPVAVL
+RRLVDEAILRHHPHAAEAENPALALYEAVIAAQAELVARWMLVGFVHGVMNTDNMTLSGE
+TIDYGPCAFLDAFDPAASFSSIDTQGRYAFGNQGPVAAWNLARLGEALVPVLDDDAGRAV
+ELAQEALGGFQATHLAAWRGGLRAKLGLSEEVTDADVAALTDRLFPVLAAARTDWTGFWV
+RLAEHVPGGRGRGRAGRGRRRTECPAECRSGRADGRRAGGGADAGPGRGRPGCRGRVAAR
+LAGAGPRRGPDAGGEPRLHPAEPPARRGPHRRRGRGPGAGAPPAGGRHRPVHPAPGPRAV
+RRAGPVGRGPVRDVLRDVRRGRRGLPYSRSPLPAPRPNSHRPTAFVWESGNLPPLSCGET
+GVPVSHTKGDEGRTLLLTRGCGGARPLTPGRATSAARSGRRGPAGPPRSRGR
+>GCF_020097155.1_00795
+MPVPALQHRFADRLPELAVPWQARPAPAPTLAALNAPLAAELGLDPAWLATDAGLAFLTG
+TEPGPGARPVAQAYAGHQFGSYSPLLGDGRALLLGELTAPDGTLHDVHLKGSGLTPFSRE
+GSDGLAALGPMLRELVVSEALHALGIPTTRALAVVATGGPVRRQRVLPGAVLVRVADSHL
+RVGTFQHAAALVHAGRAPEDLLTRLVAESLERHHPGHADDAAPALALLRAVVAAQAELVA
+RWMLMGFVHGVMNTDNMTVSGQSIDFGPCAFLDGFDPDAVFSSIDRGGRYAYGAQPRIAL
+WNLNRFAETLLPLLAPDPEAAVAAAEEALGGFAPAFDAAWQGGLAAKLGLARSADSDALA
+AELLRLLAQDRADWTASWANLSDLPLPADWLARWRALDPDPELARAANPLRVPRNRPLQA
+ALDAAEDGDLADVERILAAVREPFTPRADASDLDVPPAPGAGGEAPFVTFCGT
+>GCF_023573625.1_01924
+MTTSVPALSSHFADTFPELALPWQAQATDGPQLVLLNAGLAAELGLDAEWLATDDGVRFL
+TGEQPGPGARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVGTGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELI
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYACGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTLFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPWPEDGAPFVTYCGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001597.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abbfe6af385ec6d7daff0eb9d88f17b453241020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001597.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02003
+MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS
+VRAFAGEGVRVSIGEKEANDRFLEVARDFLA
+>GCF_003691675.1_01713
+MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS
+VRAFADEGVRVSIGEKEANDRFLEVARDFLT
+>GCF_005280335.1_00839
+MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG
+VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE
+AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP
+NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF
+SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD
+ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE
+QEANDRFLEVARDFLK
+>GCF_020097155.1_00776
+MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV
+VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE
+DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP
+NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF
+SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD
+ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER
+EANDRFLEVARAFQR
+>GCF_023573625.1_01941
+MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS
+VRAFAGEGVRVSIGEQEANDRFLEVARDFLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001606.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cbc3ebc9af8f6b878425140db36cc12e28647c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001606.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02013
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>GCF_003691675.1_01723
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>GCF_005280335.1_00829
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG
+>GCF_020097155.1_00766
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP
+>GCF_023573625.1_01951
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001609.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c3667b4a49ca993ce31cfff1941e23d01febc83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001609.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_02019
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>GCF_003691675.1_01728
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>GCF_005280335.1_02537
+MDALDLPALAGARALELPGSELTHPFGPEADVYKVRGRVFMLVLEARGAMLVNLKAVPED
+GAALREAYPAQVTPGYHMSKRHWISLGPPPADPHDDDAPARLDAALVRDLVTESYLLVLE
+RSVPRRDWPVDPATFGRG
+>GCF_020097155.1_00761
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVVKVQGKLFVVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLVVAKLPRTRRPVD
+PDTFGRA
+>GCF_023573625.1_01956
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVMKVQGKLFAVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLIVAKLPRTRRPVD
+PETFGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001610.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d15cf9758d14c59889e9c1a385aa709d15386959
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001610.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02020
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRATVHDDGAPAGHAPRCIVVWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPA
+>GCF_003691675.1_01729
+MSADRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRVTVHDDGAPAGHAPRCIVAWEQEVVLTSPWM
+RAVAHVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTSRP
+>GCF_005280335.1_00802
+MPASARRPFRFTHRWAVPRPAAEVAALLADPLGYPTWWPSVPRARRIDGAGHDGDPRVAV
+LLRGLVPVRLVMARELDDRERGRLVARLDGDLRGTVRVTVHDDDGPAGGTGGCTVAWEQE
+VVLGAGRLRAAARLPGARAAMRLSHAWAMRSARRALGARALPAGR
+>GCF_020097155.1_00760
+MSVDRPFRFTHRWSVPADARSVLALLADPAGYPRWWPAVPRVRHLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPRCIVVWEQEVVLTAPWM
+RAVDRVPGARTAMGLSHAAAMRSARRALGAKAMPTADPAPTTRP
+>GCF_023573625.1_01957
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRAHRLGPDRAAVRLRGLVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPHCVVTWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTTRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98ea83ad3b3af697f12f5a692703a1e59b2bb55a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001611.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02021
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_003691675.1_01730
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_005280335.1_00798
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI
+AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD
+PADGLLDGVSRPPLSREWNEAQAEL
+>GCF_020097155.1_00759
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>GCF_023573625.1_01958
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWDEAQAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001614.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2de99daf66c7fa9a8eb3ed6b01fa87f315a8365c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001614.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02024
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKRVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVVEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNAGADWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>GCF_003691675.1_01733
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>GCF_005280335.1_00795
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DVVGFHVAANVSRNTGVDWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>GCF_020097155.1_02090
+MTTIQKVTVFGTGVLGSQIIMQAAYHGKDVTAYDVDDKALAQLPARWEWMRGYYQRDLPD
+FDAERFDKAVSSIRTTTDVADAVTDADVVIESIPENLELKKSVWAKIGEAVPERTVLLTN
+TSSLLPSSFADSTGHPERFLALHFANLVWKNNTGEVMATAKTAPEHFDAVLAFAGEIGLV
+PVPVRKEVPGYVLNSLLIPWLDAGAKLYQGGVSDPEDIDNVWKIATGAPKGPFEVYDVVG
+FNVAYNISRVSADPLKKAFAEETLKKGIDAGTTGLGVGEGFYRYDKDGNNLGAVESWKQE
+NRG
+>GCF_023573625.1_01961
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001617.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d951a9093e7771e3ae40a3d16299c9376f81bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001617.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02027
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>GCF_003691675.1_01736
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHASLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
+>GCF_005280335.1_00792
+MLEASIPNPYTPAPLPAPADRGAQDPEETMSRDQIEALQFERLRWSLHHAYENVPAYTEH
+FDAHGVHPSDFKALEDLAKFPYTDKEFLRKNYPFGAFAAQGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTDEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDKG
+>GCF_020097155.1_00753
+MLEASIPNPYSPAPVPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYKEH
+FDNHGVHPSDFTALEDLELFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFRKLGLDPRESSLEVAILGAEPWTEAMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERREHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>GCF_023573625.1_01964
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cae7a6b62f8ce74f29aa9cf49eacf39f5d9789b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001619.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_02033
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>GCF_003691675.1_01740
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>GCF_005280335.1_00787
+MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVRLALLRRDWDSARASV
+>GCF_020097155.1_01226
+MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS
+FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW
+TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG
+DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG
+SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ
+QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG
+>GCF_023573625.1_01968
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18152613ba1d11a5a5d7fab5f7234be3b8a88bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001625.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02052
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
+>GCF_003691675.1_01758
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE
+>GCF_005280335.1_00770
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>GCF_020097155.1_00740
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>GCF_023573625.1_01986
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebcb233f575e7459d194f29afcdcce4e476b9428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001634.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02082
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>GCF_003691675.1_01787
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
+>GCF_005280335.1_00701
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG
+>GCF_020097155.1_00611
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG
+>GCF_023573625.1_02021
+MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA
+MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV
+SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84f1403b7f765ed8e2f6a07f80818a89bdbacd5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001635.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02083
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_003691675.1_01788
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_005280335.1_00700
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_020097155.1_00610
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>GCF_023573625.1_02022
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001636.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e40c0c60451120117921a2337c1d9456b561f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001636.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02084
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_003691675.1_01789
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_005280335.1_00699
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_020097155.1_00609
+MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>GCF_023573625.1_02023
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3d8700cc9b0ab3a2dd01c07d0d7784b2321e745
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001637.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02085
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>GCF_003691675.1_01790
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR
+>GCF_005280335.1_00698
+MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
+>GCF_020097155.1_00608
+MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR
+>GCF_023573625.1_02024
+MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL
+AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG
+AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER
+FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA
+PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT
+RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1337ec022d4f0a4d26932c95b0de8c133814a52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001639.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02087
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>GCF_003691675.1_01792
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>GCF_005280335.1_00696
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR
+>GCF_020097155.1_00606
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR
+>GCF_023573625.1_02026
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001641.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb281f0f93315ad01c60272d8b4ddbeb5f5082c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001641.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02092
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGARRIVDLGCGTGSLTVT
+LAGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHDALQRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSTPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWHGRPFDEAE
+HPLMIIEARPQGA
+>GCF_005280335.1_00686
+MHPDPAETNRRAYDDARVVALYDLDNPPGEDHAYFRRAAEESGAQRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPASADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQETTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYSDEGVVREGEEHLQFRSVEQVTEDLAAAGLAVDRVWSDWHGRPFDAAE
+HPLMIIEACPQGA
+>GCF_020097155.1_00413
+MTPSDPNGATYDDARLAALYDHDNPPGEDHAYFRQVADESRARRIVDLGCGTGSLTVTFA
+GEGRAVVGIDPAEAMLAVARARPGGNAVTWRQGTAELIEPASADLVVMSGNVAMHLIGEV
+WHATLRRVATGLVPGGRLVFETRNPVLRAWEDWSHGPTERTTPAGRLLETETVTAPDADG
+VVLMRSRTVFLADGALVEAEQRLQFRSAAQVRADLDAVGLTVERISGDWHRTPFDDATDR
+LMGVEARKA
+>GCF_020097155.1_00602
+MHLDPAETNRRAYDDDRVVALYDLDNPPGEDHAYVRRAAEESGARRIVDLGCGTGSLTVT
+LTGDDRAVVGIDPAEAMLRVARARPGGDRVEWRRGTAELIEPGSADLVIMSGNVAMHLIG
+QDWHGALRRIAAGLVPGGRLLFETRNPVRRAWEDWQQEPTERTTAAGRLVESEATSAPDA
+DGVVVHRWRTEYPDEGVVSEGEEHLQFRSVEQVTQDLAAAGLAVDRVWSDWRGRPFDAAE
+HPLMIIEACPQGA
+>GCF_020097155.1_00937
+MTDTNPSRGTDTYAHGHQPSVLASHATRTADNSCGYFLDRVRPGQRILDIGCGPGSITLD
+LAALVGDEGRVTGVDFSAEAIAAARLAAADRGDVVTEFLVGDVFELDLEPASFDVVHAHQ
+VMQHLTDPVAALEAMARFVKPGGILAAGRRLRAWAHQADLHVVLARSSAWSYATTESAAW
+WGNSQAERVTSSSFAQRAADQGVTPEQLTAMADDWRTWGQHPDAWFFLPHGEIIAVPSPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001645.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8acdabc59a402e06f75fb354dcf427f81a1d02a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001645.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_02103
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>GCF_003691675.1_01810
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>GCF_005280335.1_00676
+MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD
+SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR
+>GCF_020097155.1_00591
+MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA
+DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS
+>GCF_023573625.1_02043
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001646.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aa571cdcd31b8ca31f99f50cea7fa02b173a6fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001646.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02104
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>GCF_003691675.1_01811
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>GCF_005280335.1_00675
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM
+ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA
+VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV
+>GCF_020097155.1_00593
+MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF
+ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS
+LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA
+APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR
+>GCF_023573625.1_02044
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf109b5c6630c43078a50ac702d73e46e943d16c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001650.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02109
+MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>GCF_003691675.1_01816
+MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>GCF_005280335.1_00669
+MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE
+DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP
+QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFEAR
+>GCF_020097155.1_00586
+MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG
+RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY
+RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM
+QWEQGAFGPR
+>GCF_023573625.1_02049
+MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001651.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8377c0310753d6a5e6de15ffe8a61c2ac6d439f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001651.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02110
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDEAVQSTAAHLDDVNGR
+>GCF_003691675.1_01817
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGAALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDDAVQSTAAHLDDVNGR
+>GCF_005280335.1_00668
+MATKDLTLEEFGTTVSENDTVLVDFWADWCGPCKQFAPVFDAASEKHEDIVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPAPALDQLLEQVKGLDIAEVRAMAEQQAG
+EAEAEPSQDEAVQSTASHLDEVNGR
+>GCF_020097155.1_00585
+MATTDLTLEAFGTTVSENDTVLVDFWAEWCGPCKMFGPVFETASEKHQNVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGQALDQLIDQVTALDIAEVRAMAEQQGA
+QDAEPSEEEAVQSAAAQLDDVNGR
+>GCF_023573625.1_02050
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHDDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDVAEVRRLAEEQQG
+QQDDAEPGQDDAEPGQDEALQSTAAHLDDVNGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46454138e4e80cf1693011ed328cc32fb0c84192
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001652.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02113
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH
+VSAVADVVIAGAGVQGYTLAVDWLAAAVRR
+>GCF_003691675.1_01820
+MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLAAAVRR
+>GCF_005280335.1_00667
+MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT
+LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD
+ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR
+>GCF_020097155.1_00583
+MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR
+QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE
+FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR
+>GCF_023573625.1_02051
+MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG
+ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH
+VSAVADVVIAGAGVQGYALAVDWLATTVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f42b33dc805f30dc619bccaa550946796800cbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001660.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02123
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_003691675.1_01831
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_005280335.1_00656
+MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR
+IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE
+ESGELEQWLEYSRQCLP
+>GCF_020097155.1_00574
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>GCF_023573625.1_02061
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f574dafaa8a25da61fa637f2e34d2fc6d29deac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001664.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02128
+MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>GCF_003691675.1_01836
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>GCF_005280335.1_00652
+MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>GCF_020097155.1_00568
+MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>GCF_023573625.1_02066
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001668.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d085bfa4482db65e803d512c206ac5bb5158e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001668.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02132
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>GCF_003691675.1_01840
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
+>GCF_005280335.1_00648
+MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA
+RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD
+VPTTAA
+>GCF_020097155.1_00564
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA
+RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR
+LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD
+VPTTAA
+>GCF_023573625.1_02070
+MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA
+RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR
+LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD
+VPTTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001671.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59952db79bbaa5b3bda498091abf9553bdddd70b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001671.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02136
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER
+REQGGTGGDAPRA
+>GCF_003691675.1_01844
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
+>GCF_005280335.1_00636
+MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER
+REQDGTGGDAPRA
+>GCF_020097155.1_00560
+MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR
+IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA
+ERRAAQGDAGR
+>GCF_023573625.1_02074
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0227b644b4dacba7932a108efbc09ea35971febf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001679.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02145
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP
+>GCF_003691675.1_01852
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>GCF_005280335.1_00627
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP
+>GCF_020097155.1_00551
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>GCF_023573625.1_02082
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001693.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eba046935d09fc216405ec28dda4b816455bcce9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001693.fa
@@ -0,0 +1,80 @@
+>GCF_002008305.4_02164
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA
+GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ
+PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL
+AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG
+WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>GCF_003691675.1_01878
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>GCF_005280335.1_00593
+MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL
+PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP
+VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV
+GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD
+AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ
+VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA
+FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV
+VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR
+PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL
+VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE
+DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL
+ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML
+WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV
+AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL
+PARRAARLSPVAGLATV
+>GCF_020097155.1_00516
+MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ
+PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP
+RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA
+PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA
+EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF
+QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG
+ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG
+LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA
+RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD
+LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG
+QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA
+ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE
+RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG
+MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV
+AVAAVAGLLASLAPAGRAARLSPVEGLATV
+>GCF_023573625.1_02109
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001697.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80bf0f64e8892b8ed732626e868b8575f8cc7c55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001697.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02173
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
+>GCF_003691675.1_01887
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
+>GCF_005280335.1_00579
+MSRIQSTTSPSSMAELKKVLPELSHPDGSPVRVLVVDDEPMIADLLSMGLSLCGWDVVVA
+HDGASAVEQGTARRPDLAILDVMLPDMDGLEVLERLRAHWPEVPAMFLTAKDATEDRVAG
+LASGGDDYVTKPFSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGQVI
+DLTATQYNLLKFLMANVRTVLSKERILQEVWGYDFGGRANIVELYISYLRKKIDADRDPM
+IHTIRGAGYVIRPA
+>GCF_020097155.1_00506
+MTSAEHTVSPASMAELRESLPDLTHQDGSPVRVLVADAEGLEADLLSMGYSLLGWETVVA
+KDTAAAVQEGTARRPDLALLDAGLPDGGGLEVLARLRAHWAEMPAIVLASPAEAEDRIAA
+LLAGADDVVAKPFAVEEILLRSHHLVRRAGLNASTGEELVVGDLVMNTRTHEVTRGGDLI
+ELTATQFNLLKFLMANVRTVLSKDRILQDVWGYDFGGRANIVELYISYLRKRIDAGREPM
+IHTVRGAGYVIRPAEG
+>GCF_023573625.1_02118
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLERLRAHWSEMPAMFLTAKDATEDRVAGLAAGGDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3740bfbf856a5ed4b550c0926e547e211da983d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001698.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02175
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>GCF_003691675.1_01889
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
+>GCF_005280335.1_00577
+MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI
+DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG
+KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL
+GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV
+QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG
+>GCF_020097155.1_00504
+MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL
+TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK
+ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF
+GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI
+SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV
+ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK
+G
+>GCF_023573625.1_02120
+MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH
+VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG
+AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS
+WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY
+TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA
+IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001704.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ad6de715b944689e9ae9005863e98ed22486bf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001704.fa
@@ -0,0 +1,29 @@
+>GCF_002008305.4_02181
+MPLSTLRVSLPSVRRTRPAPQGVRGRIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+CDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
+>GCF_003691675.1_01895
+MPLSTLRVSLPSLRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWHVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
+>GCF_005280335.1_00569
+MLRLARPRSRRAPQGLGGRLVRAVAARPVPPVRPRARLAWHVSGALPLIGCLTSFPIGMS
+KDSMVIPGVGYQGGFSAGWHHALNQPAYFTWLSNALVAGTSLTLATRRTAPTSDAFWAVR
+TAGLGSVMVTGIVYNSVLRGREQDTVLYRFNDTLQHIVNPVLAPAVWALFDPRGQITPRR
+AGLASVIPLAWAALTMARGPRIDWYPYPFLDVPRHGARTVGVVLAGILAGFTGLMGLLGG
+LDRRLGGR
+>GCF_020097155.1_00496
+MPAWLARFTRPRPAPRPSRAARAGWWAAGALPLVGCLTSFPIGASKPTMVIPGVGYHGGF
+EAGWQHALNQPAYFTWLSNAMVAGTSLTLAARRDAPTSDAFWALRTAGLGSVMVTGIVYN
+AVLRGMEQDTLLYRFNDAVQHVVNPVLAPLVWAAFDPRGQITYRRAGLAAVVPLMWATAT
+LVRGARIDWYPYPFLDVPRLGWRGVGAAVSVVLAGFSAVLGLLGQVDRRLGTR
+>GCF_023573625.1_02126
+MPLSTLRVSLPSVRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDTFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAVTMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001705.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d158b6ff5cd9773a5fa53ac7e0f13529a238d674
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001705.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02182
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASREERLDRAVEIMSLLAGRRLSVDRETYESEMAVSDRNLALAHMLRSYGVL
+QDSAEEIVAGYVAQCAVRVTVKDLAVMGACLATGGIHPMTGERVLPSIVVRRVVSVMTSS
+GMYNAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADRAALSAATGGGAVHEAAAVAARDENDGPIRTVVLNLTRVDWIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>GCF_003691675.1_01896
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRLGIALATPTGRLHSAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLAVDRETYESEMAVSDRNLSLGHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERVLPSIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALAAATGGGAVYEAAAVAAQDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>GCF_005280335.1_00568
+MRHPFVDYLEGLLGSLEHVTEGDVARYIPILAEADPSLSAVAVATTSGRVHTAGDADAEF
+SIQSVSKPFTYAGALEDRGVELVDEYVALNPSGEAFNELSLEADSHRPDNAMINAGAIAV
+HQLLVGPGATPAERTERAVSLMSTLAGRRLRVDERTFESEMATADRNLALGHMLRSHGIL
+QDRAEDVVAGYIAQCSVMVTVRDLAVMGATLASGGLHPLTGERVLSSLVCRQVLSVMSSS
+GMYDAAGQWMAHVGIPAKSGVSGAVLGALPGQVGIGTYSPRLDPFGNSVRGVEMCRIMSE
+DLDLHIMEADVIGSTVVRSVRREGDTVHLHLQGVIRFGGGESVLAAMTELGTGADPDPVE
+WAHCFYPFSEEPDTAAGRAAAQDEGRTAAEALEQEAPVRAVVVHLERVDRVAPVGRRLIE
+DGLKRLRADGVQVRVEDPDGVLTGG
+>GCF_020097155.1_00495
+MKHPVPDYLQHLVDSLREDRRGALADYIPVLAQADPERLGIALATVTGRLHSAGDDETEF
+TIQSVSKPFAYAAALQDRGLDAVDARVGLNPSGEAFNELSLEAESKRPDNAMINAGALAV
+HQLLVGPYAGRQERLDRLVGFMSTLAGRRLEIDRETFESEMATSDRNLSLAHMLRSHGII
+QDRAEDVVAGYIAQCSVRVTVRDLALMGACLASGGVHPLTGERVLPSLVCRQVLSVMSSS
+GMYDAAGQWLVNVGIPAKSGVSGAVLGALPGQVGLAVFSPRLDEVGNSVRGVEACRRMSE
+DMDLHLMEGDSLGGTVVRFARREGDTVLLHLQGVIRFGGGEAVVTAMTDLGTGAAGGGRA
+AWSEHDYPEWEDAPHGDVAAEAGDRRPVDAADPEAARAAATGDGSVHEAAACAVAEDGLP
+IRTVVLNLERVDRVTAVGRRLIDEGVDRLRADGVAVEVVDPDGLLG
+>GCF_023573625.1_02127
+MRHPIPDYLASLITDLGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLSVDWETYESEMAVSDRNLSLAHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERMLPYIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALSAATSGGAVHEAAAVAARDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001710.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b35767e159a60f5df6d47240f9a9a753f570ea05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001710.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_02190
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKARGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAQGTTHVGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYLRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>GCF_003691675.1_01904
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMRHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>GCF_005280335.1_00554
+MAPSRRQILLTGSALLGSGLLAACSSEGGSAPASSSPAGTPAPAPSSSSAAPAGPGPAGE
+PVAWPNTALVPHLFFHSLVVDPKRAFDGDHKEAGYLDFMVTMDEFAAILPQLYAKGYVLV
+SPHELYEVGEDDVVRPKTLMVPENRTPLVFSLDDCSYYLYMEGDGFADRLIVDEDGRVRN
+EYTDADGTTHVGSYDMVPMLDDFLEEHPDFSLNGARGVLAMTGYEGVFGYRTSAREFGDS
+PTFDADVAAATEVADAMKATGWEFASHTWGHRTVPKLELDELQRDLELWHGEVEPILGPT
+DMMIYPFGADVARTGKYEADNERYQYMRSLGYRSFFLVDGTAKAWGQLEPGYYRGSRINV
+DGISLEAAISGKRPVLDEFFDSRSVLDPARPASIRGTQQSPAAPPGGQSGSASPSATG
+>GCF_020097155.1_00483
+MEYSRRHVIFGGSALLGAGLLAACAPAQDGAAPSAGGGSSSEAASSSAAPSPSSTRPVIP
+SAPEPAGKPVAWKDVAKVPHLFFHSLVVDPEKAFHVHGESDGYLNYMVTQAEFERILPQL
+WALGYVLVSPHELYEVGRDDVVRARTLMVPENRTPLIISLDDCSYYEYMEGDGFATRLLV
+DDSGRVRTEYTDQEGKTTIGANDLVPILDDFVRDHPDFTLNGAKGVLALTGYNGVLGYRS
+SPTMYPEGPELDEAVATAKEVVAAMKETGWEFASHSWSHRSMAQMSLADLKEDCERWIED
+VQPIVGPTDMLIYPFGADIAGIEKYSGPEYEHLRSLGFRSFFLVDGSSKAWGQLEPGYYR
+GSRINVDGISLAGAKDGSRPVLDEFMDVDSVLDPARPESIHAPSYVPPEERAAASSGAPS
+ASPSS
+>GCF_023573625.1_02135
+MPPPVPQPTRRQLLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWSDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGTYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRSPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001711.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c5649bb8791f0330a435a8684e662a9c95835d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001711.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_02194
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPSSLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAATPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNTRANRFYERLGFATIGARQFVVGGERVEDDWV
+RLLTVE
+>GCF_003691675.1_01907
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVA
+>GCF_005280335.1_00546
+MIQAHIDEHLNERVVAAWIADPARIVLVGGTAPDEVLGYAMLETAATPEAPVVEHLGETP
+AGHLSKVYVLAESRGTGLAETLVRDGVARLEALGFRHVWLGTNAQNARANAFYERLGFEK
+IGARTFVVGGTRVEDDWVRLLSLG
+>GCF_020097155.1_00482
+MPTSPTPRPVPAVIRPATPADVPALVRVAAETFPDACPPTTSQEAKDEHIASSLNAEVIG
+GWVAGPGHAVHLAEAPAGRDDAGRLLGYVMAELAPEEEPAVTAVLGEGAAVGCLSKLYVV
+REARGTGAAAALMAAGLDALRVRGLTHAWLGTSEENHRANAFYERVGFRTVGSRTFLVGG
+RPERDNVRLITP
+>GCF_023573625.1_02138
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001714.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d05c9e2ad6fb7e63dd508c8f5acc69f2b9fa365
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001714.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02197
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>GCF_003691675.1_01910
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>GCF_005280335.1_00547
+MATRPRREDVRAAILDHAAQVFGREGYARSSLTRIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTQAMDGVADALDDPDLPREDLVARVAEALADVVLEPTGSWPLLLHEFQSVG
+LREPAVGRAYRVLTVRRRDFLAGLLREHRVLADVPDAQVTHTAAMLLMLVHTLTVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>GCF_020097155.1_00480
+MGGLRGVRRFDTVGIQYHRYRKGKMASRPRHQDVRADLLQYATEAFERDGYGRASLAGIA
+ADAGYTKGAVYSGFGSKAALFAEVCGAQFEALTRRTLDVVGRELAVEGGGRADLVARLAA
+VLTSLTFDGDARWPLLLHEFQAVGLRDESVASEYRALTARRVRFLAEALGEHPRLAGLSA
+ERLERTSSLTLVLVHTLAVEHRLSPEAMDRRGGELSFTALLDSALPD
+>GCF_023573625.1_02141
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f5dd73361db57138c450531b1e5d564148ae01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001715.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02198
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV
+GGTVALVRGVAGTLG
+>GCF_003691675.1_01911
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV
+GGTLALVRGVAGTLG
+>GCF_005280335.1_00545
+MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL
+SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV
+HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA
+SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS
+RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA
+>GCF_020097155.1_00481
+MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG
+GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA
+PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG
+FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW
+WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL
+>GCF_023573625.1_02142
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV
+GGTVALVRGVAGTLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c03ca745ca2af039dc36c4cc443504bfda90ab7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001716.fa
@@ -0,0 +1,30 @@
+>GCF_002008305.4_02200
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>GCF_003691675.1_01913
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>GCF_005280335.1_00542
+MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS
+RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN
+LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP
+VDPEPYLRERGVELGSSWERPRRR
+>GCF_020097155.1_01787
+MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ
+TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN
+DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT
+LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA
+TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG
+QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ
+PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH
+VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL
+QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS
+>GCF_023573625.1_02144
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001717.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aafd496c27ee2d49d3f4676d915159553ab5b0d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001717.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02201
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
+>GCF_003691675.1_01914
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
+>GCF_005280335.1_00496
+MPSRLHLRPLTVADAEEMSAVLADPALYAHTGGEPPSEELLTQQFRIQTRGESADGSERW
+QNLIVVLEETGEAVGYVQATTPKDGGPTEVAWVIGVPWQGRGLGGEAAAQLVEHLAGQGV
+RELIADIAPGHAASEAVARHIGLEPSDVVVDGEVRWTGTVADRER
+>GCF_020097155.1_01297
+MTPPIHLRPLRPDDADEMVAVLADPALYTFTGGEPPTRGALSGQYAVQARGHSEDRSETW
+LNHLVVLDDTGEAVGYVQATIPVAGGAAEIAWVIGVPWQGRGHATAAARLLLDELARRGV
+SEVVADIHPGHAASAAVARRLGLRPTGHIVDGEQRWEGPVAVVDGAASAPGG
+>GCF_023573625.1_02145
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fce12485c1706e0fdcd61dc94bd4327a6496dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001719.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_02206
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>GCF_003691675.1_01919
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
+>GCF_005280335.1_00539
+MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT
+LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD
+LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV
+RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA
+DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD
+GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE
+LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD
+LELVLRARAGGMAA
+>GCF_020097155.1_00469
+MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA
+AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA
+AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG
+>GCF_023573625.1_02150
+MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN
+LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF
+RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA
+LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI
+DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD
+DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ
+RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001727.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b06637cc04e4dce8ed82981e48e234fbadeb1d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001727.fa
@@ -0,0 +1,28 @@
+>GCF_002008305.4_02244
+MTEHTSEHTPENPHVVRRGSGVPLIEVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>GCF_003691675.1_01946
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAESGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>GCF_005280335.1_00502
+MSRGGCLSGGLQSKCGEFRLQFPDRHSPRTACRPHRASAPHLRTAPHVRTFLATLDPDDA
+EPFLEMSPRLVPETWERFRDHALPGIRAVDEDAVERPSARYVLDPVPEEAGPRVEAPALI
+LTGRSWGSGPPRRRGRRGTEAPVREARSAHPLATRPAGFPSATCRGALAPWPT
+>GCF_020097155.1_02088
+MSQPAPHLVRRGSGAPLVLVHGMGVDHRLLLPLDAALEAAGGWERVYVDLPGFGGTPALP
+APGGLPELADWLDGVVGEIAGEDRFALLGNSLGGLLVREVLARRPGQVAGLAMIAPVVDP
+DPERRDVPERVVLEQDEALLAELDGDDAAPFVEMAVIQTRPVWEGFREHVLPGVLAVDED
+AVDRLEDRYALDGPLPEERFGEFDRPTLIVTGRQDDKVGWRDQLALAEHFPRLTLAMLDR
+TGHNAHLDQEAAVGAMVRNWAEDAAREL
+>GCF_023573625.1_02176
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001736.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d1e81a34ccab43abba25385eaeb4bfb4e3c7b5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001736.fa
@@ -0,0 +1,45 @@
+>GCF_002008305.4_02282
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF
+>GCF_003691675.1_01973
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>GCF_005280335.1_00454
+MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF
+>GCF_020097155.1_00406
+MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>GCF_023573625.1_02221
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5a749e837948468b5d08e299f7492d10ade6a9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001738.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_02286
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_003691675.1_01977
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_005280335.1_00451
+MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG
+RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA
+>GCF_020097155.1_00404
+MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA
+MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR
+AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS
+YLGGQPPRGVRRRNRGHA
+>GCF_023573625.1_02225
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e8240621497a16728fd4199ac90f7e34435285f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001739.fa
@@ -0,0 +1,41 @@
+>GCF_002008305.4_02287
+MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_003691675.1_01978
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_005280335.1_00450
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL
+TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS
+WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>GCF_020097155.1_00403
+MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA
+EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL
+GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP
+QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI
+SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV
+HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK
+AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP
+AATP
+>GCF_023573625.1_02226
+MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001740.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..428b5cfc6686b222788e27cf8db098e09823a3bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001740.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02289
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVQLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
+>GCF_003691675.1_01981
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
+>GCF_005280335.1_00449
+MAKLILTQEVTGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAEKLQSATVKLERTAGAEGRLFGAVQAADVAEAIEAAGLGSVDKRAVTLPA
+HIKSVGNHQAQVRLHEDVVAVVDLQVVAAKAKK
+>GCF_020097155.1_00401
+MAKLILTQEVPGLGIDGDVVEVKNGYARNYLLPRGFATVWTQGGEKQVESLKAARAARAT
+ANLEEAQALAAKLQSATVRIDRKAGAEGRLFGAVQAADVAEAIEAAGLGSVSKRSVTLPN
+HIKTVGNHEAQVRLHDEVTATVALQVVAAKGSKK
+>GCF_023573625.1_02229
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001744.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b0f8b04de32f4a0e8a9169ee266ddc7b94ba5d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001744.fa
@@ -0,0 +1,50 @@
+>GCF_002008305.4_02293
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV
+>GCF_003691675.1_01986
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
+>GCF_005280335.1_00443
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV
+>GCF_020097155.1_00396
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV
+>GCF_023573625.1_02234
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dd69149cca3f5de3d23dc5745dc625f903ff06c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001752.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02306
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID
+CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPSVKG
+>GCF_003691675.1_01999
+MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPTALKS
+>GCF_005280335.1_00430
+MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM
+FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA
+AAEIAGRGAPAAKG
+>GCF_020097155.1_00383
+MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK
+TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD
+APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP
+PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD
+ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA
+EIARRGAPQAR
+>GCF_023573625.1_02247
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPAVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001755.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b38d8e50471097014712cb99de0ca624543ac0f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001755.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02309
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSTIFGARMSDTFLNSFGDPGSAPVII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGAVLNGEVVRQSGQRVQPQRKNRRRK
+>GCF_003691675.1_02002
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSGPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK
+>GCF_005280335.1_00427
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSMIFGARMSDTFLNSFGDPGSAPLII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEQELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGTATLNGEPVRDSGQRVQPQRKNRRRK
+>GCF_020097155.1_00380
+MFDAILAPFRWIMSWLLGAFHTVLDTIGLPADSGWTWALAILLLVILIRTLLIPLFVKQI
+NAQRAMQTMQPELQKLQAKYKGKKDQLSRQAMALEQQALMREHKANPFAACLPLLIQMPF
+FFALYQVLVGARGAAERGESMDALSAETIRSFESSQIFGARMSDTLMGSIGQPGGAAVVV
+VAIVLILLMTGSMFFMQKMLMTKNMTQTALEGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRHNPTPGSLAEQELNERRAAKGLPPVGKKVASSEAKPGSAH
+TEAAQGAVVNGEVLREGGQRVQPQRKNRRKK
+>GCF_023573625.1_02250
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPVDSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSTPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001758.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d321df66cb8bd65c8318b3d3fc1430bf18f65c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001758.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_02312
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+
+>GCF_003691675.1_02005
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+>GCF_005280335.1_00424
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILAARRGKGRAELSA
+>GCF_020097155.1_00377
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSTRRGKGRAELSA
+>GCF_023573625.1_02253
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001760.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e21b0406fd3579fc870e9dc29e48cd7237f12c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001760.fa
@@ -0,0 +1,45 @@
+>GCF_003691675.1_00303
+MVELVALRKTNEVAAYVRASMDRKGDRWTVDTQLRKIRALAEAKDWNVVEVYEDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNERRRAEGIPASTWKAFGWTREGELIEEEAAA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSEFSVDAVRYLLANSLYAGFIRHYKTG
+ELYPVQGEAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEAAGPDREELLT
+ERNALVERVKELSPLLRDIHQPVLEITAAINDVKARIDEIDAELLDRSVSVAAKLLAEVD
+EPVGTAERREVVESKWKALDMDRRRMLVDELVTVTIEPIMPGHVKFDPDLVRIEPRRD
+>GCF_003691675.1_02232
+MRAAIYLRISLDRHGDGLAVERQREDCKRIIAQRGWEHVATYEDPSVSASSRTVTRPGYE
+RMVRDWQAGRFDAVVCWDLDRLTRQPRQLEDWIDAAEQRGLHLVTANGEADLGTDAGRMF
+ARIKAAVSRQEVDRKSARQVRAAQQRAELGKGWGPRRPFGFAEDKVTHDPAEAAVVRRMY
+DDFNAGVGQREICRRLAAEGVRTSTGREWTQPALRQFLRNPRNAGLRAYRGEIIGPAEWA
+PLVSESVYRAALDRMDAPTKRVGGSGAKHLLIGVARCGVCDSPVGTNYTATHKRQYACRA
+GHVARSAEAVDAYVSEVAVGVLSTRGAAAFTRHDDAGQVELSAEADRIRARQEALAVEFA
+DGTLTAAQLRAANARMAERLEQVTAAMVAAEGNAALRPLLEAESVAAGWERLDIPRRRAV
+IDTLMNVRILRTSQGSRFDPASVEITPRTG
+>GCF_005280335.1_02196
+MVSVVGGRVDYSVVGLQNPMRISEMPGKTAKITVSGRMPNTRGSITRTGYSYSMTSKRAV
+IYTRISRDDRGVEAGVTRQEEDCRAKAAGLGFEVVRVYTDNDIGASTRSRKVRPEYAQML
+EAARRGAFGAILAYSTSRLTRRPREAEDLIDLVERHGVQIKTVVSGDWNLETADGRAVVR
+TLAAWDAAEAERTAERVARACEQRAAEGRTHGAVPYGWTRDADGTEHLHPERAQVIRDAA
+AHVLEGGSLRSFTLDLNARGVGSPRGGKWTAPQLKQLLLRERNAGRLVRRDPNNPRHRPV
+VGKGIWPQILDEETHDRLVAHLTDPTRRKSRGSELKHMMSGILICGVCGARCRLMPGGKS
+PDGTPRPPSYGCRECFGVKRRVAQVDEWVSYMARVRLAEKDAPALLAGDDEGARKAQRER
+DEARAKLDRAADAYAEGLIDSHQLTRISANLHKKREDAEARLARARPLGGLSFDRGASPV
+QVWRRAPVAVRRTLVEMMMTVTLLPGGRGSRFDPEQHLRIVMNDLKTSVSDILVTSGTVP
+DRPTGSEDSDPPRRE
+>GCF_005280335.1_02198
+MQVEEDDRRVVAVVEDPVREPVVCEAARRVLAGESLNSIARALNERGAPTAATDREEASR
+LWTASKVRQMLQRPGYAGLRVYRGEGVGKAAWEPLIEREQWDELQALFESSRAAQGPQDH
+RAAYLLTGIARCGVCGSKLVRRATRSGKVVRKDGTVAPKRRYDTYACAAGIDRAGAGFHV
+SMSMVHLDDYVSRLVVERLSRPDVLECLAGTEGTQSDERVALRAEIAGYREHLERARAYA
+AEHLRMDLLIDQEARLQPKIDTAERRLRELAAVDPEVRRLAEAADVRATWDALDLEGQRH
+VVRVRMTPSVLPRTRPGRRGLDPERVDVTWLSDCLESP
+>GCF_005280335.1_02372
+MVELVSLRKTNEVAAYVRASMDRKGDRWTVETQLRKIRALAEAKDWEVVEVYDDNAVSAT
+KKRRAGTRWAEMLDDARAGRFSMVVAVDMDRLLRSTKDLNTLIDLGLRVVTVDGEIDLST
+ADGEFRATMLAALARFEARRKAERQIRSNDRRRAEGIPASSWKAFGWTREGELIEAEADA
+VRRAFDAFLGEPSLSIRRIREDLNSAGHLTARGSAFSVDAVRYLLANPLYAGYIKHYASG
+ELYPVQGDAFPPIVGEQTWRAAVAKLEDNVRRSARQGNQPKYLLSTIGLCGKCGATLVSG
+TNSRKQPTYRCGEQFHLTRQREPVDAMVTEAVLTRLSSVDVHDLVMPQEDDGPDREALLT
+ERNALVERVKELSPLLLDVRQPVLEITEAIRGGKARIDQIDAEILDRSVSVAAKLLGDVD
+ESLGTMERREVVESKWKALDMDRRRMLVDELVTVTIEPIAPGHVKFDPDLIRIEPRRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001763.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de42088485a495e93fba8bd1b5c64624f272f8d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001763.fa
@@ -0,0 +1,47 @@
+>GCF_003691675.1_01860
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
+>GCF_005280335.1_00614
+MLLERIYDEDLAQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHVSGEGGEDWTYGFEGNLLHDGDVITLGNITVTAQHTPGHTPEH
+LSYLITDGAFAQAPGYYLTGDFVFSGDLGRPDLLDEAAGFQDTRFAGAKQLFRSLKEKFV
+GLPDHVQVFPGHGSGSACGKALGALPSTTVGYERTYAWWAEYVANDDEQGFVDELLDGQP
+DAHAYFARMKKQNKLGPAVLGELTPLAELTGEQAVARVAAGDVLADTRSVDEIHAGTVPG
+ALALPAKDKAATHIGWAYDPEQDDAAIILLADDQGDAEAIRSHMIRVGVDAADAFVTSLD
+GFELQPAAVISPEELQRRIDAGDVVPATADAAPGEGGLALLDVRNRTEHAEGTVPASGGA
+EAAQLNSGKVLFHQGELPKDATLVTFCQSGLRNVVAAQSLRRAGFDVVELEGSYLGWLGR
+TRA
+>GCF_005280335.1_02660
+MLLERIYDEDLAQAGYFIGCQAKGEAVVIDARRDIADYLALAAKHGMRIVAVTETHIHAD
+YLSGTRELAAAVGAEVYVSGEGGADWQYGFDARRLYDRDTITIGNITIQARHTPGHTPEH
+LVFLVTDGAFASEPGYLISGDFVFAGDLGRPDLLDEAAGGVDTRFEGARQLFTSLREVFL
+TLPDHVQVHPGHGSGSACGKALGALPSTTVGYERANAWWSRHLAADDEQGFIEELLDGQP
+DAHAYFARMKKQNREGPAVLGERGPVPELAVAEVARRLEADETTFVDTRPPAQAHQGTVA
+GSLNIPDGSKTATYAAWAYDPEADSRPLVLLAEDQTAAQAIADRLLRVGIDQTAGYVTTI
+DGLPRFVPPLIEPAELAGFDAALLLDVRQRGEYAAGHIPGATQLSAARVLWHKDELPRSG
+TIVTYCQSGMRNTVAASALRRAGHAVVELDGSYNAWRAWQETTSETALA
+>GCF_020097155.1_00538
+MLLERIYDEDLSQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHLSGEGGEDWTYGFEGHLLHDGDTIQLGNITVQAMHTPGHTPEH
+LSYLVTDGAFAAAPGYYLTGDFVFSGDLGRPDLLDEAAGLQDTRFAGATQLFQSLKEKFV
+NLPGHVQVFPGHGSGSACGKALGALPSTTVGYESTYAWWAEYVENDDEQGFVGELLDGQP
+DAHAYFARMKRQNKQGPAVLGELTPLAELTGEQAVARVSAGDVLADTRPVDQIHAGTVPG
+ALALPAKDKTATHIGWAYDPESDDAAIILLADAQDDAEQIRAHLIRVGVDAADAFVTSLD
+AFDLRPTAVISPEELERRIQDGGVVPATADAAPAEDGLALLDVRNRTEHADGTVPASDDA
+EAAQLSAGKVLFHQDQLPKEATIVTFCQSGLRNVVAAQALRRAGFDVVELDGSHLGWLGR
+SQA
+>GCF_023573625.1_02090
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001767.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78c99f9be1c8725951c4c0d5a336e0e53b33c28e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001767.fa
@@ -0,0 +1,24 @@
+>GCF_005280335.1_00149
+MEVPFTFDAELREGRLDLAEITGGGGAQVLGFDMLPESFTTMKLTTADEPYAPVGPMKPE
+GSPEGVLVQEPRHGDLVPVVASWDPSVVDRFIYVADAGFTGKDTPAPDGEHTVPETVETG
+SATAWWLAAAGALGAGALLRLRPARRGA
+>GCF_005280335.1_01863
+MTITASTTAPTAPSRRVRLAASTPDAHAAEDVDVRVRPEGGDAWTTVAHRSGADPVGAVS
+SRDIQEAIGTPERGRAARQRLGQCRRHGRAGDLA
+>GCF_020097155.1_01752
+MDHVASHPRIRPASMRLITAAGTVGLAAAVLAAPASATPHLGEQAVWGCVYDTAGVYTFT
+DQETGATASSASVPFVLQDAAADPEAHTAEDVTVAVRPAGSDAADAVQIPFAGGDPVGAF
+ETRDIVAALGPDVRQAVVEVRVDGVTEAATVLEVETGTNAADQACFAYEYGTEVMGPQVE
+RIDVPLHQPADLGRPADGSFAFGVSSTPAAVEVTVEGETHSLPVAGVWQEGSFFGVDEPV
+AALKEVDGGYGYKEWMSEALARFDGTDYALVYGEDADGVTRSRLALLHPYVDRAVEDAAA
+PAEGGHTVPSKVQTGDEAAWWLAGVAALGAGALVAARRRLGLAA
+>GCF_020097155.1_01759
+MVYLQGGPSSGTPGGGVTVLAEEPQHGRLVVVPGEQGALPYAESHVLAQLGAGEDPAPTA
+PDAEHAVPGKVQTGDEAAWWAVGLGALGAGALVAARRRFGLGEAR
+>GCF_020097155.1_01765
+MSARRVVIALRGARTRPAPITEDTLKKTTPRLAAAAAGVALITGLGAAPASAATWTSAHG
+VPSGLFDTSLTSEGLLGFSLVDNFTADQVKVVVTAADGTQTPVPFEFYGESDGGVVLLED
+VRAAAGGADQPYTLTVDAAGQEAFGLTYTPGAGYEDVDAEDFVAFEDWATVSTRSVPVDV
+DGWLYEPLAVDEAGNAASGVAAVVTVQPQHGTVTVGSGAYLYTPAEGFEGLDTFTVVLTS
+DGIKRTVEYSAYVQDIEGEQGTAPSVDAPVAPAEPVEEPAPTEEPAPTDPSDEPTPSTTA
+PSTPAETGEETAPTTPADGHEVPGKVQTGGEPAWWLAGAAALGAGALVVARRRLGLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001768.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acdb3f5fa92a6cf4504ec9652b4c16722f384a1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001768.fa
@@ -0,0 +1,26 @@
+>GCF_005280335.1_00388
+MARCTVERLMRAAGLRGISRAKGPRTTVPGRGPDERQDLVQRDFTAAAPNQLWVADITYC
+RTFSGWVYAAFIIDVFSRRVLGWQLSKSLRTDLALDTLEMAFWTRQRAGQDVAGLRHHSD
+KGVQYVAVRYTQRLAQAGAVASVGSTGDSYDNALAEAFNSLFKAELIRNKGPFKSIEDLE
+IAVAEYIDWFNHRRVHGEIRLVPPVEFEDVYHHENPVPAPAGTALTSL
+>GCF_020097155.1_00330
+MHTCCRLLGVSRQGYYRYQKRPTSATELRRRWLTGLIREIHIASRGTYGYRRIHAELTMG
+MNIPCSSRLVWVLMTRAGIGGLPGPARIKRLKGVATADDLVNRKFHRLELNELWVTDITE
+HPTREGKVYCAAVLDACSRKIIGWAIDSKQDSTLVVNALDMAIRARQPDPGGIVHADHGV
+QFTSWVFTQKIRSAGLLPSFGTVGDGLDNAMMESFWSSMQIELLNRKKWKTRIELANAIF
+EYIEVFYNRHRRHSSLEYATPNDYDLARTPQALATTGS
+>GCF_020097155.1_00656
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGVYGARKVHAQLRREGLQVARCTVERLMRAAGLRGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGLQYVAVRYTQRLAQAGAVASVGSTGDSYD
+NALAEAFNSLFKAELIRNKGPFKSIEDLEIAVAEYIDWFNHRRVHGEIRLVPPVEFEDV
+>GCF_020097155.1_01209
+MQIGAWAQGGEIELANAIFEYLEVLYNRRRRHSCLECATPYDYDPAGTPRALTTTGS
+>GCF_020097155.1_01831
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGLYGARKVHAQLRREGLQVARCTVERLMRAAGLGGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGVQYVAVRTPSGWPRPAQSPRSARRGILTI
+SVLAEAFNSLFKAELIRNKGPFTSIEDLAIAVAEYVDWFNHRRVHGEIRLVPPVEFEDVY
+HHENPAPAPAGTALTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001769.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1935de5f29211c3c05ebab3463185fdc70ed7e4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001769.fa
@@ -0,0 +1,35 @@
+>GCF_005280335.1_00518
+MKAWQFSGTGKPLELNEVPEPTPGPGEVVVDVKAAGICHSDVSAIDDAGWMPLFPELPHT
+MGHENAGVISAVGEGMDHWKVGDRVGLAPMNSKGEAIGYHTWEGGFGPKLRATDDNLVKL
+PDEVPFDLGAMATDAGLTAYHAVVAKGGVKKGMKVGIIGLGGLGYIGAKVAALMGAEVYG
+AEVNPKTRELKDEIGLTAVAESILEFKDVGLELVVDYAGFGTTTAEGITALKKDGVFVQV
+GMGKLEAPLNTYELITKTISVLGSNSGTKEDLAGIYELMQRGELNPPINRITQADIPDAI
+ETLRAGGVIGRYIAMYDDAK
+>GCF_005280335.1_00811
+MHQAYAVYEGDTAIHEIEVETPEATGRSVLLKVLRSGVCHTDTHLREGGYDLGSRGTMSL
+TDRGVPYPLVMGHEVVGEVTAVGDEVQDVRVGQRMLVYPWIGCGECRMCREGRDNACAAG
+KNLGVARHGGYAETLWVPDAKYLVDIGDLDPSWTATLACSGITAYSAVDQVLPLDEEESV
+VVIGAGGLGLTAIALLSARGHRTVVAVDRSEKNLELARQMGASATVVSDDDVAAALKEAL
+GGGAAAVIDFVNNGATATLGFDSLAKAGQMVQVGLFGGEVTLPNALLSLKMIRISGSFVG
+TLQQMKDLVQIARTTDLPKIPIIERQLSAEQVAASLDDLTAGTVSGRVVLTA
+>GCF_005280335.1_00946
+MTTMKAVRFTAYKTFPELKEIERPTPGPGEVLLKVAGAGACHSDVAVYDEFEAGMNPLVD
+PEYTLGHETSGWVEELGEGVTGFEVGSAQLVYGPVGCGHCPACSRGQDTYCQNVAEMDYA
+GIGLGRDGGMAEYVTVPARNLVPLGDADPVPASALADAGLTPYHAIKLALPRLNRAGTYA
+LVVGLGGLGLMAVQILKDLTGATVIATDMKPEAMAEAEKYGAVTVPSGEDQVARIREITG
+GRGVDAAFDFVGIAATARAALDSAAVQSRVTIVGIGNGSTIDWSFLSTPYEAELVTTYWG
+TVEELHELAGLYRDGKVEPLYTTYAMDGALQAYRDLQDGKISGRAVVVPHGQA
+>GCF_005280335.1_02387
+MKALYESGPHAGFEFTERPEPECGAHDVKIRVFTTGICGTDLHIEAYDAAAQAMIQAPMI
+PGHEFYGEVVEVGDLVEHVEVGHRVSGEGHVVCGMCRNCRAGRRQMCINTVSVGVQRDGA
+FAEYVVIPEANVWVHKGEHVTPELGAIFDPLGNAVHTALSFPLVGEDVLITGAGPIGLMA
+IPIARHAGARYIAITDVSAERLELARSMGADAAIDVSATRIREAQRELGLAEGFDVGLEM
+SGRASALQEMVANMNHGGKIALLGLPAEEIAIDWQTVVTHMLTIKGIYGREMFETWYAMA
+AMLQTNATLRERVESVVTDVIAAADWKRGFDAARAGATGKIVLDWRNL
+>GCF_020097155.1_00886
+MVTMRAVRFEAYQQFPALKDVEKPVPGPGEALLKVAGAGACHSDVAVYSEFQPGMNPLID
+PEYTLGHETSGWVEELGDGVVGLEKGEAMLVYGPTGCGRCRACSRGQDTYCENVAAMAAA
+AVGLGRDGGMAEYVSVPARNLVPLGDADPIPASALADAGLTPYHAVKLALPTLGRPGACA
+LVVGLGGLGLMAVQIIKALTGATVIATDMKEDAMAQAEAYGAVTVPGGEGQVERIRELTG
+GRGVDAAFDFVGVAATARLALDCAAVQSRVTIVGLGNGSTIDWSFLSTPYEAELVSTYWG
+TLEELHEVARLYRDGRIEPLHTTYSLDDALQAYRDLQDGKVAGRAVVVPHGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001770.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b624ad72eb179ae2f198275e67425f138ef5e007
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001770.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00012
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW
+>GCF_003691675.1_02030
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW
+>GCF_005280335.1_00384
+MSDEIFEHETTETMTREQAAARLRELADQLSRQNEVRIEHAGRDVVVTVPDQVELEVELE
+IEEGGESELEISLSW
+>GCF_023573625.1_00012
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNKVRIEHGGRDVVVTVPDRVGLEVELE
+VEDDGDAELEITLSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001773.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bc9751fad736111ede63794408f9fab0714152f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001773.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00051
+MSTTLQPARTDGVASEAPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEVTQLELPAELAELLSSQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTGLEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMRGVIESTAGIRGTDA
+>GCF_003691675.1_02064
+MSTTLQPAQADVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+KHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAALEAGDYGNRLFLSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
+>GCF_005280335.1_00352
+MSTSLHPPQAVIGEPEVLEDVRADVVSHPAWLRLKAAATALQGLQAKDGSVPDPADHPAA
+GGHVETITAAVAELAPLFPHDAAYLAALPRDFARWRDGGFGVPDFLDSLVAFQPQEHRVD
+GIRHLVVFPMYTQNGSSSRHVEALLVEAIWPEFIAQLEAGDYGNRLFLSLRLLDFTPGYE
+TNSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVAAAAEITRLDLPEDAAELVADQD
+LAEQTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDLTAFRETVRIEREL
+SARAAAGEELTAVQAQTLRHAKLVQYAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHR
+RHVVQWRDVKLTIDWDRLAEAVVELGDAIDRLYWESIDRPKTVHWLKAYELVASVVAPHP
+ASVWAQGLPREVLAGPPKEMTDLVLDDEFPLSMFFEALGKKLRGVIESTAGIRAADA
+>GCF_023573625.1_00046
+MSTTLQPARTDVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLTALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLANAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001774.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ea1a277bb7b266ea37fe553fd0ecb75053e9a54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001774.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_00052
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYILFVRVGSPRELEALVT
+EIRQTASVATRTTVVLQTFYEHRPMLELPAED
+>GCF_003691675.1_02065
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPAED
+>GCF_005280335.1_00351
+MDDPVDARLAAEVSRDPRATLAQLSERVGLSASAVQARLRKLESTGVITGYQAILDPEAV
+GKPLAAFIEITPLDPRQPDDAPELLEPIAAIEACHSVAGDAAYMLFVRVGSPRELEALVS
+EIRHTASVNTRTTVVLQTFYEHRPMLPLPDAGE
+>GCF_023573625.1_00047
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001775.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8017ebf7a8be0c7643af257353cbc261393360da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001775.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00059
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+MSLGDYTST
+>GCF_003691675.1_02072
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPDAPAGDADRAAWDRAPSYAEQ
+EGQTRPAYGQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTDGVGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
+>GCF_005280335.1_00336
+MTEPHPAHDPHRRADGGQPSWYGGGASGGGSSAASWPDGPAADADRAGWEQAPSYAEQQA
+APAYGGDAGHGQDGYAPAGYAPAPGHGRPAYGFGAPLAPGQTEGTGRSVASMILGIVSIV
+GGFTLVVPPIVGVILGHLGLKREPNGRGMAIAGLVMNYLSLAFVLLGVVLLTILVAAGMA
+ASEYSTY
+>GCF_023573625.1_00054
+MTDPHASHDPRREAARPSWYGSEAGAGSSGTGSSAAGWPAAPTGDADRAAWDRAPSYAEQ
+EGQTRPAYDQPYGYGQDANTVPAYGYGQGTPGHGFGAPLQPGQTEGIGRSVASMILGIIS
+VVGGFTFLLPPIVGVVLGHIGLKREPHGRGMAIAGLVMNYVSLALLLLAVVFLVILVIAG
+ISLGDYTST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001785.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e30aff39dd738afe90f1b86b43c5c44ceceeabb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001785.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_00177
+MTATQDAPAVDPRPAAALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDDAGPCGSGAAVAAEDVRPDTGAEGAVKPELRRRGAGTAEPANA
+>GCF_003691675.1_02170
+MTATQDAAAVDPRPAAALDPEALVDRVEAGHRLTAEEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDGAGSCGSGAAVASEAGAAEDARPDTGAEGTVKPELRRRGAGTAEPANA
+>GCF_005280335.1_00225
+MTAAQDAAVVAPALDPEELVDRIEAGHRLTAAEAVAVLDAPDAETFRLVAAASRLRERHF
+GRTVKVNYLVSLKTGLCPEDCTYCSQRLGTEAQILKYTWLKPDEAVRQAGLGIAGGASRV
+CMVASGTGPTDRDVDRVTEMIGRLKDEHPQVEVCACLGKLKDGQAERLKAAGVDAYNHNL
+NTAESHYESICTSHTYADRVDTVERATAAGLSSCSGLIAGMGETHAQLAEAVLALRELDS
+DSIPVNFLMPFDGTPLAGHVQLTPLECLRILAVVRLACPDKELRIAGGREMHLRSLQAVG
+LQVANSIFLGDYLTSEGQDAEADLSMIADAGFTVLGAAAAPADDDGAPDGGCCGGGGCGE
+GGVEDASTRGGTSPSPSPAPRRRGAGTAEPANA
+>GCF_023573625.1_00169
+MTATQDAAAVDPRPADALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERAQQAAADDGAPAGCCG
+GGCVGTHDNSKNGAAATPSKPVLRRRGAGTGAAANA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001786.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2e3e96becab9ff204f01fa2b5e5bf89660c235e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001786.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00199
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG
+>GCF_003691675.1_02195
+MARPQTVLTVVAAHRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRRMDAAARTMDVDFVVHGASDDGAAPGRDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAVGVALI
+EVTDARDEVPLTAPAGVEVRWLHRGDPFTPETTRFAAAVEDAAWREGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPAGQIFEDGTTGG
+>GCF_005280335.1_00194
+MTRPATPGRPARPQTVLTVVRTERLTPHMVRVSLGGDEFAAFHARWAEKGATDQYIKLLF
+ADPALGLTPPYDLDALRERLAPEQMPVRRTYSVRAVDVAAGTVDVDFVVHGDDGLAGPWA
+ASVQPGEQVCFGGPGGNYRPDPAADWHLFAGDEAALPAIAAGLEDLATTAPDAVGTALIE
+VEGPEDEQPVTAPAGVEVRWLHRGAEFTPQSTRWAAALREEPWREGRVHAFVHGEREQVK
+AARAYLADERGVDRRDLSVSAYWAFGRAEETFQAEKQTPLGQIFPDGTTGG
+>GCF_023573625.1_00202
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001793.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1de0b5c6b18246902ff768aaa6d9ff1f88e7da8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001793.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00247
+MSEKTAPTETAPVIPHFVHGERREGASGRHSDVYHPATGRVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSMRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVVMPDADLEMTADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>GCF_003691675.1_02259
+MSQKTAPTETAPVIPHFVHGERREGASGRHGDVYHPATGGVAGRVPLASAEEIDAALASA
+EEGFAAWSRLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERIKGLTVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGAELVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>GCF_020097155.1_00091
+MSQQSQTQQTIPHFVHGARTGTDAARTSDVFDPSTGQVQARVALASPEEVTAAVDSAAEA
+FRTWSAMNPQRRGRVLLTWVDLINANADELAETLSREHGKTFEDAKGDIQRGVEVVEFAA
+GAPHLLKGEFSTSAGTGIDVHSLRQPLGVVAGITPFNFPAMIPLWKAGIALAAGNTFVLK
+PSERDPSVPVRLAELALEAGLPAGALNVVHGDKAAVDALIDDPRVKAVGFVGSTPIAQSI
+YEHAARRGKRAQCFGGAKNHAVIMPDADLEMAADALIGAAFGSAGERCMAISVAVPVGEE
+TADRLVALLRERMASLTVGPSLDPSSDFGPVVSAQAKERIESLIQAGVDEGAELVVDGRG
+VVVEGHEGGFYVGATLFDRVRKGMRIHAEEVFGPVLCVVRAKDYEEALSLPSDHEYGNGV
+AIFTRDGDTARDFSTRVECGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLKFYT
+KTKTVTTRWPSGPRQGGAAASEGASFVMPAGS
+>GCF_023573625.1_00247
+MSQKTAPTETAPVIPHFVHGEQREGASGRHSDVYHPATGSVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTVPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001795.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90d29bf4f2aac7b46b8a6d875844a83bd2087f85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001795.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHKEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>GCF_003691675.1_02265
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>GCF_005280335.1_00116
+MYTRSRNDVEKVEWGGGTSERLLTAKDEMGFAVAHTIVRAGSSSKLQYRHHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>GCF_023573625.1_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001796.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b73a97b07b1f621940f30acd847fa7cdc4124729
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001796.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_00272
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>GCF_003691675.1_02287
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>GCF_005280335.1_00084
+MDALGWTTLAISLLALVAAGWSAFESWRLGRVERQRDQRQEDRERQEQARQVAAWMCVVA
+EREHNLAATVRRRWFLAIENSSQVPVYDGHATITSKYPVPALEAAMFPPGRTYFELGKNE
+WGYGVQSDELAIVPRPLTNAERFRVTSLAFTDAAGTRWTRDEQGRLAEGPAAADTGAMST
+GT
+>GCF_023573625.1_00270
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001801.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d59bebe0acd3d226f7af8304cb703a858fa3ae82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001801.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00302
+MALALVLVGCAAPQGDEGTAAGSSGATDAAVSSPASVDGSEASSSQGRSSDAASSPAAAS
+SGEGSPSAAADPAGPAVPLAARSHEGVPMRAFTAEERPPQFVLFSFDGGRQDARWKTFLD
+AAADSDAKFTVFQSAINLIETANRENYTAPGNTPGYVGTEFGGDEAEVAQRIENINTAHA
+AGHEIGTHYAGHLCALATYGGDKWSTAEWEQEYGSFRDILSDPAAYNPGSSLPALEVTPE
+DVKGGRLPCLDGQWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQEDGIWEFEMPMTWSPV
+LAEKGAASPFVMAMDYNFWISGNGGRDIPEDVARLTDFQYRTYRYMYDSALAGNRAPLVF
+GNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQDPEVLAAWRDQARSAT
+GTDAEALGW
+>GCF_003691675.1_00010
+MSFPRRSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SANGSEASSSQGRSSDAASSGEGSPSAAADPAVPLAARSHEDVPMRAFTAEERPPQFVLF
+SFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPGYVGTEFGGD
+EAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGSFTDILSDPG
+AYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAAASGVAWPYQ
+EDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVARLTDFQYRTYR
+YMYDSAFAGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQQMIAWLELQ
+DPEVLAAWRDQARSATGTDAEALGW
+>GCF_005280335.1_00052
+MPLHRQPAPFRARRVWGTSVALALVLAGCAAPQEGDAQGAASETSSSSAPAPSASAPSDA
+GPASPSGSTGTDASETAAAPSSSASGDSAGPTASADPATPLAARSHEGVPMRAYAADERP
+PQFVLFSFDGGRQDARWKTFMDAAEDSGAKFTVYQTGINLIESANRENYAAPGNEPGYVG
+TELGGDAAEVAQRIGNINAAHAAGHEIGTHYNGHLCSPTPHGGDKWTTAEWEQEYSTFEE
+IITDPGAFNPGSALPALDITPEDIKGGRPPCLDGQWDQLVPMWKEHGLVYDTSRSASATG
+VAWPYQEDGIWQFEMPIVWSPVLAEQGKPSPLVMAMDYNFWISGNGGKDDPADTARLTAF
+QHRTYRYMFSSAHAGNRAPLVFGNHFNDWGLNAFNPAVEQTMREVCDEPDTYCVTYQQMV
+DWLELQDPAVLEAWRAQPRSATGDDAAALG
+>GCF_023573625.1_00309
+MSFPRPSARTVDTPSPRRRRWWGTSVALALVLAGCAAPQGDEGTAAGSSGATDAAVSSPA
+SADGSEASSSQGRSSDAASSQAASSFGEGSPSAAADPADPALPLAARSHEGVPMRAFTAE
+ERPPQFVLFSFDGGRQDARWKTFLDAAADSDAKFTVFQSAINLIETANRENYTAPGNEPG
+YVGTEFGGDEAEVAQRIENINTAHAAGHEIGTHYAGHLCAPTRYGADQWSTAEWKQEYGS
+FTDILSDPGAYNPGSSLPALEVTPDDVKGGRLPCLDGEWDQLVPMWKDNGLEYDTSRAAA
+ASGVAWPYQEDGIWEFEMPMTWSPVLAEKDAASPFVMAMDYNFWISGNGGKDIPEDVSRL
+TDFQYRTYRYMYDSAFVGNRAPLVFGNHFNDWGLNAFNPAVEKVMREVCVEEDTYCVTYQ
+QMIAWLELQDPEVLAAWRDQARSATGTDAEALSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001810.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dafbb01d8cbff600f7b1555aec06791c4e84a2cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001810.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00431
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASTLRNLLPGAAQDIADSLPEGSAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRRSNAARIMGALFASIAIFVTLLGTIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>GCF_003691675.1_00152
+MASDHRPPHPVSPHPDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
+>GCF_005280335.1_02526
+MASDPRPPNPASPDPASPDGFRPGDGRPVVGPEDARRRIAGHSGPHARPLIRPNERTPGV
+FRALVGLTVASAAVYVVSLLLGLRPGAAEEIAATLPADASRSPAMTAESIQAALTGSVWV
+AVLLGLGVYALVLVGLLRRSNTARIVGAIVAALAVFVTLLGAIRLFVFPAESVVAPLLLG
+LLFALVNAAWLVCAFNPGLATTFVRRDAGPRRPA
+>GCF_023573625.1_00434
+MASDHRPPHPVSPDSDDLDGGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGVFRAL
+LGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWFATLL
+GLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLGGLFA
+LVNAAWLVCAFNPGLATTFLRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001811.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..295e6b90c529b1aca59d86f0942c9bf76c361cc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001811.fa
@@ -0,0 +1,28 @@
+>GCF_002008305.4_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLQDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>GCF_003691675.1_00181
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAAGILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAAAPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>GCF_020097155.1_02368
+MSEPSIPAPTTASVPDSTGLRLLAVHAHPDDESSKGAATMAAYAAAGAEVLVVTCTGGEA
+GSVLNPSYAHPVRAERDIAGVRHAEMAAAARALGVRHRWLGFLDSGLPEGDPLPALPDHC
+FAEVPLETAAAPLVAVVRRFRPHVILSYDEAGGYPHPDHIRAHEVTRVAWERAGDADAYP
+GTGPAWEPLKLYYDRAFHPAKYQALHEGFLAAGEESPFTDRLEMHARMEAMREVLRRREE
+GEEVPDPEHLPPFVPPVHEVTTQIPVQDFLDERDAALRAHATQVDPEGMFFAAPNELQRS
+TWPWEDYALIESRVRTVPPETDLFAGVR
+>GCF_023573625.1_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGVRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001813.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90f7c278e4483354b8ac1c34fe391a24b6e7364a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001813.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_00510
+MAPAEKRVPGPRFRELDGLRGIAALAVVFSHYTGAHNSHYPQDPAAFHDAAWGAAGVQLF
+FIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVVLLLLHPVPGFPFTWSQAF
+LNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRVVLWGSLAWSVISW
+AVVLFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQTGQHRGWVAAAAV
+SAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLAPVQWYGKISYSLYILHAIPG
+YILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGLTRVRSVVDARTGH
+PRSLEPAR
+>GCF_003691675.1_00230
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGVAALAVVFSHYTGAHNSHYPQDPAAF
+HDAAWGAAGVQLFFIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVGLLLLH
+PVPGFPFTWGQALLNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSIAWSVISWGVVSFTAPHVGWDPQRDPMWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLPPIQWYGK
+ISYSLYILHAIPGYILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVDARTGGPRSPGKALG
+>GCF_020097155.1_02324
+MTAASSNEPGAATVPPIEKRHPGPRFRELDGLRGIAALAVVLYHFTGHFAARFPAAPRAF
+HDFWWGEYGVQLFFLLSGFVILMTAWRAKRPSDFAISRVARLYPPYWISLAVAVSLLLWR
+PMPGFPIDPATVVANVTMVQRWFLFPNVVEVYWTLAVEMQFYVIVFVLLLVTRCRLRGRV
+LLWAAAAWTAVSWVVILAAFRVTSDNPQADPTWVKLLTNATVAEYGPLFVTGMLFYLVRE
+TGRHPGWAIASAASTALGATLLRGSEHGVMVAAVCALAWLVWRVGEQWLGKHARTGLVSL
+RDHVSPRAVASKREAAR
+>GCF_023573625.1_00509
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGIAALAVVFSHYAAQHNSHFPEDPPPF
+HGFEWGAAGVQLFFIISGFVIFMSARRASRPSDFAISRAARLYPPYWISLVFAVVLLLLH
+PVPGFPFTWGQALVNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSLAWSVISWGVVSFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSSFVMRGMPLAFEVLVVVLLAVTVMLRERTSVLLLAPIQWYGK
+ISYSLYILHAIPGYILIHTLWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVEARTGHPRSLEPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001817.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d906477f1fa421a692f14daf143c1bbc38036e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001817.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_00576
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>GCF_003691675.1_00308
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>GCF_005280335.1_02357
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRVAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>GCF_023573625.1_00577
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGAVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001819.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4bab7f0cfe84fb365d6e0abeeeed3496ff46c6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001819.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_00578
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>GCF_003691675.1_00310
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>GCF_005280335.1_02355
+MPQSRALSRGVRLSAMSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLVELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEPPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>GCF_023573625.1_00579
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPGLSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001820.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35a5656bcd274a484b38d3efe90e1c3f8c5b4acd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001820.fa
@@ -0,0 +1,23 @@
+>GCF_002008305.4_00581
+MVPLMVVTLFTVVASQIRGAGERLPALAAVVPLFAAFAAVMVALGVVAARWTHLDVPAGR
+ALVFSGATRNSLVMLPLALALPASLDPAPLVVVTQTLVELGVMVSLVRLVPRLLPLHGQS
+AGAGARRTVT
+>GCF_003691675.1_00314
+MPSSPPRRALVAALLVGVLLVLLAPCVDYVIAFTALAGGAAERLLAAAPLLMLVQLVVLP
+VLLRVVAGEAAVAAVDVGPFVRALVLLILAPLALAALLQWGTARGRGGVRRTAAGVVRGC
+TAAMVPLMVVTLFTVVASQIRGVGERLPALAAVVPLFAAFAAVMVALGVVAARWARLDVP
+AGRALVFSGVTRNSLVVLPLALALPASLDPAPLVVVTQTLVELGAMVSLVRLVPRLLPLH
+GQSAGAGAGRTVT
+>GCF_005280335.1_02352
+MESAQSRRAAAVAWMERHQAALYAAGIAAGAVVGWVVPGAGRLAVLVEPVLGLLLLATFL
+AVPFAALGAALRDVRFLAALLVLNFAVVPAVVFGLSRFVAHDDALLVGVLLVLLAPCVDY
+VIAFTGLAGGAAERLLAAAPLLMLLQLLLLPVLLRVCAGPAAVAAVDVGPFVRALVLLIL
+LPLALGALVQGVARRGAPGPRRAARAVEAATGAAMVPLMAATLFLVVASQVRAVGERLPA
+LAGAVPVFVGFVAVMVPLGLAVAALARVDARSGRALVFSGATRNSLVVLPLALALPPSLD
+PAPLVVVTQTLVELVAMAVLVRLVPRLLPERAAPAEEAALAVRPEPDVTGS
+>GCF_023573625.1_00582
+MPGADAWAVLVEPVLALLLLATFLAVPFAALGAGLRDGRFLGALLVLNFVVVPAVVFGLS
+RFVAHDDALLVGVLLVLLAPCVDYVIAFTALAGGAAVAAVDVGPFVRALVMLILVPLALA
+ALLQWGAVRGRGGVRDTAAGVVRGFTVAMVPLMVVTLFTVVASQIRGVGERLPALAAVVP
+LFVAFAVVMVALGVVAARWARLDVPAGRALVSSGATRNSLVVLPLALALPASLDPAPLVV
+VTQTLVELGAMVSLVRLVPRLLPLHGQSAGAGAGRTVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001821.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4e0d92a6238a96b997af7dbacd7777590e63e75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001821.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00624
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLRLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAVAAA
+>GCF_002008305.4_00638
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>GCF_005280335.1_00752
+MESFFALLQKNVLDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHT
+PADPA
+>GCF_023573625.1_00593
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001823.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0539aabb553ae56dce8e83a21b8a01cc7eda72ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001823.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_00628
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADTVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTTTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>GCF_005280335.1_00400
+MTSSLTTRRTFLGASVGALALAGLTACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEGTSVHWHGL
+ALRNDADGVQGLTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMDHGSMSQDSSSGMP
+MKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDTAYR
+VGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGHAYG
+IIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYDWGI
+NGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVIIKP
+RQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>GCF_020097155.1_02201
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>GCF_023573625.1_00603
+MTSSLTTRRTFLGASVGALALAGLAACADPVISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRHTIVFDFEADNPGQWLTHCHNAYHAVAGMMGVFSYIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001825.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aeb712001d403eac0282300e684ee8e6ad572c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001825.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00632
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>GCF_005280335.1_00404
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>GCF_020097155.1_02197
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
+>GCF_023573625.1_00599
+MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV
+AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001827.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6b5c3879abb6579fb405643a9d43a9dd69fd4e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001827.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_00639
+MTLMQIPTDHGTIGLNVEESGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLYGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFEGS
+GKRTHKAIDGSRVELVKDAPHGFNTSHSEEFNRILLEFLAE
+>GCF_003691675.1_00376
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAAVSPHYRVITYDRRGF
+GVSEKPTGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
+>GCF_020097155.1_02186
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPMTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARHMSRFGADRIHSVVF
+AGAVPPYLLKTEDNPDGPLTEKQAAEMRAGLEKDREAFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRKEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPTLVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
+>GCF_023573625.1_00608
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GVSEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGSDRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001829.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9989fd060284ca4d7ec02e45a3abd9d672354da2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001829.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_00646
+MSVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>GCF_003691675.1_00383
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>GCF_005280335.1_02317
+MRLIDVGLREGHEYRVRDTWLTVPNVITLVRLALVPVFVWLTVTDQFLAAFLTLAFLSST
+DWVDGYIARRFDMISTVGRWLDPVADRLSLVTVALTFVLTGIAPAWLVLSILIPDVVLTL
+VCLRLFGGSPDLKVTVLGKVRTALLLAGTPLLLLARVPGVDQDLWGGLALVLVGAGCVLH
+VLAAVDYLVRAVRKARELRAAGVDPRDRRARPAQGA
+>GCF_023573625.1_00616
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDVVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001831.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f08ce5fc7646a531f9463dac5297811c010b57d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001831.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_00665
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFTDARVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYATQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEIGEGTTEVQLMLIARELGL
+>GCF_003691675.1_00402
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>GCF_005280335.1_02297
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEFGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTQEQKEAWLPDL
+VAGRHLAGFGLTEPGAGSDAGGTQTTAVLEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGADGKPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGTRGRGFANFLEILDEGRIAIAALATGAAQGCVDESIAYAKQRTSFGQRIGEFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>GCF_023573625.1_00635
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001834.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56e717562bb77e3461f1cdf68960dfa98205903f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001834.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00678
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
+>GCF_003691675.1_00415
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLLL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
+>GCF_020097155.1_02146
+MSPRTVVRTCVGCRSQADQQELMRVALEPGTTPPTVVWDPLRRRPGRGAWVHPGPECLQL
+ALRRRAFHRAFRGQVDPDGLEAGTRASAARPTDEGGSEI
+>GCF_023573625.1_00648
+MTSRTVVRTCIGCRSRADRQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001835.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c6a0ffe1bcc7a3ec7456e3e8ad0242018618355
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001835.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_00698
+METASPPTQPEHAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDDGPSP
+TDEPPEPDTAALRGIAPLVDVDADVTTTTRMGGGSRRTSTVYVKGWTGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+GETMSRE
+>GCF_003691675.1_00435
+METASPPTQPERAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGRGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIAPLGDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMSRE
+>GCF_005280335.1_02256
+MSSASPPFRSASDPSAQDPSASDPRVAADGREEDPHAPADGRPPRVVGLVAGPGYPWVLV
+RRIARDFEQRLQERMPAPHGWRVETRQESLPVGADGGMVLEEPVRALADEHGWDTVIAVV
+DLPRFEDGRGVVADVVPQLRLGVVCVPALGLITPARRLRETVLRVVDHLDTVPEVDPPDG
+ELDVQSSDRSAEVEEDGAADTEELRALTPLGGTEAGVSTTTGMGGGRREASTVYVKGRTG
+TLRLLAGMVKANRPLRMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPWRLAAVTVLS
+IVLLVAWLIATNGLWTRGTRHRHSSRLDNLSTVITVGLACTLVYAVLFATLFLVAVMIIP
+VDYLGGELERASDLSDYANLVWLAASMGTMAGAVGSSLDDSERIRNATYSLREWHRRRGW
+DEAREAADEPAAASRE
+>GCF_023573625.1_00668
+METASPPTPPEHAQQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIASLVDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001838.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0335ee4ca0730f07ae538a18482208bc27e254c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001838.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00846
+MNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTPAALLAAMSLDEST
+QIHEQAGQLWEVLPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTRALTVAGG
+AVFFFGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLHLRPAPGH
+LQVTADGVPDAGADDVVLGAGPGPAARLDDCD
+>GCF_003691675.1_00568
+MSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTR
+ALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLH
+LRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
+>GCF_005280335.1_02089
+MVSMKRSTEQSDVPAPLADPGSGAGSVTASGAVRPAEADPAAGQPVQGRWARRVALTLIG
+VSVALAAWSFAIPFLFGLGVRELPWWRQFFDLNHETNLTAWWSSGLLLLGAIGFAVVGLV
+RRSLRADRPLALLAWLTPSALLAAMSLDEFTQIHERLGEVWDALPFTPENPLHAFQGLIL
+GVPIALAVIALLALTAMMLPRRTRALTVTGIVVFFVGAIGLEAVPLVFNIARASWAYHAV
+THLEELTEMIGSSLLIVAPWVHLHLRRAPGSLLVTTDGLPAAAEHDDAAPAGR
+>GCF_023573625.1_00805
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTP
+AALLAAMSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVA
+LPRRTRALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVA
+PWAHLHLRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001839.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9423bbcb4887ff7fd26fee70fb10dfe8802ce35f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001839.fa
@@ -0,0 +1,48 @@
+>GCF_002008305.4_00858
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALAPDTSARAADVVRDWQSDVLALVQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLEHRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHV
+PSAAEAGEEPR
+>GCF_003691675.1_00580
+MAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQIDDYVLPR
+LDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADTHWFTGP
+RVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVADQNRAL
+ARQLLEAADLWIFTTTAHRYADAVPWQLLDEAADRDITVAVVLGRVPEGAAEDITPDLRR
+MLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARRTVDGVL
+GQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVLSRWQDF
+VGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAAAEQIER
+RWASEPAGRALVAGRDLGALTPDASARAADVVRDWQSDVLALIQEEGAGKRTRARLAATG
+VNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRADELLEL
+RVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTEPEHAPSAAEA
+GEESR
+>GCF_020097155.1_01971
+MESTDLTSPSAAAPIGVDTAVRRVRAHLDALELPFATATVGADRAEAERTRHQIDDYVLP
+RLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHHPDDAHWFTG
+SRVLPDLARVTVHRSASAGPVEPDSQAMDTVALVAEPSLPQGIAIVDAPDIDSVADQNRA
+LARQLLEAADLWIFTTTAHRYADAVPWELLDQAAARDITVAVVLGRVPQGAGEAIAPDLR
+RMLVEHGLPEAPIHVIPETRFGEDGLLPAEHVADLRAWLTSLAEDAQARSAVARRTVDGV
+LTQLAVRVEALAEAEHGQQETAARLAGIVADSTELALETVHRATSDGTLLRGEVLARWQD
+FVGTGEFFRGLESAVGRVRDRLGALVRGRPAPPEEVEDALETGLHAVLVEAVASAVEQVE
+RRWRSEPAGRALVEGRDLGSLPAGTSERAATLVREWQGDVLALIQEEGAGRRTRARLAAF
+GVNGAAVALMVISFASTAGLSGIELGIAGGAAAVGQKLLESIFGEDAVRRMARRASELLD
+ERVRVLLEDVVGGRFLPLLRLERDAEDTAALRALVPTLRRGVAAGVDGPQPDAAPDAPRR
+EAADAAIEEDAR
+>GCF_023573625.1_00817
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVESALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALTPDTSARAADVVRDWQTDVLALIQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLERRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHA
+PSAAEAGEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001840.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb5c35154c192636ee1b56cada5663064287d3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001840.fa
@@ -0,0 +1,52 @@
+>GCF_002008305.4_00946
+MSTPAVTRPGRPRARFALSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAMYAGTVATAGLLQVQARGVGADTTLARIIHRVEAAQEAR
+ARTQQFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPIVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDHPGVAQAVARQVGVDDVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>GCF_003691675.1_00665
+MSTLAVTRPGRTRARFTLSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAVYAGTVATAGLLQVEARGVGADTTLARIIHRVEAAQEAR
+ARTQRFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPVVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDQPGVAQAVARQVGVDHVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>GCF_003691675.1_01109
+MVTLAVAAVLLVAGLVVEWTIHSEPVALALFWGAILIGGVYPLRSAIRAVRHKRLTITVL
+LVVAAIGAIALGVIEEAAMLVVIFSLGEAMEAYATDKARGSISALMELAPPTANRLNDDG
+ATKTVAVEELHPGDVVLVRPGERLPTDGAVIDGASWVDASPVTGESVPVEATAGTEVFGG
+SLNGNGVLRIEVTKEYYDTVLARVIEQVEEAQANRSGAERFADKFGAVYTPAMFALAIAV
+ALVLPLLGFEWREAIYRALVVLVVSCSCALIISVPVSVVTAIARGARDGILIKGGIYLER
+LADIKAVAFDKTGTLTRGRPTLAQVTPLDGISEDEALTLAAAVETGSEHPIATAIVAGAR
+DRGLTIPAVQDARALPGAGMEATLDGRTLHIGRPTDEDRTDGTAGPALAHAEAEGCTAVV
+LRDDTRPLAVVAVADQLRPDAESTLTELRDLGVERVLMLTGDNATVARSTAQALGLDDYR
+AELLPEDKSAAIRELREKHGVIAMVGDGVNDAPALANADLAIAMGAASTDVALETADVAL
+MADELDRLPAAIRLSRRARNNIKINIALSLTVVAILIVAALAGWMSLTTGLLLNEGSAAL
+IILNGLRMLRPGRGETRRAQVDFGTRQGSDLNSGRPCAPGSTTDGHSVAAGSSYDQREHG
+R
+>GCF_005280335.1_01991
+MSTAETTRTGERRGRTGPRLPHRWRRPALAGLLIVLSLILAPEQVAQGTAHPVAAALMLA
+AAVVAGAGIVRSAVAALRVKTIGIDLLVATAAIGATLLGNFWEAAAVTFLFALGHALEDA
+TLAKTRSALGDLVATAPETAVVLEADGTQRTVAAHEVPAGATVLVKAGARVPVDGVVLTG
+TGAVDEASITGESLPAEKSDGDDVYAGTVATAGLLHVQARGVGADTTLARIIHRVEEAQE
+ARARTQQFMDRFSRWYTPAIMVLALVTGLITRDVPLALTLLVIGCPGALVISIPVAIVAG
+IGRGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVALEDGREDEVLGWAA
+RLEAASDHPLAAPIVAAGRDRGLLSGAMATDVDVVLGRGLTGTVEGRTVAVGNVALLRES
+GADADRTARVEAVAAELAAAGRTPMAVAVDDVPVGVLAVADTVRPEAAGMIRELHRIGVR
+EVVMLTGDQPGVAHAVARQVGVDRVRAGLLPEDKLDAITAMQAEGRVVAMVGDGVNDAPA
+LASADIGVAMGAAGSGVAIETADIALMGDRLELLPQALGLAQRTVGVMRQNIAVSLVTVA
+ALLAGVFAGGVTMSIGMLVHEASVLLVIANAMRLLRPAAGSGRGGSRAAQSRSTTSNSSS
+SAPVATGAGRPSDSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001846.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc55d53ca40c54a7f8dbaaa62de2e867b6f8b373
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001846.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01064
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEVGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>GCF_003691675.1_00783
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGRALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>GCF_020097155.1_01712
+MFTGIITHLGTVLSLEERPETDTAVLTVDAGGALDGLPAGGSLAVDGVCLTALDDDAASA
+APGVFRADLMGQTLRMTSLGGRRPGDRVNLERCLRPTDHLDGHVVQGHVDGTGTVLAVSP
+HGDWTTLRIGLPARLARYVAAQGAIALQGVSLTVTGVSPADAREHWFEVGLIPATLEATT
+LGRLAAGDTVNLETDVLARYAERLAAIPAPTTEEPHA
+>GCF_023573625.1_01011
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDEPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001847.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faae65a5ff368686e693c4a6c12f40c6ce5cb5a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001847.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01067
+MNEKQLEPDLSLRAQRRKPTPAPQTQAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
+>GCF_003691675.1_00786
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGRV
+>GCF_020097155.1_02229
+MNEKQLEPDLSLRAQRRKPTPAPHTPAPGAVIPVEPATASDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALVRAHLMN
+>GCF_023573625.1_01014
+MNEKQLEPDLSLRAQRRKPTPAPQTPAPGAVIPAEPATTSDPAGGYAPLARRGAPTVALN
+VRVPEAIRDAVRREAATNPATPSQAAVIEALGHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001849.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ee5d405db1466d40e481efc1ce3d4f72dd1e3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001849.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01077
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>GCF_003691675.1_00796
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>GCF_005280335.1_02323
+MDPILLLILGTVVILVIILANGFFVAQEFAYMSVDRVRLAAAAENGDEAARRALAVTRRT
+SFMLSGAQLGITVTGLLVGYVAEPMVGEALTQLLGGTAIPASVVIAVSTVGVLLVATVVQ
+MIVGELYPKNLAIANPDPLARALARPTQVYLALFGWLIWVFDKSAEALLRLLRIEPVHDV
+DSTATAQDLDRIVEDSRDSGTLPAELSVLLDRILDFPERDAEHAMVPRSQTDEVGPETTV
+AEVRALMAAAHTRYPVISADHQPLGVVHLQDVLALGHAPAPDLLVTDVMRPATVVPTVMP
+LPDVTRALDDADDQLACVIDEHGGFVGVLTLEDLAEELVGDLRDEHDDEAHEEIVPVVVG
+ESWALRGDVHLDELERAIGHPLPEGEAETVSGLLIESLGRLPEEGERVAVDLPEDTRDYG
+GDVLYDRRLEVDVRRVERHVPADVEVHLVETPREDETEEDPR
+>GCF_023573625.1_01026
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001850.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c348fc05d47248acc8d416585acd8b67cb54c0ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001850.fa
@@ -0,0 +1,26 @@
+>GCF_002008305.4_01111
+MKEAGLWIGFYVALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>GCF_003691675.1_00830
+MKEAGLWIGFYVALALVFAGLLFTLGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>GCF_020097155.1_01674
+MDVLTPAFEITTLVVLGVILLFDLLYVLKRPHEPSMKEAGLWIGFYVTLALIFAGLLYVL
+GDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQVPRRYQQEVLMVGIIIALVARAIFI
+AIGAVAIEHLTWVFYIFGVFLLWTAWHQLQDDDDGEEAEPGIVGRLTRRLNVAEDFDGNK
+LRTTVDGKRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIVLTANIFALMGLRQL
+YFLLGGLMDRLVYLKHGLAFILAFIGVKLILHALHENELPFINGGNPVPVPEISTFLSLA
+VILGTLVVATVASLVWGKAADEGDARRAESATRMKQVSDAARRDGR
+>GCF_023573625.1_01061
+MALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQVPRRYQQEVLM
+VGIIITLIARAVFIAVGAVAIEHLTWVFYIFGAFLLWTAWQQLKDDGEDEESEPGVVARL
+TRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIV
+LTANIFALMGLRQLYFLLGGLMDRLVFLKHGLAFILAFIGVKLVFHALHENELPFINGGH
+PVTAVPEISTFVSLGVIVGTLVLATVASLTRGPHQRARRRPAPPAAGRGVVVRPGRLTGD
+VGEYPEHCGRQHAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001851.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e8fe56b46bb3d880b61fb1c95c232d7c4c675f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001851.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_01112
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>GCF_003691675.1_00831
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLAEDADPAERERAAALMD
+RWTARAEALDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>GCF_005280335.1_01781
+MEINGLTWGLTITLIVGLLAFDYFAHVRKAHTPTIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTIFIL
+LGAAVIAAWSDVFYLFGLFLLVIAGGQLKGEMAGDADDAKDEADNIMVRMVKRFLPASDR
+FDGDKLFTLENGKRVMTPMLLVMIAIGATDILFAFDSIPAIFGVTTEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVTIPT
+TLSLVVVVVILAITVVVSLYSPKGQALRALQNAEKFSYRYSKLDETADPAERSRAAALMD
+EWTAKAEGLDQKWRDELLEHKDTWSGIIRTAHETRLADPRDDDARGVSERIVRQDGPTV
+>GCF_023573625.1_01062
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIATWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001852.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..965f3d2d374eecf7593caf11816710d2ef1bd6ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001852.fa
@@ -0,0 +1,13 @@
+>GCF_002008305.4_01145
+MIGAVPGEPGMDLLGALASGRLDPAAGASTARSPHAAVDGPERPVCSRRGCTAEAAWALE
+WNNPRVHAPDRVKTWLACTDHRPFLDDFLSARGFLRRSRPLDPAATQAPEVDTPETPQEP
+PRP
+>GCF_003691675.1_00864
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
+>GCF_020097155.1_01641
+MTGPDLLGALAAGLDPSLPAVRREPSAEGPAAVTADGAPVCSARGCRAAAAWVLEWNNPR
+VHAPDRVKTWAACPDHREHLSDFLASRGFLRRTRPLHAAAGPAATDPTTPGEPRR
+>GCF_023573625.1_01095
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001853.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..257f7c9c868a7c00f16c512416044294935614f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001853.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_01155
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>GCF_003691675.1_00874
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>GCF_005280335.1_01734
+MNALSLNPRGGAEHLARHAGLVAALRERPVVVETEAAGDRAALRAANELGLRRVGRELRF
+LVR
+>GCF_023573625.1_01105
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001858.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b00a8e90d771a28668bc9cd1327f829cde23e896
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001858.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01290
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>GCF_003691675.1_01009
+MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
+>GCF_020097155.1_00710
+MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVSALTRALQGV
+ATGLLDDHLKHCVLDAAKLSDEAAVEKIQEATDAINRLVRS
+>GCF_023573625.1_01248
+MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS
+ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001859.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e4dc9d66804cd9912524081cd5caf2ed72061d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001859.fa
@@ -0,0 +1,37 @@
+>GCF_002008305.4_01306
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>GCF_003691675.1_01029
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>GCF_020097155.1_01482
+MAELRLTGTTEDGHALRLAAPDGTEHTLERTPFLRRLALDDVARPDAVPAAEPADGAAPA
+SPAQADEPSAEAPAPEVPRPAPSPAQEPAAPVTAVAEQADVRAAATAEAQPLSPRDIQAR
+IRAGASVEQVARESGNAFSRVRTYGYPVLAERGYIAQQARAVQVWVGGPDLYSGTVADGG
+PTTLGALAEHRVRELGTDPASLEWDAWRESGGVAWTVVARFPLPPRGRALTAEEPPARWS
+FRPAGGRLDPENAWARILSDAEAWDVFTAEEPLTREDDAAAPQQGGGEEASGGDAPAAVT
+PLGASPSSVGVDADLLEILRARRGRRVGQDAESDDALAHLIARGVAEREARQDGAEADHT
+EQAETEPAAPGRAARLLRGLPSLREEVAKDGADGRPPVEADSPAAEAAPAVDAAGREDAV
+TPQAPGKTDAGKTVAGPSGADRTETGQAGTMQADAEPSDAPVAAPQEEEPARTARRERPA
+MPTPRPRARSAARRASVPSWDDIVFGKKSD
+>GCF_023573625.1_01264
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPRADAEEPVDATTHADDAAEEGERAPDVPSGPARPDEDLALTPRIDPRPVADDST
+ADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRTYGH
+PVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLEWDA
+WREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAWDLV
+PRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDALAHL
+IAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADVADA
+GVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001860.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6470407fe1b8bf9cacd800520824981312b2d6c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001860.fa
@@ -0,0 +1,28 @@
+>GCF_002008305.4_01315
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTAVR
+TLRARARHRDAVELVATGPADAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>GCF_005280335.1_01577
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTVVR
+TLRARARHRDAVELVATGPTDAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>GCF_005280335.1_02666
+MTAGILTMALCTGLVALAVFGPWLLRHAAPALVRVPRLAIVVVAGGIGVWLVTLLAIGPV
+LAWAGAGPALLPERAAEVCQRCLTAANPFSADTTETLIPAVLLLALPVALALALGAGLAR
+QMVRRSSRSRDAARTLLHGARRQLLHGHEVALVDAEHPFALTFPDRHGGIVLSTGAVRAL
+GPGELAAVLAHEHAHLHQRHHLITALVDSIAAYLRWVPLIRAVADALPHYLEIAADDQAR
+RHAGTRALVSALVKLGERTHPAMPQHSCPVALHAAGPERIRHLVHPSAGLAGALPAVAIA
+AYLVGMAALAALVHLPYVSAALTGCTI
+>GCF_020097155.1_01473
+MSFSVLVLAAVALCLAGPVPVLLGRAAWPSRSPGLAVLAWQAVALAGGLALVGTPLLWGL
+HPWGDGLLDAVPALLADLTSPDSGIARPGSAPAEVHLLAVGAGLTVALHLLLTTAVTALR
+TLRARSRHRAALELIATDPERADDWPGGPRGARELPVDLPLAYCVPGVPGGGTPLTVVSR
+GLLERLSPEELRAVLLHERAHLAQHHGLLRLAFASWARACAWLPSAETARAGVVLVTEML
+ADDAARRTAPAPVLARALALTVRPAEAPGASASGPDAEPDAESGGLGRRVARLLDPPAPV
+PGAVAGAAAAACLALPLAVLAVILGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001864.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b088ef44945dac2dfde4733ed75cb2fff8163500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001864.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01409
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPTAAADGTVQFLLDIIPGSLPMLPTLFIALLVGFALQQMGPADAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLVGRWVGELDGERARRVLSGE
+LQFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFAMAADGDRNPAR
+>GCF_003691675.1_01139
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAIGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGYLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
+>GCF_020097155.1_01397
+MTHASPAEAVPVKKKDRTHWLYISVIASVILGAAVGLLFPEFGKSLKPLGDGFVSLIKMM
+IGPVIFCTIVLGIGSIAKAATVGKVGGLALLYFITMSTFALAIGLVVGNFVHPGEGLKLT
+PYDPNKPKAPLDSTVQFLLDIIPGSMPVLPVLFVALLVGFALQQMGPAGAPLLRGLTLIQ
+GVVFRILMMIMWVAPLGAFGAIAAVVGSTGWSAIGAMLLLMGAFYLTCILFITLVLGTIL
+KVVTGLNIFSLLKYLGREYLLIFATSSSESALPRLIAKMEHAGVDKSVVGVTVPTGYSFN
+LDGTAIYLTMAALFVSNAMGMEMNLGEQVGLLLFMIIASKGAAGVTGAGLATLAAGLQAH
+RPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGQWVGELDGDRARRVLGGELKFD
+EAMVAGHGDAVLEDAKAHPSMVEQTGGSHAASTY
+>GCF_023573625.1_01359
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALAYFMTMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGSLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001870.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..765103467f9eaaf8cb3563677ca8bde228d8daf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001870.fa
@@ -0,0 +1,47 @@
+>GCF_002008305.4_01470
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQSGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADADAVGRVADVAATAAD
+APPCARQDEQALTAPTRPVRRVPPGDPADGPAAGDRTGEDAAEEAR
+>GCF_003691675.1_01202
+MTVSGPDVSAAPAAESGAEPVEPAAARPRSWGPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQSEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPDSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPNPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRHVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVSRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYMVPMDRDRA
+DGHVAHVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AVQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVATAAPPSA
+RQAEQALTAPTRPVRVVPAEDPAHGSAPGDPTGDDPAEEAR
+>GCF_020097155.1_01332
+MTAPAEPPQPAETGDPDETGATSAPASAGPSTSAAPPRAGLRRRLRRRWNGSLQLRTAVL
+AGLLTLLASLMISGLITQQVAQALFDARHQQVEAEARRGLARVQSTFANAAATDQQATDA
+LVSQTMRALELDGGTTIRRRFRLEPLPGGTAASVGTVSSQGLDADVIPQDLRDAVASGPG
+VYDASIALPAADGNTRPGLAYGTQVVLPPGATYALYLVYDLSDVQESLDSVLGVLLMFGS
+GFLLVTVLVSWWAAHSVVRPVQQAATAAESISGGNLAVRMPVRGDDEMARLGTSFNRMAD
+SIQAQITQLAQLSRMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLY
+HQVDRFQAMLADLLEITRFDAGAAQLALEDTDLLALARDVVLTAAPLADQAKVPVYLVPL
+PLEEGLDCVAQVDPRRIERILRNLVNNAIEHAEGSPVDVLVAADEGAVSVAVVDEGIGMS
+PEQVQRVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGVGSVFMVTLP
+RRNGAESPVRRAVLPMPPSYDRGGRRLAADLHTPVTGPEGTGVHDAAALPERGREQEL
+>GCF_023573625.1_01420
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTRPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGTSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPARKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVTAAAADAP
+PSARQAEQALTAPTRPVRMVPPADGTAAGGWTGDDGAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001871.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0b8d3c8f7910a20cfaa12a35fce27d51889066a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001871.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01476
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>GCF_003691675.1_01208
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>GCF_020097155.1_01326
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVALELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVSSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>GCF_023573625.1_01426
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001874.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85a9d467289775a65e183887da34bcacef16b3de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001874.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_01514
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>GCF_003691675.1_01223
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>GCF_005280335.1_01411
+MSNDPRTPGSDDGRDPLEEMLRQLFGGNGPDPDEIRRAMEGMGGPGGMPFDPSQLDPAMM
+QQAMAQFQAMMNPGPGSEGPVNWTLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGATQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASMLSGIQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGVPIAGHRLAMVPVNVEEF
+GDGLSVPDDQVRIYLALREAARMRLFLHSPWLERDLYAAIEQYAAGIRLDTEGIEQAARS
+VDPMDPESMQAVFDGSSFIAAPDATQRAALAQLELLVALVEGWVDVVVAEAATPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEQGKEYREEIWRHPER
+QPTAEDLEDPAGYAGRRTAADASTDSLDDDLRKLLEGGFGDAPKEG
+>GCF_023573625.1_01441
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWSLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAISMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYTGRRSAADASTESLDDELRKLLEGGFGDAPREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001878.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..741ef692a40885254cb37ab39350067035850648
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001878.fa
@@ -0,0 +1,28 @@
+>GCF_002008305.4_01592
+MTRTPPAVAPPAAETGGESLLTVLIALGVNAVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>GCF_003691675.1_01304
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>GCF_020097155.1_01221
+MSHSDDIRPSVAAHPDDGDATSDPALAPPQAEDRPEGLVTVVIALAVNVAVAVVKSVVAA
+LTGSAAMVAEASHSWADAGNEVFLLVAERRAARPADARHPLGYGRAAYVWSMVAAFGLFA
+VGAAVSVWHGITAWSAPEEEGGGHLIGYVVLAVAFVLEAVSFGNAHRRVSAGAQEHRVSR
+SRFLARTSDPTLRAVWAEDSAALVGIGIAAAAIALHQLTGDARWDAAGSILVGVLLGAVA
+VFLLSKNMAFLVGEVADPAVRVRVLRWLLERPEVLSVSYLHLEYVGPGRLAVVGAVDLAA
+DEVESLAAVALQRVEDALLAHPVVAAAVLSLSNPSHAPLRLEDEEAAARR
+>GCF_023573625.1_01519
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001879.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a84178953456e6a0202193362cd01648427e6b2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001879.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01614
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWSAATGAHFARRGNRFYPALHRAGL
+TRHLVDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>GCF_003691675.1_01324
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAVLGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>GCF_005280335.1_01285
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRASARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQETPWPGTRLFVAPNPSGLNAHATVDSLAADYRAA
+GAAAGLVD
+>GCF_020097155.1_01189
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALYRAGL
+TRHLIDASGGYKAEDLAELHARGIGISNLVPRATARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001881.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26168cd0736a60b3db6656eb0dce3515b11bfbf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001881.fa
@@ -0,0 +1,49 @@
+>GCF_002008305.4_01655
+MDTPTPPHPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAIVGLSVGYVSYRRGRVPLMSSIIAPLFGDSPRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIVSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSNWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTRGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIIMLAVFFITTADSAS
+IVNSQLSQRGDPAPRRMITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDDADGPAGAGPSGR
+>GCF_003691675.1_01360
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDGADGPAGAGPSGR
+>GCF_023573625.1_01552
+MNWPVFAGTAGIVVGFALWAMLLPAQADSVISATVSWIAESFGWYYVLTAGVVVVFVVVV
+ALSRLGRVRLGPDHAVPQFSMFTWSAMLFAAGIGVDLMFFATSGPATNLLTPPDLEPMSD
+EAARMAPLWTIFHYGIPGWAMYALMGMAFGLFAYRYHMPLSIRSAIAPIFGRRVHGGIGH
+AAEIGATVGTIFGISVSLGIGVVFLNAGLALILDVPVTTGVQIALMALAVGITIISTVSG
+VDKGIRRLSELNVYLAVVILLWVLVTGRTTDLLNALVQNIGDFFASFPSMMMRTFAYTDG
+TAAYPAEQWMSDWTLFFWAWWIAWSPFVSLFLARISRGRTLREFVLGVLLIPFAFIMLWV
+SIMGNAAIGLFRDGDDALLQEAVTAPEAGFFSLLQQFPGATFLIGLAVFTGLFFYVTSAD
+SGSLIMAKMTSKGSVEDSDGAPWLRITWAVITGLLTLSMLFIDGVYTLQKATVIVGLPLS
+VLVYLVMISLWRVLHSESLAMDSRTASLPHVLSGRVRDANSRATWRQRLARRMNFATAKQ
+AAAYVDREVSPALSEVAAELREHGADVDVTRGTHPESGVPWVDLTVRFPGQTDFKYQVYP
+VAYPVPSFAGSLSAAQDTYVQLEVFSAKGSRGRDVMGYSREQLCANILDDYEAHLAFMTM
+TGDDSLLAARIDAEAPEVWTDADHSPATDALPTVALQTTDPETEGARP
+>GCF_023573625.1_01585
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMLHAGWLFALLAIGMVVFLLALAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAASEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAQGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDEDGADGPAGAGPSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001885.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0f6fb68510ce18694ca1d8d75553d360d042f30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001885.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_01766
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQAGDV
+AGRHAADPVAEGTWADFLAEAARVSDEDLAVREAATGPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>GCF_003691675.1_01473
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLQVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>GCF_005280335.1_01111
+MTPSPSVQESYTRGPSDVPMLEQTLAQNLDDAARRSGARPAVVECGPDGDPATDRSWTYE
+QLREESVTVAKALMAAGYEPGDRIGLWSPNVAEWTSLLYGAARAGVILVNLNPAYRAHEL
+TYVVEQCGMRGLVVAPADAHQDRPDIARDVACGGCPELRQLIILPTAGPITAESYAHAVD
+GVLDCRPEPTPVSEGTWSAFLAGADRVSDEELAARESAVSPEDPVNLQYTSGTTGFPKGV
+TLTHRNVLNNGFHIGELLGYSQEDTVVIPVPFFHCFGMVIGVIAAVSHGSLCVIPARGFE
+PVATLRAAAATRATSLYGVPAMFIAMLARPEADELDLSTLRTGVMAGSTCPVEVMRRVID
+RFHMAEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPVSGEVVPRGS
+TGELCTRGYSVMRGYWNDEEKTAEVLDAEGWMHSGDLASMDEGGSVRIEGRIKDLVIRGG
+ENISPREVEEFLYTHPDVQDVQVVGVPDERYGEQLMACLIMKDGTRPLTPEDVRAFCEGK
+IAHFKIPAHVRVLDAFPMTVSGKVRKVELRAEGAKLVEGGDRD
+>GCF_023573625.1_01695
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADELDLTTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGEVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001892.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93a450301912686e0d6b087f5e74ccdfe3bccc0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001892.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01879
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>GCF_003691675.1_01575
+MIKQPWGLARLPAMTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRAL
+AYLMARAAAGEPVTASDLGAHLHLTRASATALVDRLAAAGHVRRHRDEGDRRRVLVEHTD
+TARRDGQRAFEPMSQRLSAALEGFSAAELRAAVRVLEAATAALTDPAPEDP
+>GCF_005280335.1_00980
+MTPQPAAAPAEHVAVVHALRAFSEGAEHAVDEAGRGIGLHRTDLKALAHLMRCADEDRPV
+TATDLGAHLHLTRAATTAVVDRLVASGHARRRRDDVDRRRVLVEHTDSARRDGAAAFLPM
+SLRISGALTPFTAEELRAALRVIEAATAALQAPPDAPAAPVPG
+>GCF_023573625.1_01799
+MTTQPPSAPAEHLAVVHALRVFSESAEHAVDEAGRGVGLHRTDLRALAYLMARAAAGEPV
+TASDLGAHLHLTRASATALVDRLAAAGHVRRRRDEGDRRRVLVEHTDTARRDGQRAFQPM
+SQRLSAALEGFSVAELRAAVRVLEAATAALTDPTPEDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001894.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf2c3f5d4ab248c05e2a6b5356a10c44206c800e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001894.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_01893
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>GCF_003691675.1_01589
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>GCF_020097155.1_00903
+MHGTTLALVELGAVLFLLGVLGRLAARIGMSPVPLYLLGGLLIGVGGLLFSGADPSGTLR
+SPVAAIGDFSSLAAEIGVVLLLLTLGLEYSARELMTGLRGSWRSGLLDVALNFTPGAAAG
+WLLGWGPVGAVVLGGITYISSSGIIAKVLNDLGRVGNRETPVMLSVLVFEDLAMAVYLPL
+MTALVAGSAFAAGLRAVGIALVVVAAVLFTALRFGPQISRLVYSPEQETFLLKVLGLALL
+VAGVAGALQVSAGVGAFLLGIAISGAAAKQARSVLEPLRDMFAALFFVLFGMNVDPRTLP
+PVLLGALALAVVTAATKVATGYLAARAAGIGVAGRWRAGATLTIRGEFSIVIAGLATASG
+TLPAEVSAFATAFVLILAVAGPLLTRSADGFGRRRAAAARVREARRARQAPLV
+>GCF_023573625.1_01813
+MAGRWRAGAALTIRGKFSIVIAGPVLTRYADAFGRSRARAATRRVQAREVAVADPVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001895.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4136b5e352a491b89837c6c6189f357e468ef1bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001895.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01895
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
+>GCF_003691675.1_01591
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFGAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGG
+>GCF_005280335.1_00963
+MTRQSDLKTLIRARMAVTGERYTAAAAALAHEWETAERFHATVLARFFDGERLRSIPALR
+KPRVAVLLELLRRFAPDRAYTEPEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRMAD
+AGPDVDPRFAADLPVDLERRLRQLRAGR
+>GCF_023573625.1_01815
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001897.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c5db561e5d30bf7ffb1a0fd3162da15ef5d4a5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001897.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_01912
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VQMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDSLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSVRTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPAWLLVMGALAWLVSVFIAVRGFVPMVTM
+ITGA
+>GCF_003691675.1_01608
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
+>GCF_020097155.1_00883
+MSHADPTAHARGDAAAGEAVQASSSNRRTALLGAMFLMATSAIGPGFITQTATFTVQLGA
+AFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANSVLPGLGWVLAVLVFVGGLVFNIG
+NIAGTGLGANAMLGVDPLIGGAVSAVIALLVFLSKRAGVALDRIVVVLGAVMILLMLYVA
+VTSAPPVGEALRQSVFPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDDVEAIT
+RSSVLSILVTGVMRVLLFLAILGVVASGVALAKDNLAASAFQAAAGDIGLRMFGIVLWAA
+ALTSVIGASYTSVSFVTKSTTTTRTRNLLTVAFIVVCTVLYLALRQTPQTLLVFAGAFNG
+MILPIGFAALLWVAWRRRDLLGGYRYPTWLLVIGALSWLLSVFIAVRGFLPMVQMITGA
+>GCF_023573625.1_01832
+MSHADIPYAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001899.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07fae9c101135f01dff1a17bf224a033f6d83fd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001899.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_01914
+MRVPTRDGVTGDDLAPGAGDGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>GCF_003691675.1_01610
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>GCF_020097155.1_00881
+MTAPAAQGAADALRRRIGEARLQPGERLGEVALAAELGVSRNSLREAFSELAVEGLVVRR
+PHRGVFVAAPGAEDVRGLYRTRRVIQLGALQHGWLTPAAEERIGRSAELLGRPEPAVREL
+GDANHLLHLGIVDLAASPDLSRVMSSVLARVRLSFLPLDLETGLHQAFAERNRWIAGRLL
+AGDLDAVHAMLEGYLDEAEAFVLRHLDGAAHGLRG
+>GCF_023573625.1_01834
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAMFGDYLDEAEQFVLAHLAAVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001901.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3943f9a947746458537dedbcb6f0bba09735d4c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001901.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01917
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
+>GCF_003691675.1_01613
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN
+TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVAIKAFA
+>GCF_020097155.1_00878
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG
+VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN
+TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL
+VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV
+RRALEDAGVTIASFA
+>GCF_023573625.1_01837
+MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG
+VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN
+TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL
+VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV
+RRALEGAGVSIKAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001902.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d177f574fb63b0cbd5468e740f36c421c689584
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001902.fa
@@ -0,0 +1,88 @@
+>GCF_002008305.4_01931
+MTAMFSAQDHDDLDRVLSATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATAHPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDGGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPVDPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGAEADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEKLVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALILPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>GCF_003691675.1_01627
+MTATFSAQDHDDLDRVLGVTGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRRMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASVTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSEADGAGASWLETARALDTQAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALVPPAAEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>GCF_005280335.1_00929
+MTPTFSAQDHDDLDRVLTATGGIPDPADLQHLADDAVAQVRRWLADARGHEADFAAQQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAQQAPGFLPPALRAVFGVGGRAAPL
+VPRVAVPVARRVLRRMVSHLIVDARDRQLGEAIAALRDERTRLNVNLLGEAILGKGEADR
+RLEGIAGLIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLYELARDNGTFINL
+DMEEYHDLDLTLNVFTGLLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMELMQASLMGWPVATVASKQEADTNYKRVLNYALTPEHLRHVRIGVA
+GHNLFDVALAHRLMDRRGLGPEQVEFEMLLGMATGQAAAVKADVGSLLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADEALFAREEERFRASLAHLDAEVPRPSRGQDR
+SRGEDGVRPAAVDGFANTPDTDPSLPGNRAWARGILEAIPGSALGAERARAHRVGTAEAA
+RAAIADTQAPGAAWGALTGAQRAEALDAVGRALHAGRGRLLEVAAAETGKTLDQGDPEIS
+EAVDFAHYYARLARGLDEVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+AAPQSERTGAVAWELIVQGLRDSGLFDDGGPLAAHDPADLVRLVTMADEDEEEVGTALVT
+DPAVERLILTGGWDTAKLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVHSAFGH
+AGQKCSASSLVVLVGSVATSERFHRQLLDAASSLHVAHPADPRAQMGPVIEEPGEKLRRG
+LTELGEGERWALRPRELDATGRLWSPGIRSGVRPGADAHLTEYFGPVLSVMTAATLNEAI
+DIVNAVDFGLTSGLHSLDPDEIAHWLERVHAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWVDAPSSTSESPAADRAGEGTAAGTPAAAERSWLDAARALDERAW
+AATFGSGTDVSALAAERNVLRHLPVPVLVRRASGPAEHLLRVVSAGLRAGAPMTVSIAPT
+PAAQAPGTDDLSAEALRGQVDELVRTAGAGRAEGAAPVSVVVEDAAAFHDRARQLAQIPP
+AAEGGGDARIRLVADWAQDREGARAAGAALHAALGDTPDVAVYAGPVVSAGEVELLPFLH
+EQALSVTAHRFGTPDHLTDAIL
+>GCF_023573625.1_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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001903.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1017ea8725d0a6d8620a1c6147881e2b1fc0af8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001903.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01940
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
+>GCF_003691675.1_01636
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQRRRSSGLGGALVGTLGGLAL
+RELSRRGAGGTTRGRGSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTVGGGF
+>GCF_005280335.1_00919
+MGILSGITRALGGSRRRPTIGANTYGRRRSSGAGGALLGTLGGLALRELSRRSSGGTARG
+YGGQAGYGRTTGGYGRTSGGLGGLLGGLGGMGAGRSSSRGGGLLGGLLSGPMNSRSGRRT
+TGGRF
+>GCF_023573625.1_01859
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001904.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..355554044f681b3b0c6f4f7d169615975fb372c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001904.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01946
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+>GCF_005280335.1_00916
+MTEDHRAPSASGYWYVSSPNSVGPVEVLNVLRAYREAERRMRRRTRDSMRMGETDLLALR
+HLLRESRAGRPVRQRDLAAALEISPASASALVDRLIRDGYARRSPHPADRRSVIIETTAR
+TDDEVRATLGRMHRSMLDAVESLSPDELAAVAKFLTALTRSVDEAAEDALEHGTEH
+>GCF_020097155.1_00848
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLQADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+>GCF_023573625.1_01865
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001906.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c4853eb3dc581ed6518774fcee70c29f7463545
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001906.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_01977
+MTVGLTLYVLMWPVLVLAVLVSIARGFFADWAAARREGRSII
+>GCF_003691675.1_01670
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARRQGRSII
+>GCF_005280335.1_00881
+MTLGLTLYVLMWPVLVLAVLASIAAAFFKDWREARREGRSII
+>GCF_023573625.1_01902
+MTVGLTLYVLMWPVLVLAVLVAIARGFVADWAAARREGRSII
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001908.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f377a69542f5c93634c86f54ce428ff83279abe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001908.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01996
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>GCF_003691675.1_01690
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY
+>GCF_020097155.1_00797
+MPVRLNAQPLVRDLFTPEARAARGGRPAAGMFLSSGDVTAAEICAGAGMDYLLIDGEHAP
+LSLESVLAQLRAVAGYGVPVMTRVPSLDAVLVKQFLDLGAQTLLVPMVDTAEQAAEAVRA
+VRYPPHGVRGVGSALARSGRWNRIDGYLTHDADHVGLFVQIETAAGVENARSIAETSGVD
+GIFVGPSDLSASMGLIGQQTHPDVVAAVQSVIAAANAAGTVVGVNAFAEPQARAYAEAGA
+DFVNVGADVALLARAAEALADTWCPTPEAAADDDAGSRASY
+>GCF_023573625.1_01922
+MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP
+LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA
+ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV
+DGIDGVFIGPSDLSASLGLLGQQSHPEVVAAVEEVIAKVKAAGKFVGVNAFVPAQADAYA
+AAGADYVNVGADVALLARAAEALADRWCPAPSDAAGDGEGAPRASY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001911.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bab6a63be0a308b9a4c907dd6b8b2c2224ad4f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001911.fa
@@ -0,0 +1,40 @@
+>GCF_002008305.4_02032
+MTELTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPMFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGATD
+>GCF_003691675.1_01739
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVISSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+EIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAG
+>GCF_005280335.1_00788
+MTERTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLATGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAEG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPDDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQGVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVST
+AGEPLPPSVLEWGRSALGTEIRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAA
+QIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVVDPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
+>GCF_023573625.1_01967
+MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLT
+FGELADRSRRLAAGLAARGVTRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAG
+AARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWDALADSAPLAEDVAVGGDGPI
+ALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT
+LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVAEDAPLRLRRVST
+AGEPLPPSVLEWGRAALGTEIRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAA
+EIRGGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYLTGDTARQDDDGWFFFSSRDD
+DVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVAAFVVPAGAVADPDAL
+AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001912.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2584a06211bab2385bc6599ab1e5453fa21af1e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001912.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02037
+MVGITLRHMEYLVAVIDEGSMTAAAARLHVTQATVSMALAECERRLGVPLLVRQPAKGVA
+ATLAGHRMAVQARRILGLVHEMEASVPAMPGELAGDLEVGCVPSLSPQAVPVLAEHFSRR
+HPRVTLHYREGAATDLQREVLQGRLEMAVMFSRQQAPGLRSIEVARAQLKVMLPEGHRLA
+AAHEVAFADVAQEPAILIDLPPSTERSLEFMRAAGVEPTLRWSSNNLATVASLVGAGLGW
+SLRYTLPGEQPAARGLVEIPVADPTPPNAVCAVVPDGDRVDQRVRHALEVLRRVLSEEEG
+RPDVDCA
+>GCF_005280335.1_00142
+MEPLNLSSPGLSPAVWRVTTVSRVEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIK
+QLEAALGVTLLERTTRRVDLTDAGRLLLDRSRQLLTDLASLEHDVREVGRGAAGILRVGF
+VGSATYRLMPAIVRAARDAMPGVRLQITGEKITPALEDALLENRLDVAVLRPPVRAAELT
+LTPVEAGRLLLAVPAGHRLAAEDGPVALADLVDEEFVSYPRDSALTAIVQEAARRVGFRP
+RLVQRAGETSTVMAFVAAGLGVAVVPDDVRRPGAVSGVAFRPLSDMPDVELAVAAKADAR
+SPLVPAFVELACRTAAALAEAGEDPTPDPDRPAQET
+>GCF_005280335.1_00807
+MDVHQAKAFLAVAEELHFGRAAGRLQIAQPALSRTVKQLERSLGTDLFVRSTRRVELTAA
+GLALLEPARTLVQASQTAREAVQSALAGETGTVRLGFAGASTHGVVGQLARSVRRRRPGL
+TLEIHSSQFSHLGLERVLEGSLDVAIGRWDFIPHELASRVIAHEEAIVALPADHPHAQET
+GPIDVGLLRDEPWVTLPSGLGSALANRLTTLATSAGFAPRVVQQAPDSFTQMVLVAAGLG
+CAVTLDSVRDNSATPGVVYRPVAGDNPPLEVRMLWRSLDASPALRAVLDLAPAAEPAGVA
+PARTDAAD
+>GCF_020097155.1_00104
+MEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIKQLEAELGVRLLDRTTRRVDLTEA
+GRLMLERTRSLLADLASLEHDDDIASAVKPELLLDVQQGADGNSTVYDFVLDPVSEKTHP
+TAIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001913.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f98a32f7baca5185d7c11bdbaa57d2280ffcead
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001913.fa
@@ -0,0 +1,31 @@
+>GCF_002008305.4_02044
+MRRLAEVTGLVPVEYPTTRQLGASPESRARDLNAAFADPQIRAVIATVGGEDQITVIGHL
+DADAVRADPKPFLGYSDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAAL
+LTGGRLEITEPGESEDHGVDWLDPRALTEFGTREPVPGPHDDGARGVGAGASPWRWAGPR
+RAVTGRTWGGCLEVLPWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGES
+GVLGAVDAVLAARPPTRSFEVPRGAEERARRRAEQADVVLEEVGRYNPDAVVCVGVPFGH
+TRPQWVLPHGGVMTVDGAERRVWAEYC
+>GCF_003691675.1_01750
+MASRYAPGMTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEY
+PTTRQLGASAEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVRADPKPFLGY
+SDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASMRAAMLTGGRLEITEPGESE
+DHGVDWLDPRALTEFGERDPVPCPHDDGARGVGEGASPWRWAGPRRAVTGRTWGGCLEVL
+PWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPP
+TSSFEAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTV
+DGVERRVWAEFG
+>GCF_005280335.1_00772
+MEHTLVRPPKAAPGDRIAVVSPSFAAPGFAPEVHEQAMRRLRELTGLEPVEYPTTRELGA
+SPEDRARDLNAAFADPRIRAVFATVGGEDQITVIGHLDAAAVRADPKPFLGYSDNTNLHQ
+WLWAHGVASFHGGSTQVHLGPGPGVDAVHAASLRAALLTGERLEITEPGESEDVGVDWQD
+PRALAEFGQREPVAADDDGLGGPGASPWRWAGPQRSVTGRTWGGNLEVLQWVLAAGRGPV
+DVAALRGGVLLLETSEELPSATDVRRMLRVLGERGILGEVAAVLAARPPVSDFDVRPDAQ
+ERARLRRAQADVMVETVHRYNPDAVVCVGVPFGHTRPQWILPHGGEMTVDGVEKRVWAEF
+G
+>GCF_023573625.1_01978
+MTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEYPTTRQLGA
+SPEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVSADPKPFLGYSDNTNLHQ
+WLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAALLTGGRLEITEPGESEDHGVDWLD
+PRALTEFGTREPVPGLHDDGARGVGGAPGAGASPWRWAGPQRAVTGRTWGGCLEVLPWVM
+AAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPPTSSF
+EAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTVDGVE
+RRVWAEFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001917.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9364cda3d80b788fd602c7d3892f3ba1041c500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001917.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_02054
+MLVLLILATRLPGVVAGERLSVWDVAYLLLAVVVLVSEWRDYRAAVRRARR
+>GCF_003691675.1_01760
+MTIRPHSDPVTPDATWRDVPVLGFTVAAGIAVLFCLVWLLRDGLTTDYTWGLLLSPVLMS
+VPGAAVMVLWERLLARVPRLAATLVAVAALLALGLVLAWWLVEVNAQTHLFTGSTFWLLA
+VAPVCAGLAWLAHRLLPPARRPVGEPPAALDDDAWARRLAGVLRLRKDLPDARVAEIVRD
+ARARGAAAGRPLAEELGSPESYAAGFQKDRVAAPRRRAWAVTALVLLILATRLPGVVAGE
+RLSAWDVAYLLVAVVVLVWTWLDYRAAVRRARR
+>GCF_005280335.1_00766
+MSTHDHDHDPADPRRATTSAPASLEPEIEAMHAARGNEEDRDWALLLVGVLVVDGVSTAA
+ARRHLRRAAEAVAQSGEGPDELFGTPVEFAAQMRADAAEAGEPIVDSTPDASWRDVPVVG
+FTVAAAISVLFFVVWLVRDGLTTEYSWGLLAGPVLMSLLGVGAMTLWERLLPRVSRLVAV
+LAAGAAFVVVVGGLAGWLVTGGGTETLFTGSTFWLLALAPVHAALAWLANRVLPEARPVA
+TSSADPLDDDAWARELAGTLRLRMQLSDARIREIVREAQAHAADAGRPLAEEFGAPAGYA
+SRFAKDGVAGKRRMAWFFTALAGLVVLTNVAGAVEDGGIDAWSVAQILVLVLVVGVSWRE
+YRAAVRRRDAVAPGAGGR
+>GCF_023573625.1_01988
+MLLILATRLPGVVAGERPSAWDVAYLLLAVVVLVSEWCGYRAAVRRARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001925.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd7adce992276f321aa5dda37648ea9471e6ae68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001925.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_02116
+MRPDRHSAPTSAAALAREAAILAGAGAAILLQVAHRPVGAGVAGHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPARDAVVDRVRAAHGSVRGVDAGGRPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
+>GCF_003691675.1_01824
+MRPDRHSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPLRDAVVDRVRAAHRPVRGLDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRMPELGDAVAVRATRRDVRSVWENGGDV
+>GCF_005280335.1_00664
+MPREAHGPVSAAGLAREAAILAGAGAAILLQVAHRPVAAGVAAHSRFTEDPMRRLRHTLG
+YIYAVTLPEAAGARDAVVARVRAAHAPVRGADHEGRPYNAADADAQLWVAATLYWAGEQV
+RRRLWGALDPADADRLYRGFAPLATSLEVPAAAWPADRAAFAAYWDARIAGLEVTDDARA
+VAADLFSGRGVPAPLRAALPLARFVTAGLLPARARAGLGWDWSRRDSIREARLWVLTRTL
+YRPLPAAVRGVVVRGILRGLRRMSEAGGPAS
+>GCF_023573625.1_02054
+MRPDRRSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAASLRDAVVDRVRAAHRPVRGVDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGHGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001928.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08b3974cf61aed4f30c5eab3dbd536c7793a07dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001928.fa
@@ -0,0 +1,35 @@
+>GCF_002008305.4_02155
+MSTAAPAPARPTTATSRPPADSPLDSRLPAILRAEPVSRHMRIVLYVIVGLMVLGEILTL
+VLGPMVAAGLSADPELAAIFEEDGGLTGERREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGSAFGLAGLVEADHAHLTPQAFSGGVILGAAMVTRYSHRVFVWFALGALILLTVAGE
+ALTDGTWADEDSLKGVMVVTLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPEKRAASEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELEELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSELEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLMAGPLGGCWVVRAELPLR
+>GCF_003691675.1_01868
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+MLGPTVAAGLSADPELAGILEEDGGLTGEGREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGCTFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGTWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPDKRAAAEKAIEEAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEAQLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLGGCWVVRAELPLR
+>GCF_005280335.1_00602
+MATVSIGRPDSPVWGPFGARRLSLRIRLIVWISLAVVFGIDVVLAFSGTGVTAAEALPQL
+AGEYLLIGLIAQHAPLGVIAYAIAFTAGARWWDYEALSIVFAGAALMLGLSAQRGLLLLA
+GGLFAAWFVIAGPVLGSFSTAAAVAFAVSAALGVAAGLGLRWLARRFDSALRLAEERQTQ
+LEQAQRDERHRLALELHDVVGHGLTVIALQAGMLPTVTSPVQRTEVEQAIADTARQSLTD
+LRTMLGVLRGSAPGLGPAEDAEPPRPVRELVAEYRDRLTAAGFDVHVRLEAEAEVPDSLR
+HTLRRIVQEASTNVLRHAEPGGRVDVEIRHDGCETSVLVRSPLPARRRQEPAPHSGYGLA
+GMDERVRILGGRITHGPVDGSWVLDVTLPSQERAAQA
+>GCF_023573625.1_02098
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+VLGPTVAAGLSADPELAALLEEDGGLTGEGREPLLRWVLFLAGVLVTLLFGWQPTLAAVF
+VLLGSAFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGSWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQKDPEKRAAAEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLDGCWVVRAELPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001930.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2153841964bfb05b4fb56b0581d3025edd8db9cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001930.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_02171
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDAR
+>GCF_003691675.1_01885
+MTDIRRTATALTLAAAVVTGLGAPAAVAQTTAPATEAATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVGGAHRDHDVHRVDDRAGDVRAEGADTR
+RPGTGDAR
+>GCF_020097155.1_00507
+MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD
+NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD
+AGHRAGGTDGTPGNGR
+>GCF_023573625.1_02116
+MTDIRRTATALTLGAAVVTGLGAPAAVAQTTAPATETATTAPASESPAPQEEEKDDNGNW
+GLWGLAGLLGLAGLAGRRKREVHAEPVRRDHHVAGAHRDHDVHRVDDRAGDVRTEGADAR
+RREADGTLGDATRRPGTGDSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001931.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aec70b1064afd90c130a4d770836f16023bee7cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001931.fa
@@ -0,0 +1,44 @@
+>GCF_002008305.4_02172
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALDRFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSATGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>GCF_003691675.1_01886
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>GCF_005280335.1_00580
+MSSAPPDPADASSGRGGPRPRRQSSLARRTGAGVVVILLITLTAFALFAGNTTRALTAES
+ASRNTTAAWTRAAEQLASLEAGTAFDAEPTAGDPQVPGTLGQPEGTVVALVSPADLEDHQ
+AGTLRGHRVGKAGESVPLDARQSHDIIHAIRGEPIGAPVDAAVSGEGYRFKALPMTSPGP
+WVGADQLLVVGVPTGALTAVSRRGLLMVVLGLSLTVVVTALAVFLWLRRGLAPLGEVAAM
+AERVAGMDLAHTGIDRRQTRMPKRLLQGPDEVVVVAEAMDRFTGAVEDALEERRRQEQQL
+RSFIADASHELRTPLASVRGYAEMIAMTEDLSETGRRSLDRVLHQAGRMSALVDDMLLLE
+RLESVSRGRAVGLAPSGEVPAADPVDLPEVLLEAVVDARAAWPDHQWVLDLPETLGEEGQ
+GCVTGDPAQLARLVGNLLSNGAKHTPAGTTVTTSLRIGRPLPHQVVVSVHDDGGGIPAEH
+RERLFERFARGASAGGPGREPSTGLGLAIVRSIARSHGGEASVASEAGWTRFDVVLPCAR
+WTARAQAEAAGRGGPEAPEGTGAPRE
+>GCF_023573625.1_02117
+MSSGLPETAAVPSGHGSTRRTQPTSLARRIGAGVLLILVATILAYSFFAAGITKALLAES
+ASRDASEAWIRASEQLTAPSPGGGGDARPGEGYLRAPGTLGQPEGTVVALVPLSGLEAHQ
+QDALTGHRVGDTGESVPLTAQEAHDLLHAVRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVARQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001934.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d78c6cdddf01a7e63edcaa89d31de8467aecb53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001934.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_02192
+MPHATLASVTRRPDAPPPADPRARAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>GCF_003691675.1_01905
+MPRATLASVTRRPDAPPPADPRTRAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>GCF_005280335.1_00550
+MPRATLASVTHHPDAPPPADPRTRAALRAVLTVLAVLAVLFAAVVLTLAYGPAR
+>GCF_023573625.1_02136
+MPHATLASVTRRPDAPPPVDPRTRAALRAVLTVLAVMAVLFAAVVLMLAYGPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001936.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7070908b1e983e3e31cba78e7b4981bc8c45b2b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001936.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_02203
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>GCF_003691675.1_01916
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>GCF_005280335.1_00540
+MTHHDDDRSALAAGETYLVHILETSTPPGNPEHYRITDAVEAHHAETGSWDIEAAGPDAA
+RELLARHGR
+>GCF_023573625.1_02147
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001943.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..264146438c048cb2bc907187bc7464c4a52311e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001943.fa
@@ -0,0 +1,36 @@
+>GCF_002008305.4_02222
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARLGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>GCF_003691675.1_01938
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAANPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAIGAFTAFLDDADVALVGVEPGGRSAAKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFASVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDARILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>GCF_020097155.1_00461
+MTHRNPEDNALRAADAARPEPRTLAEATDLVHTPDLTAGADGMFGTYGGAVLPPELAGPM
+AEVAEAYEEARHDPEFYAEYRRLLRDVVGRPSPLTPLDRLSDELGGARIVLKREDLNHTG
+AHKINHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGSIDVAKQHP
+NVVRMRLLGATVVSVDREGRSLKEAVDSAFDVYASDPAHYLFAIGSVVGPHPFPTIVRDF
+QAVVGREARAQFLERYGALPSAVVAAVGGGSNAMGAFTAFLDDADVRLIGVEPGGRSATK
+GEHAMSMAQGVDGVLHGMATKVLQDEQGVPDPVHSIASGLDYPGVGPQHARLAQLGRVEY
+VAEDDAAVLEAFQRLTKLEGIIPALESAHAVARAIRMAPGLGTDQRILVNLSGRGDKDVD
+YVAETLGLTGDADEVVR
+>GCF_023573625.1_02161
+MTHRNPEDNALRGAAEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001948.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6455f2c55a50ab9a4ac45c6d1ebddbd78b8af65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001948.fa
@@ -0,0 +1,22 @@
+>GCF_002008305.4_02273
+MPHSDPVPEPFVLTLGSVLDAAGLDPHEVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HLGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGGLQSMVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSNTPQAQIDAAEKHYKEALMTRRFGLNRN
+>GCF_003691675.1_01965
+MESTQPVPEPFVLTLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HVGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERHRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGDLQSLVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWAAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSSTPQAQIDAAEKHYKEALMTRRFGLNRN
+>GCF_005280335.1_00459
+MESTQPFVLSLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQHHVGK
+FPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEERLVV
+EWSADPVNWAKRGPLAARFPVLEIADPSTEAFPGFDHVLLSYGDLQSMVTETRYAGWRTA
+LEAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPAQPER
+YTFSLLRVFGSNTPQVQIDAAEKHYKEALMTRRFGLNRN
+>GCF_020097155.1_00408
+MPLLASLEERLVVEWSADPVNWVKRGHLAARFPVLEIADSTTEAFPGFDHVLLSYGDLQS
+MVTETRYAGWRTALQAVHGIYLIADDAASQCYVGKADGERGVLGRWEAYARDGHGGNVAI
+RDALELDPAQPERYTFSLLRVFGSNTPQAQIDAAEKHYKDALMTRRFGLNRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001950.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6074d8fc8c751d664715f1259ab1d4f702e161ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001950.fa
@@ -0,0 +1,32 @@
+>GCF_002008305.4_02284
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAETITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>GCF_003691675.1_01975
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>GCF_005280335.1_00453
+MPSPTPFHAEADSFLGRADVVGLDALFSDQEKATALAVRAFVDEHLRPHIASWYEDAVFP
+REIVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIH
+KHGSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQETGGDWVIDGVKRWIG
+LATLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVR
+LPASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLAS
+HQLTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIARDAREM
+LGGNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>GCF_023573625.1_02223
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001954.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..967cb7994e2ad6f701522a22be357047ef59717a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001954.fa
@@ -0,0 +1,33 @@
+>GCF_003691675.1_00238
+MTWVVTGGAGYIGAHVVRALQGAGMDVAVVDDLSTGFADFVPADVPLLRADVGDVGQVAT
+YLTRVGAAGVVHVAGYKFAGESVREPLHTYRVNVRGTLGVLEAMERAGVPAIVFSSSAAV
+YGTPDVERVTEATATAPESPYGESKLIGEWLLADQGRATGLRHTSLRYFNVVGSADPALS
+DTSPHNLFPLVFRALDRGERPRLFGADHPTPDGTCVRDYVHVADVARAHVAAARALAESR
+ALAPVYNLGSGAGTSVRQIMEAVGRVTGRDVDPVVEPRRPGDPARIVADGSLAARDLGWE
+NRHTVEDMVRSAWEARRPPETR
+>GCF_005280335.1_01224
+MPHDESMCMMNVSAPEPTRPQLPPLARHALLIIWDSVSWILALLAFLVVRYDFGLSPTQW
+DWVLAFTLIAVVGQVAAGLVTQFYLGRHRVGSFSDAGWTAVIVCAIALAIGLALSVAAPA
+FPRGVALTMPPLALVIMLAGRFLVRNVAAGRPRADASAAVPAIVYGAGNAGHQVSQLMRQ
+AEEPPYRIVGFVDDDKGKSRLRIHGLGVRGRGTDLAEVAAELGAEAVIYAISNADAEHVE
+WVSRVCTEEGLDLVVVPPLREMVGGKVTLGSLRHLSVTDLLGRRPISTDISAISDYVSGK
+VVLVTGAGGSIGSELAVQLHHLGPAKLLLLDRDESALHGVQLDIYGNGLLDTDDIILCDI
+RDEQALQAVFEHHRPQVVFHAAALKHLPMLERFPLEGWRTNVLGTRNVLQAAHSVGVQRF
+VNISTDKAAAPTSVLGATKRLAERLTAWHATTYDLPYLSVRFGNVLGSRGSVLISFRNQI
+EKGGPVTVTHPDVTRYFMTIPEACELVLQAGAIGNPGEVLVLDMGQPVKILDVAKRMIAE
+SGQNIDIHFTGLRPGEKMHEVLFSNAEANATSQHPMISEVQVPDLDPVVVAELPSDRESI
+LAMIDDEPPVERADDTQTPGLDQAGARP
+>GCF_005280335.1_02437
+MTWVVTGGAGYIGAHVVRAFRERGLPVAVVDDLSTGHREFVPDGVPFFHADVTDTAALTA
+VLRENEAEGVVHVAGYKYAGESVRVPLTAYRANVQGTASVLDAMAAAQVQSVVFSSSAAV
+YGTPAVERVTEDTPPAPESPYGESKLIGEWLLRDQERAVGIRHTSLRYFNVVGSGWADIT
+DLSPHNLFPLVFSALERGERPHIFGDDYPTPDGTCIRDYVHVQDVAEAHVAAARALTSGV
+GLHSVYNLGSGQGTSVHEIMAAVRDVTGVTDPPEVLDRRPGDPARIVADGTLAAQDLGWR
+MRHSVEDMVRSAWDAHRRLGISASGDE
+>GCF_023573625.1_00844
+MRLLVTGGAGYIGSHFVSVARQQGRADIVVVDDFSTGLRQRVPADVPVYTIDLASDAAVA
+TLTTLLKEESIDVVVHFAAKKVVADSVVQPEDYFRSNVGATVNVLAAMRAAGAASMIFSS
+SAAVYGEPDSSIVFEDTPTVPINPYGQSKLVSELALANASRAWGLRAVALRYFNVAGAED
+AILADTTTTNLMPAIRDVITRGQRLSVFGDDYPTVDGTCVRDYVHVVDLAEAHLAALPAV
+QGSTDPATRIYNVGTGSGSSVLEVVDAFRRRPGVDLDYDIQPRRPGDPGALTANVSLIEK
+ELGWVARYTRDDIVTSVIDFPPRLVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001957.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..602281d68f33c2635e4e0d239c7f18d5c9102aa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001957.fa
@@ -0,0 +1,26 @@
+>GCF_003691675.1_00323
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>GCF_005280335.1_02273
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>GCF_020097155.1_01825
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLCFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYRTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>GCF_023573625.1_00592
+MRVAGMNGVRRGRPVRTTVPAKDGCRAGDLLNRDFTAAAPNTKWVADFTYVRTWAGFVYV
+AFVLDCYSQRILAWHAATAKTTPLVLTPLRTALWDRDRHGHPVQPGELIAHSDAGSQYTS
+LRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADVEYAT
+AGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001960.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d562936d0bd4a0ee889f0944dc46378e6151fdd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001960.fa
@@ -0,0 +1,28 @@
+>GCF_003691675.1_01645
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKARLLISALGHRVFESADGSH
+AAAAAGRATQAPEAAPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDDA
+>GCF_005280335.1_00903
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>GCF_020097155.1_00842
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>GCF_023573625.1_01875
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKAKLLISALGHRVFESADGSH
+AAAAAGRATQAPEAEPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001967.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6013f10f875c90dee61aa6eb3a7b20288fb1757f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001967.fa
@@ -0,0 +1,36 @@
+>GCF_003691675.1_01702
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
+>GCF_005280335.1_00849
+MTLADAYVFDAVRTPFGKIGGKLAGTRPDDLAAHVIRTIVDRAPGLEGLRRESAQDVADE
+LKGRPIEAGTDRARPDRIDEVVFGNANGAGEENRNVGRMASLLAGLPVSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVMLVGGVESMSRAPWVLPKTSRPFPLHNLEAVNTTLGWRLI
+NDAMPKDWTISLGESTERLRERFGITRERQDEFAARSHQLTAKAWEEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRKEDGTVTAGNASPMNDGASAALLGSEKGAEILGLQ
+PIARIAGRATAANEPDFFGYAPVEAVNLALKRAGIGWKDVAAVELNEAFAAQSLACLDAW
+GVDPEIVNAWGGAIAVGHPLGASGTRVLGTLARRLQDTGDRWGVAALCIGVGQGIAVVLE
+NVDAR
+>GCF_020097155.1_00786
+MCVDRTSLARPRGRAYGEAMSLTDAYVFDAVRTPFGKIGGKLAGVRPDDMAAHVVRALVD
+RAPGLEGLRAESAQAVADAAAGHPIEAGTDAAAPQKIDDVVFGNANGAGEENRNVGRMAT
+LLAGLPLSIPGTTVNRLCGSSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTSR
+PFPMHNLEAANTTLGWRLINDAMPSQWTVSLGEATEQLRERFDVSRERQDEFAARSHQLT
+AKAWDEGRYDDLVTVVPGTDLERDETVRPDSTPETLAGLRTVFRKENGTVTAGNASPMND
+GASAAFLGSEKGAEVLGLPPIARIAGRATAANEPNFFGYAPVEAANVALRRAGITWKDVA
+AVELNEAFAAQSLVCVDAWGVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLQATGER
+WGVAALCIGVGQGIAVVLENVDAR
+>GCF_023573625.1_01930
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001970.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0e5cbe2f56d725e3939249c3c8df59880a17067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001970.fa
@@ -0,0 +1,24 @@
+>GCF_003691675.1_01707
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
+>GCF_005280335.1_00845
+MAQPTVTTTLLKAAKSPARVLLVGAGLGTGVHALWSLAAQRMAEDTLVIGYDLPGHGASA
+PHADPYTIAELADAVVAAVARLKDEGAIPADVPLAYAGVSLNGCVALQLALEHADVVSGV
+AVVCSAAKIGEAKAWHERAELVEKAGTPTMVAGSAERWFAPGFIERHPERTTDLLHTLQE
+ADRHSYARLCEALAGFDVRERLGEIRVPVLTVHGAHDAVTPPAAGEEIAAAVPGTTVVAL
+DDAAHQAPLEQPVATAEALAAFLTTVQEAAK
+>GCF_020097155.1_00778
+MTTPEVAVTLLKPAEAPTRVLVAGAGLGTGVEALWSLAARELPADTLVVGWDLPGHGASA
+PHDAPLTVADLADAVAAAVGRLRAEGTIPADVPVHYAGVSLNGCVALQLALDHADTFASA
+TVICSAAKIGEKDAWLERAELVESAGTPTQVEGSSKRWFAEVFIAEHPERATGLLHTLQQ
+ADRHSYARLCEALAEFDVRGRLGEDTVPLMTIHGVEDQVTAPAAGEEIAAAVPGTVVHAF
+EHTAHQAPLEQPERTAEALAAFLAR
+>GCF_023573625.1_01935
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001974.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d372b171b486b78a05dad2aa00a17920a2113d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001974.fa
@@ -0,0 +1,20 @@
+>GCF_003691675.1_01859
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
+>GCF_005280335.1_00615
+MTAMTLTPVSPEELLERTEAGTAFVIDVRTPAEFAVEHIAGSYNVPLDTLKEHVRDVAER
+LHGDVVLVCASGARASDAQQRLTGAGFTEAAVLSGGIGSYAQAGGDVVRRGTGWGMERQV
+RMTAGSLVLAGVIASQIGSKRLALLAGGVGGGLVYSALSNTCAMVSVLDRMPWNRQDRER
+PASEVLGALPAGAARKA
+>GCF_020097155.1_00539
+MTVNVTPITPADLQRELAQHPDTVVIDVRTPGEFEAQHIAGSYNVPLDLIQEHAAEVAAR
+LDGKAVLVCQSGSRAGTALDRLAEAGFTQARVLRGGIGAYAQAGGRVSGTGSRWSMERQV
+RMTAGSLALAGAVASQLGPKRFGLVPAAIGAGLSWSAVSNTCAMASVLSTMPWNRPTEQR
+SADQVLGALPGADADGARG
+>GCF_023573625.1_02089
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001980.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b8c44ebf3ed67b6be19fa1374dea59688b9ca26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001980.fa
@@ -0,0 +1,31 @@
+>GCF_005280335.1_02247
+MSSLNTVKDTATAAGTAELETDILVIGWGKGGKTLARTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARSTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRSRAPRRRRLRPRPPRSSRHRRSARAA
+>GCF_020097155.1_00402
+MSEQKTTTPDLDPTGQAIATQAPLAERYDHVIVGGGMAAAKAVESIRELAPEASVAVVSA
+DTAAPVYRPDLSKTLWADADAHVEDSILATPDSEGTAPGERTAYRLGAEVTAIDPQAHTV
+TVDGRTVGYGSLLLATGAEPVAAGIPQSERVHTYRTVADYRRLKEASGPGTTAVVVGGGY
+IGTELAAGLTMAGTDVTLVVPHRPLLARMLPAELSAAVEATFQEKGVRIAEGRLASAAES
+GDAVTARLEDGTELRADLLVLALGVRPRATLAEAAGLALADQGVRVDDRLRTSAPDVYAA
+GDIATFPDALLGERRVEHADAAETQGATAGRNMVGADQAYTHTPFFWADLFDYGYEAIGE
+LDTRHRTVVDLATGEDGRPDPSTAVVYYADEAGHVRGVLLWNVWDSVPQARALIERTAQE
+PVADLGSLKGRIPLG
+>GCF_020097155.1_00715
+MTPQHVLILGSGAAGAAAARTLASRDDVRVTLVTRTGETPYTRMLIKGIAFGQTPPEMIK
+LPLPQIEVIADTVLKVDTSAKQAQLTSGAQVSYDALIVATGSMPRSLPADVFGGDDAGQG
+RVTALHSVGDALGIRKLLTGLGRPARVAIYGGGIIAAETASSLQADGHMVTLVSRSSVPG
+VGAFGAPVAERLAADHAAKVQARFGRTLQHVDETESGVTITLNDGNPVVADFLLLALGTT
+PAAPSPWTNGIDVDDHLRAAADHVYAAGGVATHHDEALDAWRIDHWEDAAAQGAHAARAA
+LHDLGVSDDPGAYLPRSPYMAMVYGQMISGVGYTAGADAHLEAGEEFIVRHEIDGIVVGV
+TGIDAVGTVYQWGQQLHGVRA
+>GCF_020097155.1_02120
+MSSLDTVKDTVTTAGTAELETDILVIGWGKGGKTLAKTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARFTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRTRAPRRAVVVGSGPVGLELASMLAGFGAEVTVLVRGEQILPDESDAVRDSLV
+EALQDRGVRLATGASATGFAEADGGLRVDLEEGEPIAADIVVLATGRASTAEALDPAAAG
+IELDEKGFIAVDEHLRTSAPDVWAVGDVNGGPQQTYISLDDHRIVTGQLAGDGAYSRADR
+VAVPTTVFTTPPLGSVGMTAEQAREAGHEVKVASKPVAKIAAMPRPKIEEDAHGVIEVVV
+DAATDLVLGARLHCVEAQELVNLVALAMRADVTASALRDGIWTHPSATEALNEVLGELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001984.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b47d6a4a9e0f37da5d3d014ffea84386a652ac57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001984.fa
@@ -0,0 +1,24 @@
+>GCF_020097155.1_00661
+MDTPVMASLPAGVITLRDARRSQTREVTLEAFEIAVHPVHDQGSGLPWAPFTWFDAVAYC
+NELSRASGLQEAYTWQGRTVDWDTAADGYRLPTEAEWEYACRAGTTSPTYGLVEDIAWTS
+LDDVDSPQPVGSKAPNAWGLHDMLGNVWEWCWDYADPARYGDYRSLRGGGWADEPWSVRA
+SVRRGSAPNAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLWEIAR
+>GCF_020097155.1_00698
+MNQPSMATLSSGKITLRDARRRTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTRAGGGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+ISLDHLEGPQPVGMKKANPYGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLREI
+FA
+>GCF_020097155.1_00722
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLRDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTHAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+TSLDHLEGPQPVGMKKANPHGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAICGPLPVGWTPLREI
+FA
+>GCF_020097155.1_01398
+MQGAIDDDMMLTGAVDEWRFIVQTLADRLDQAAHAAGTPVSTAADVDAGTPAGTVSSDHQ
+AGPDMVVIPAGTYTAGSTDAEHEAWGVPENRRDFELPQREVTIAEPFALGRTEVTVEQFQ
+AFVDDTGYQVCGGSRWWDPEDPSAMTFNPELSYLDPGFEQTPDSPSVALTRQDAQAYVDW
+LSETTGESDRLPTEDEWEWAARGGADTAFFWGDTLDEAARYANTYDTVSQAVNGFPWESL
+SVTDRFAHTAPVGSFEADGFGLYDVTGNARAFMADDWIEDLSGTAGDGSVHDGPVPFPVV
+RGGAWNYQPQNLRLDYRGAYLSAEVATTMFGFRVVRDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001985.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b702af24be44d747d0f35d702ae49fa094876b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001985.fa
@@ -0,0 +1,12 @@
+>GCF_020097155.1_00674
+MAYLFLIIAIIFEVAGALSLRMATSGSKKKGLWLLAVLGGYGIAFFGITMALVEGLALGV
+AYGIWAASGVALTAVLSRILFKEPLTKVMAAGIGLIIVGVLMIELGAAH
+>GCF_020097155.1_00675
+MKWVFLAGAIALEVTGSLSLKAAVDAPGFFALVAVGYIGAFTLLAGALKQGMPLGVGYGI
+WGAAGVALTAILSAVIFGEPLTALMTLGIAVVIGGVLCVELGSQAATKKREGTV
+>GCF_020097155.1_02225
+MQWLFLAGAVLSEVAATLCLRVAAAGRRGFYAAVAVGYVLAFVFLTLALRAGIGLGVAYG
+IWAAAGVALTAIASHVLFKEPLTRTMILGILLIMAGVLVIEIGSSSH
+>GCF_020097155.1_02226
+MTKWFLLAGAVGSEVIASLSLKAALTHPALYAVVLLGYVSAFTFLTLVLKRGMALGVAYG
+IWGALGVAATAVLSAVLFDERITAMMGIGIALVIAGVLMVELGSHHTPDTDEQQAGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001987.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c747b9f2e2dc9451a2370012ae14a2c488fbdb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001987.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVAVSVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>GCF_003691675.1_02045
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>GCF_023573625.1_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001989.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe81a96a806ecb817df75d289b7e56915b63f86f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001989.fa
@@ -0,0 +1,13 @@
+>GCF_002008305.4_00029
+MSHASTVPPAADAPSRWGRAAGLSGLVMPAVLAAFSLYLLLGSLTMDTDGADFPGPDFFP
+LILSVAGLVIAAALAVEVVRVRQAPEG
+>GCF_003691675.1_02047
+MSQASTVSPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
+>GCF_023573625.1_00029
+MSHASTVPPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001994.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e9ec2151b10832b35ea39efa426bd8b7d269543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001994.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_00167
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>GCF_002008305.4_02078
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>GCF_003691675.1_01781
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPLPPPTHPDSRFYGTTEVPNRLEKLAGTVQDKLHRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001999.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9359e10b03d30ca383fbd4529d016a915ea6111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0001999.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_00274
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVVGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARIE
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVAREVLG
+>GCF_003691675.1_02289
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGSEVGAKLLTLTPDNPERGLPAIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDAGRAAALAARIT
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVARVVLG
+>GCF_023573625.1_00272
+MSTPISTAPGLPWIDGPAVRSALSPCAAVDALEAALAAGLDPEADAPRTRVATAAGQLLQ
+MPSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGAPGQAPRAVLDGVELTGLRTS
+AVSTLGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARI
+EAELGVTASTADSEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDA
+LARRATVAVESRDSAAREAGDVTLAVASGALAGIEDTVTLAELVAGTARRREGEPALFVT
+TGMPWQDLVVASAVARVVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002001.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ffbfc6d548f500e1fed245545a21822f27f9a60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002001.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00378
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGASMWVGLTGTEELA
+GVKRLLPGGAVTELIIEGWSGMALHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRT
+>GCF_005280335.1_02585
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGAAMWVGLTGTEELA
+GVKRLLPGGAVTELIVEGWDGMVLHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRA
+>GCF_023573625.1_00384
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGASMWVGLTGTEELA
+GVKRLLPGGAVTELIIEGWSGMALHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002005.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38a9835fef336468f165fa198e2412164f45884c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002005.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00498
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>GCF_003691675.1_00219
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>GCF_023573625.1_00497
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002009.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab7d21e4fcee59123e2109bae2532e8acdc8089c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002009.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00528
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVA
+GLADHRPAALQPFMVAEADLVLAAAQEHMRFALREVPQAVARVFTVLELAALVRILDARN
+GRDWIPAGRGVRAFAAEAAHHRALARSSAQPLDVVDPFRGPVEGYAEMIRIMDPALETIA
+DALARAVTPTP
+>GCF_003691675.1_00249
+MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVTPTP
+>GCF_023573625.1_00528
+MLIVCTGNVCRSAYASRALQGRLAVLAPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT
+GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD
+GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA
+DALARAVSLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002012.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fa46aecce97077c82b7a6d28ce80db8dcf2734e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002012.fa
@@ -0,0 +1,17 @@
+>GCF_002008305.4_00600
+MTSPWVEDDELTDWEAPAAADDDGQTGTPLPYVDPEIAAELAGEGPPVWMGTRWREIEAE
+HQWEAWNTLRRWVDWFVAEYRLVTSVVPPCWYKHSDLTAELYAAMCMEYKVWEEQAPGLG
+PMMMWHPHVEMLTARLRRMVDEAGCAKIGQHKEPEAYGDRPAFNLDYDEDDFTAWAATTC
+EQHALERPEAGVKYVRARVFNGDGEEIALSNPVGLASRRTSTGVTAELMMTSSTPLAPGL
+RLTVPSATPGLEVGWQTSVNGHDWE
+>GCF_020097155.1_01802
+MSTHSPEPDDQYDDPGILDDQPDMFDTNALPEPPHPINWNLLSAQDLEAELLELNRWVDW
+LRHTYGLPASVIPPYWHRHPELLWELSALHLHWLCAYDPEQNGSAPLGWHRDFADARHRL
+RDWVTASGTRLDRDRPTRQTTWPGEEPQPTHGESVITDRDADFVQFIIDQVNERQAAEDA
+FYASLDDRIDPATGEVRDDVLGPEGG
+>GCF_020097155.1_02241
+MASPWVEDDEPDWSETAPLQDEGPTETSLPYVDPEVAAELAQEGPPVWMGTRWREIEAEH
+QWQAWNHLRRWVDWFVAEYRLGTSIVPACWYRHPDVTAELYAAMCMEYKVWDEQAPGLGP
+MMMWHPHVEMMTARLRRMVDEAGCAKIGRHKDPEAYGNRGAYELDYDESDWTRWAATERE
+EELIERPTEGVKYVRAKVVDSDGNVLGHSAPVGLRPVPNVVGVEAKVRVTSSTPAEPRMA
+VAVSSGRDDLGIEWEMSPDGAEWSTRPNDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002014.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1df9fbf46f37ec18d9477221959e30be2c78ac1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002014.fa
@@ -0,0 +1,11 @@
+>GCF_002008305.4_00613
+MTMIKEPGVSPTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSA
+HLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHSGPAATG
+ALPHDAGH
+>GCF_003691675.1_01773
+MSPAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVSAHLACLAGC
+GLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGPDGPAAA
+>GCF_020097155.1_00703
+MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVSKH
+VGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHTHH
+ASDTDKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002017.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90a8908ea78b0178662f8f0afbcd6a877d1c6893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002017.fa
@@ -0,0 +1,11 @@
+>GCF_002008305.4_00808
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESHDVEGDELRAFVRFQSRDG
+>GCF_003691675.1_00540
+MTDSPIAADRDGIRYLSGVIPAADGGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIAS
+ELLRRVFARFGQVRQHVLLTDTEERQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
+>GCF_023573625.1_00777
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002021.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..016eda1832c910cbf6cf5acf1dca2a85da8c5ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002021.fa
@@ -0,0 +1,15 @@
+>GCF_002008305.4_00944
+MRMDLPLAPMDEPEPCAARVPLFTGLDLEQLRRVSALARPLVLEAGDALHLAGDRTDRLC
+VVHSGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVAATRLCTFSHAE
+VARLLAEHPGIGGRVMRTLAVRLAEAEQRLAREHQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLDPDALEALAAE
+>GCF_003691675.1_00663
+MRMDLPLIPVDEPEPCAARVPLFTGLDLEQLRRVSALARPIVLEAGDALHLAGDRTDRLC
+VVHTGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVVATRLCTFSHAE
+VARLLAEHPGIGGRVMRALAVRLAEAEQRLAWERQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLNPDALEALAAE
+>GCF_005280335.1_01993
+MRRELTLTPVGEAEPCAARVPLFAGLEPDQLRRVSALARPFALEPGDVLHLPGARTERLW
+VVHTGGLALSLTSPTGRERVVRMAGPGDSVGEQEFLTGAAARHGVRAVAPTRLCTFSHEE
+IAGLMAEHPGIGRRVMRTLAVRLADAERRLAQERQPVAARIAGHLLELPAVHASGTPTVL
+LTAPKKDVASLLGTTPEAFSRGLRRLVDDGVVAVDGPRVRLLDADALEGLAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002025.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17c35bc27f53c0ed55e9b8396bf60a0d351b8d9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002025.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_01038
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>GCF_003691675.1_00751
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>GCF_023573625.1_00980
+MARHGRDEDEAHEAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVLGCAMMGF
+ALGIAWMYVERGRDGRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002029.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8915c74f4ad67085038193933778cadefa240f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002029.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_01314
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>GCF_005280335.1_01578
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>GCF_020097155.1_01474
+MARARLEGAVLDALWDHPDGLTAQELRVRLEREDGAPAVTTVLTALSRLTAKGHVRRVGA
+RRPQVFAAARTREQHAAGLLQDILGSSPDHEAVLAAFVGGISDADAAALRRLLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002032.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..830da7b6433826bfb79f14b3e250ecd1a5ea5eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002032.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_01391
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>GCF_003691675.1_01123
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>GCF_023573625.1_01342
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002035.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5f1a35fcf85924396a6b9d9fb18b197bdee2ac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002035.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01507
+MRESGVMSRDVISDEVWAVIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPER
+FGNWNTIYKNVNRWAAQGVWERVLEKTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRP
+TGGLDELQEISGRAG
+>GCF_020097155.1_01747
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
+>GCF_020097155.1_02235
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002036.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19d0fbe0d376d0f8c8c350d62f2d60d6f6607168
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002036.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01593
+MTDSPLHLDRPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLAAGRALEAGVVSPIQAFG
+LDDFETACAAVGLVRA
+>GCF_003691675.1_01305
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAEAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVGALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRIVADVHLSGPNAYTLTGDLMAWGARQLAAGQAREAGVVSPIQAFG
+LDDFETACTAAGLVRA
+>GCF_023573625.1_01520
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEIGFVKD
+LKADLDATARRTGATLLPALGFEYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLVAGRAREAGVVSPIQAFG
+LDDFETACAAVGLVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002037.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12d7b2b6c04a3e800ab5da42dbe68aaef1411089
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002037.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01596
+MRALVLQSYGGREAMALTDVPAPTAGAGEVLIRTRAVGLNPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDAVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
+>GCF_003691675.1_01308
+MRALVLQSYGGREAMALTDVPAPTAGAGEVLIRTRAVGLNPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDAVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
+>GCF_023573625.1_01523
+MRALVLQSYGGREAMALTDVPAPTVGAGEVLIRTRAVGLSPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDTVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002040.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69ae5e2827372eec0119294d8cf4c54bfffa816c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002040.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_01618
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIAYGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGAGRVIVGAGGSATTDGGTGAAAALGVRFLDAAGEEFVPTGHTLTRIARIDSSPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDTDTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPAGLRR
+>GCF_005280335.1_01278
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVIVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLTRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGPQGAAHVFGPQKGADPAAVASLDTGLVHLAGLVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAADRAIPVIVLAGSVGQDADTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPARLTR
+>GCF_020097155.1_01185
+MQSIIVIPDSFKGALSSREAGSAIATGLASATDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVVVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLIRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGAGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDADILYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDIGRLVMACSPAGLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002044.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caa362941dc49a8a5b05fe19e12fc4265febe57d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002044.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_01897
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>GCF_003691675.1_01593
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRSEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>GCF_023573625.1_01817
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002045.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29765ba2793b05e8323163215799f15f4d0193b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002045.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01945
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCARLAMSAARAVTVFPEVAEARFAI
+TGTPSAPELEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>GCF_020097155.1_00849
+MTATLEAPQAMGRTLSAAPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>GCF_023573625.1_01864
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002046.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e36d2a8072b47084280f3d62fab41f8d1000e0fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002046.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_01961
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTPAPLDVRVDVLRDALDLTLPTRLASAHLLGTLRWCRDSAEVAALKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCRHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDAEPLPEPPAHALDADEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>GCF_003691675.1_01654
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTLAPLDVRVDVLRDALDLTLPTRLASVHLLGTLRWCRDSAEVAELKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCCHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDTEPLSESPAHALDVDEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>GCF_023573625.1_01887
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLMTAVHGVSADGRLVVA
+HAPNLLGSLGAFHTLAPLDVRVDVLRDALDLTVPTRLASVHLLGTLRWCRDSAEVAELGL
+RGRVADLVADVGPRVRVGVIETQRILLHDVDGVAVFCRHTLPLTSRGLIDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVGTGPLPESPAHALDADEAGVTLLRVRDGEA
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002048.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7fd7b71af4dacea43eaf63264d4c1dfef351a4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002048.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_01964
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPEEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAKRRHRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>GCF_003691675.1_01656
+MSTHRLSSTALGFAAGLGTAAAVTAARRIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAQRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>GCF_023573625.1_01890
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMGAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEKRRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTTAKRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002050.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b024677105edd1dc1d7a4007917439d1bc2d839
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002050.fa
@@ -0,0 +1,20 @@
+>GCF_002008305.4_02041
+MPRPLAPLATSLPTILTVPEGREAGLSRARLRAPDLVAIGHGLRMSRDVEATWTDYLRAV
+QSLNPSGVFSHATAARIWGMWIPGRLLEDPRVHLAKERGHGGRTSRSGLVMHQLQPDAPV
+IEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAEARRLGHLPPRATTVDEMR
+RLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAGFPEPQVNPPIRLSSGETV
+RVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDWAVTWVAGEVFTRGGRPRF
+VGDLSRLMRRQATRRGAVLPPGLPGE
+>GCF_005280335.1_00777
+MRMSRGVEATWTDYLRAIQSLNPSGVFSHATAARIWEMWIPGRLFEDPRVHLAKERGRGG
+RTSRPGLVMHQLQPDAPVIEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAE
+ARRLGHLPPRATTVDEMRRLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAG
+FPEPQVNPPIRLSAGETVRVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDW
+AVTWVAGEVFTRGGWPRFVGDLSRLIRRQAARHGTVLPPRLPGE
+>GCF_020097155.1_00745
+MADPSRATPPRLVTTATLRSRGVAPWELRRREYTGRGRSLWGAAGVEFTLLDHVRALQEL
+HPTGVFSHATAARLWGMWLPRDLLQEPSVDIAKVKGRGGWPSREGIRGHHLDPAAQVVRL
+HGVRVTSPAWTWVDLAARLSVEDLVVAGDSLLPDEHGATARSLGRLPCRASTVAELRRTA
+ATRKNVRGVVRARHVVGLLREGADSPAESRLRHRIVEAGFPEPEVNPALRLHDGRIVRPD
+LCWRALRMCLEFDGDHHRTERAQWQEDRARRRGLEADGWSVTWVAGEVFTRAGWGRFRGD
+LAATMRRQAHQEGVVLPPSLPGEEASLW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002056.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1441465f3c0a3b77b0ef399435a9415a62c6c59f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002056.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_02165
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRADGRRAAGAPGSAPANRLRN
+>GCF_003691675.1_01879
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
+>GCF_023573625.1_02110
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSAP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002060.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24df77e15356e0e08f4445add55f841e82b97857
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002060.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_02204
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>GCF_003691675.1_01917
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>GCF_023573625.1_02148
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002061.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcf992882fb351b1aa6131d662960b5bf7133111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002061.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_02205
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>GCF_003691675.1_01918
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETPLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>GCF_023573625.1_02149
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002062.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c363814dd1cd04917283c1cbdb628b42fe43d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002062.fa
@@ -0,0 +1,33 @@
+>GCF_002008305.4_02210
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>GCF_003691675.1_01923
+MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAF
+LLFQLAAAGDWVVFALTLAVTIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYV
+AFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLEEGGDLYLLTLRDGEPVLGGA
+DQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR
+GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFT
+DPELRDPLLRVTVWTFAFAFLSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPA
+FLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLSVLVVNLWLGFPYMFLVTTGA
+LQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG
+PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKAL
+EEIDK
+>GCF_005280335.1_00534
+MSTSSTTSARPDAPHEDPADAGRRGLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLF
+QLAAAGDWVVFAVTLAVTLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFT
+NYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLEQGGDLHLLTVRDGQAVLGGADEP
+LAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSRAYV
+YSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPS
+LRDPLLRVLVWTFAFAFLSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLS
+GLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFSVIVVNLWLGFPYMFLVTTGALQS
+LPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGGPRF
+ADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEI
+DS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002063.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..629dc22dab7c838fb69b46d951b58288983bb88e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002063.fa
@@ -0,0 +1,27 @@
+>GCF_002008305.4_02211
+MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTATASPSQDLS
+EAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYSVENIAILRNTE
+LAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNIE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+FAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>GCF_003691675.1_01924
+MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTAAASPSQDLS
+EAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYSVENIAVLRNTE
+LAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNVE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+YAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>GCF_005280335.1_00533
+MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA
+ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI
+TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS
+VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS
+MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA
+AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN
+YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW
+GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002068.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5ad4eb61f8f72c29ee1388562cdae0b2ddee05f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002068.fa
@@ -0,0 +1,21 @@
+>GCF_002008305.4_02258
+MTTKVGFIAAASHALQNGPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLIGPEDYIGSW
+>GCF_005280335.1_00472
+MTTKAGLIAAASHALQNGPQLFARVEDGGVVIGGRGGEVVPDSTGLYAVVAQDPDAVWAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVERLGLEPVAV
+ASAGRFTLTQESGEQLTTWMRCHLAVRVWQAPAGFAEVTPLGGIEKPVIDTHTPPLNLTY
+GGTSPEAQQLRRRIREARTAMAEQAKRGVDVVEADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEHELGRLLHDALERSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTQGLLGPEDYIGSW
+>GCF_023573625.1_02189
+MTTKAGLIVAASHALQNSPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPSQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLLGPEDYIGSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002073.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6a606a1e10e3c30aa441b4bcf436cb067facb67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002073.fa
@@ -0,0 +1,24 @@
+>GCF_002008305.4_02288
+MPSAPPPSDLAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLAALTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>GCF_003691675.1_01980
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>GCF_023573625.1_02228
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTALGYDA
+LFRACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVVAAVGIPVMYLLSGGVGVALLLYYRLVHGGRAIARRLSPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002078.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ff1d78ee57eb03e42b858f326e423b7097f221c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002078.fa
@@ -0,0 +1,25 @@
+>GCF_003691675.1_00357
+MTAGVDRPADGKVAVERVDRPGRRGMRLLGPAFVAAVAYVDPGNVAANLTAGAQYGYLLV
+WVLVAANLMAMLVQYLSAKLGLVTGRSLPELLGHRLPRGRRLAYWVQAEIVAAATDLAEV
+IGGAIALHILFGIPLLAGGVIVGVVSMILLGVQSRRGQQPFEFVVVGLLAVITLGFVSGL
+FYGPISWGEAVAGMVPRFEGTQTVLLAAGMLGATVMPHAIYVHSALARDRHQGAHAHPGT
+LGRLLRATRWDVGLSLLVAGSVNIAMLLLAAANLSGVSGTDSIEGAHAAITTALGPAVGV
+LFGVGLLASGLASTAVGSYAGSEIMGGLLRWRIPQMLRRVLTLIPALLVIASGVDPTWAL
+VLSQVLLSIGIPFAMIPLVRLTGARAVMGRHANSTPLQTVAWVVVALIVALNAVLLWLTL
+TGQG
+>GCF_020097155.1_00671
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
+>GCF_023573625.1_02013
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002083.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4dc3074116cee048c7586728b3a22e4014ba457e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002083.fa
@@ -0,0 +1,9 @@
+>GCF_003691675.1_00913
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
+>GCF_005280335.1_01694
+MTIVTDKRDRPLHATIAILLAILTGGYLAPWAVAATRGKSNVWTVFWVNLLAGWTVIGWA
+IALYMSLTSHRTARVWGARR
+>GCF_023573625.1_01144
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002087.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d33b5878db5cb0a1bd95e1f0b9e0b655704ba6c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002087.fa
@@ -0,0 +1,10 @@
+>GCF_003691675.1_01652
+MKISDRVRAMRKELLLTQQQLADLAGVSDATVRQIERGTGKSTLKSVLSVMEVLGLELEV
+TG
+>GCF_020097155.1_00207
+MSRQPASVPLTSALDTAPFGREMRALRRGAGLTQAQAADRMGVSLRWLKYLEAGTRRPRL
+QDVGRVAVMDPLTGRMATSVLQTLTPAGKITPSGPRLSLAHLARLAGWPLEPMDPSVSDA
+VTPEALAVVADVLDAAHALLDQADPHMEDLEALAATRNVSAVVHRLDHVYAALAAEDAR
+>GCF_020097155.1_00836
+MAQPHPSPLVPVGERVRAARREMGLTQQELADLAGVSDATVRQIEHGTGKGTLGSLMAVL
+EVLGLHLEVNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002092.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1052ee52e7f003ac83d6292fd44b5290c4691bb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002092.fa
@@ -0,0 +1,24 @@
+>GCF_003691675.1_01711
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
+>GCF_005280335.1_00841
+MTQQPVTRTRVGIVGGGPAGLMLSHLLSKQGIDNVVLESRDHETIANTHRAGILEQPSVD
+MLTGTGVDGRVKTVGDEHRGIFLRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARER
+DGGDVRFETEVVEVLDIDSDTPGVRFRSVAGGEQGPVEELRCDILVGADGSRSTVRKALQ
+AGTEGKDYFTAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPAT
+RVEDWSDDRIWERLQKIVDGPDGLTLKTGPIIDKTVLGFRSFVRTPMDHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLFEALDSWASTGSRDLLDAYSDTVLARVWKAQNFSSWMTTM
+LHARPEASEFEDMRVRGELLNVVSSRFGQQYLAEQYTGWPHR
+>GCF_023573625.1_01939
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002093.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7417ca7b205697a24c91d5f9bbceea2ab961c816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002093.fa
@@ -0,0 +1,18 @@
+>GCF_003691675.1_01712
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLLDVQAVLHQHTQLAVLDAEGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
+>GCF_005280335.1_00840
+MSGTLDRLIRILSSFDAERPAMTVAALARRADLPLPTAYRWVERLVGAELLQKDDDGLVR
+PGLRLWEMASRSAPSMSLARTAMPFLVDVQSVLRQNTQLAVLDDEGVLVLERLSSQGAVV
+NQAAVAGRLPPFTTSLGLVLLAHSPADVAERFIARHRRQLGVAVEHHPSEAGGAAPAGAR
+VRVTAPTEPHLRALLAGIRREGYAAVDGALDEEARGIAVPVTRADGTVVAALGAVVPCEA
+PYTPGVPPLLMTAARGIARAVGGDSH
+>GCF_023573625.1_01940
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLVDVQSVLRQHTQLAVLDDDGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002097.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4be58d62b5a4b54fa71755166b962c80c0d3c03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002097.fa
@@ -0,0 +1,32 @@
+>GCF_003691675.1_01795
+MVSNRLETESGWRRSRLHGVRADDTLTTATLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFASDRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALSVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRCLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPPVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAAMAAQVHGASAPMFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTVAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+>GCF_005280335.1_00693
+MVSNRLEAESGWRRSQLHGVRADDALTTTTLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFAADRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALNVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRHLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPAVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAALAAQVHGASAPTFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTAAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+>GCF_005280335.1_00810
+MAPEPPQADPERIRRARHELAARGLIAGSVPPALVGEQIEQSWRRSVAHEVSLDAVPQGG
+ADLDPALPLRRAAETVVRRWAEGLGQLRVSLVVADATGRILVRRALDTRDEDALDAARAA
+VGYGFGEQDLGTNGLGTPLQVKGDVYISGAEHFTDGLAGLTCAGTPVLDPVTGRAVGALA
+VASRADEAHPLMLGVARQAAAEVMEALRDETAGPDLEIARAFRGLRGPDRAVLVMSADTV
+MTDLPGLARIDAQTQAVLWETLRRRSPGEEPVRLSLPGLEGEALARRLPGAEAAYALEFD
+AVPAPEPALGRAAAAPRSGPPAGGGPERGAGTAPSVGVHPSEMAVAYDGIGDALTAAAEQ
+TGLVELTGPRGSGKRFQAVRWLRDRALAAGTADAPDPLHVELADVTGPQGEDLLRRVAAR
+GRAVVVAGTLPTAAETAQARAGLRTTVARVVLEHPEAPRVVLLRSVDASAEDDVAGQVRL
+PALAEVPQDIPALLARLSERLHPGAPPPRFSPEALQRILAWPWPDNMAGLSRLVSLLPGL
+RRGATVQVEDLPAALRAGPGSRLTRMEQAERDAIVAALREHGGNRSAAAAALGIGRATLY
+RRLKALRITV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002101.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b42f4faf709573c2d6588206f4a2127a58c10a35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002101.fa
@@ -0,0 +1,33 @@
+>GCF_003691675.1_02132
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
+>GCF_005280335.1_00268
+MATRLRQRLLSAAALTAAGALLITGCAESQRDSGGSAGGSGSNGDAAQVDGSFIFAASSD
+PKTLDPAFASDGESFRVSRQIFEGLVGTEPGTADPAPLLAESWESSEDGLTHTFKLKEGV
+TFHDGEPFNGEAVCANFDRWYNFTGIQQAETVSYYYGKLFRGFADAPENAVYESCEANGD
+AEATVTLAQPFAGFIASLSLPAFAMQSPKALEEYKADEIGGSAESPQMSEYARAYPTGTG
+PYKFDSWSVGEDIKLSAYEDYWGEGGDVTDITFRVIDDPVARRQALEAGDIDGYDLVAPA
+DTQALSDAGFNVVARDPFTILYLGLNQQQEELKDVKVRQAIAHAIDKEALIGQTLPEGTE
+PATQFIPKSVNGFSEDVTKYEYDPEKAKQLLAEAGYADGFTIDFNYPTGVSRPYMPTPEQ
+VFSNLSNQLSQVGIQVEAKPAKWSPDYLNQVQGTADHGLHLLGWTGDYNDTDNFVGVFFG
+QEKPEFGFDNPELFSALEEARGVPTLEEQTPMYEEINKQISDFVPAIPLAHPAPSLAFDK
+RVASYPASPVNDEVFTEIDLTE
+>GCF_023573625.1_00124
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002107.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44ba8ede450ef6c88dcdcc68cbde9956e0d2d061
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002107.fa
@@ -0,0 +1,18 @@
+>GCF_005280335.1_00591
+MSEHTATPARAGSPAWIDYSATDFAAQQAFYEALFGWTFTDSGEEFGHYRMIAKDGASVG
+GAMDADQMTAMTGEAPAPAAWTVYLRTEDMAATLAAVREHGGTVLVDAMPVGDLGTMAMV
+AGPGGEAVGFWQADTFEGHDLPLTPGTSVWFELLSTRFDEAVEFYQAVAGWQPTLMGDDG
+APEDGHAAADAEDAAQDGPRYATDHPGEGATAGLCDATQWLPANAVGYWRMYIAVEDTDR
+ALEVIREHDGKVLDGPQDSPFGRVTTVQDPAGATFQINEALPGQE
+>GCF_005280335.1_01322
+MSITPGQPVWIDLGTTDLERSKAFYRDLFDWNFSDTGGEFGHYHMVDAGVPVGGLGPNVD
+AEGNIDASMPVWWTVYLKVEDVDATLAAVREHGGHVHVEPMQIGDMGRMAIVAAPSGAAF
+GVWEVGSFEGFDTEGRPGTPVWFEALTKDFDADAAFYAAVLGWKNVPMREGSSDEGAAEE
+DGAGMRYVTDAAGDDASAGLFDAAAFLPAEVPSHWRVYFAVPDTDAAVEKVLALGGAVVE
+PAQDSPYGRVAAVADDLGGTFMVIA
+>GCF_020097155.1_00514
+MSAQHTAIPSGSPIWIDYSAGDFATQQAFYSALFGWTFQDQGEDYGHYTMVRAGDAVIGG
+AMDGELSAQFSGGPVQPAAWTVYLKTEDIARTLGLVAEHGGQVIVEAMPVGELGSMALAM
+TPGGEAVGFWQPGEFSGHDLPLTPGTSVWFEVMSKDFAADAEFYRAVCGWDVVPMGPDGQ
+QDDAAPDEDGMPAYATDHTGEQATAGLCDAAAWLPEAVPSHWRVYFQTTDMDASVKVVEE
+KGGRIVDGPMDSPFGVVASVVDPAGATFQLNQPPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002110.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06f07f1f3e394c327f05459cab65a41ac705d949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002110.fa
@@ -0,0 +1,15 @@
+>GCF_005280335.1_00898
+MTLTTRDAQTWEQMWLPLWPLASDDLRAGIYRTARKDARGKRYIEANPQALSNLLVVDVD
+HEDALMRALWGRHDWLPNAVVENPTNGHAHAVWALAEPVTRTEYAQRKPLAFAAAVTEGL
+RRSVDGDAAYSGLITKNPQHASWHTSWTSDRLYSLGELASRLEEAGHMPAPAWRRSRRQN
+PVGLGRNCSIFETARHWAYREAKRIRQRHEHATAEDSRDYYAAVLAHVHELNAAFSEPLP
+ANEARDIAASIHRWVTTRFYGWTDARTVQQATLSTLQAVRGRKGGTKSGEKRRSTVEDRA
+RLIVGEDA
+>GCF_005280335.1_01314
+MDARETQAWGQMWLPLWPLASDDLKAGIYRTPRATARGRRYIEANPQALSNLLVVDVDHE
+DALMRSLWDRRGWLPNAVVENPENGHAHAVWALGRV
+>GCF_005280335.1_01316
+MVKTIVRHALAEPITRTEYARRKPLAFAAAVTEGLRRSVDGDKAYSGLMTKNPEHTSWNT
+SWISNELYSLGQLAEHLDTAGFLPAPSWKRTRRRRPVGLGRNCSIFETARVWAYRELRHH
+WGDPEGLRVAIVERVHELNAEFSEPLPAREALDIAHSIHRWITTQSRMWQDGPVVYEATF
+TAMQSARGRKGGAKSAEKRRAVVEDRARLIVGENA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002111.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73457fc7ced0d718fc76e12b0f59cfa0dead200d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002111.fa
@@ -0,0 +1,28 @@
+>GCF_005280335.1_01076
+MTARADRDDVALIILGATGDLTSRLLLPGLAGALAAHDLPRITLVGSSHSEHDTQEWQGI
+VREALKGTALDAAAVDDLVERAVWRTADATDADDLRALFAAAREAAGPEAVPVLYFALSP
+GIARESVDALAGMDDLPDRLRLALEKPFGEDEASARELNAVLADIVEEDRVFRVDHFLGE
+SMVTALLGLRTANRLLGRVWDGRDVERVDVVVDEAIGLEGRAEFYDGTGALEDMLQSHLL
+QVLAMTALEPPARVAADELHDAVVEVLRATRVWQDDPVAASRRARYTAGEADGRPVPAYA
+DEEGVDPRRRTETLAEVTLAVDTDRWRGVPFRLRSGKALERTRWEVALTLRAPEDVPEGL
+SPAAGRDRIVVGLQPRGVRIELAVDGADTPFDAERRALTAGLGEEHVDAYGEVLRGILTG
+EPLLSVRGDAAEECWRILAPVIAAWEADEVPLDEYPAGSAGPEGWD
+>GCF_020097155.1_01011
+MASADTAARDVALIILGATGDLTSRLLLPGLGRALAAHEMPRVTLVGSARSEHGEDEWRT
+VVREALAETPLDADAAEDLAGRAVWCAADASDPDDLRGLFAAAAEAVGSDDVVPVVYFAV
+GPGVAEQAVEALGGMDDVPEGLRLALEKPFGRDEESARRLNAALAEVVDEDRIFRVDHFL
+GESMVTALVGLRTANRTLARVWSAADVERVDVVADESIALEGRAEFYDGTGALQDMLQSH
+LLQVLAMAALEPPARVDAAGLQGAVVEVLRTTRLWDDDAAASSRRARYTAGVLDGTRTPA
+YADEEGVDASRGTETLAEVTLAVDTDRWRGVPFRLRSGKALAETRWEVILTLRAPEDVPE
+GLSAAGRPERIVVGLNPRGVRVELAVDGADTPFDARRTPLAAELGAERVDAYGEVLRGLL
+TGDPLLSVAAEASGLGWKILEPVIAAWEADEVPLEEYPAGSAGPEGWD
+>GCF_023573625.1_01719
+MPDVQNPCPAGASPAPDDDRAAASVALVIVGATGDLTRRLLLPGLARALTVHDLPEVTLV
+GSAHSDGHSLEERRGVIEEAVGETDLDADARAGLVERAVWRTADASDPEDLGALLVAARE
+AAGEEAVVVLYLALDPDLAAEACAALEQVEDRPTGLRIVLEKPFGSDQRSARELNALLGR
+IAEEEDVFRVDHFLRESMVSGLLTLRTANRVLERVWSAADVEHVDIVADESLALEGRAGF
+YDGTGALEDMLQSHLLQVLAMVALEPPRRLTPDALQDAVVEVLRATRVRDDDAVASSRRA
+RYTAGTVGGQDVPDYVAEEGVDPENGTETLAEVELEVRTDRWAGVPFRLRSGKALEPRRW
+EVVLSLRPPEGVPAGLEAAAGRERIVVGLDPRALRVELAVDGPDTPFVAERSVLAADLAE
+EDVDAYGEVMRGVLTGDRMLSVGGDAAEECWRILAPVIEAWDAGRVPLDEYAAGSSGPGD
+WPER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002115.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df5ab0565e8618d606c5b36a0aded94a4e2953f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002115.fa
@@ -0,0 +1,37 @@
+>GCF_005280335.1_02329
+MDGFRRSLDGQFVTVDGHDYSEVTRPKLAQADQQERLPDGSERPLPTRTLHLMAAEDGTA
+PVDLNDWERQVLDSEAAEPSLRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFVFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGMPSVGSRPSLRSRGSCGCWT
+>GCF_020097155.1_00346
+MRYTLKDYQADAVAEILANIERAQRLRREGHLPTMALTATTGGGKTVIAAAVIEALFFGS
+DTFDFLADPGAVVLWFSDDPTLNAQSRHRLEAAAPDLIGRMTDLNAGYTKPALDPRTVYF
+INTQKFAKTSRMVRGFQPSGTEGQDTFAGLDPRVRPDMVPQTIYDIIAATIQNPDLTLYF
+FLDEAHKGMGTTARAQAEQKTIVKRLIAGQPGVPPMPVVFGISATLQRFTNAMDGIRGRL
+GLDPVQVDPARIQKSGLLKDNILLNIPHPDEVGSFETVLLRSAVRQLLESEAAWDAYVAE
+QRADHPGAEIERVVPLMVLQTPNSVTPSDIAGYLRTIMDVWPEMPAGAVAHVFGEKEAIQ
+AAGLFIPHIDPEKVQDTKRVRILLAKEAVTTGWDCPRAEVLMSFRTVSDLTKITQTLGRM
+VRTPLARRIPGNDELNSVLCLLPNFDEKAARQVVKDLTNDEVPNPIIDPVVDPDPRPEVT
+PPSGGAGASSGGGTEPANPEVPGHGTHATDRVAEPSADGQGTPARPGGLHQGETRGASGG
+GQGGAVGPVVLTDRVKVTPIENGPLWDLFDSLPTETTPSRGLGPVPLLTALGQYLSEDGL
+RPDAGEEAHRHLHGTLDYRAGQFREDVDKAVKDILEVRVRTILADRATGKERIGMFTERA
+DLAVVREAYQRAARAFTADVSRTYVNHIVGPDADEDDLREAYARVAGMASVPDIVADVKE
+EASRLVGRWFQEHRTDIKALADDRQAAYKALMEQSTEPQRGNLAKPVNWQESPVDVDKKP
+LPTRTDHILTAEDGTYPLTLNRVESSVVDQEMRRRGAIAWYRNPSRVKDESLAIAYRDGN
+AWRTMRPDFLFFHEDAQGRVRASIVDPHGHHLSDALPKLRGLARYAEQYGDEFMRIEGLT
+EVNGKMRALDMQDPKVREAVEVATSARALYESDAAVDY
+>GCF_020097155.1_00693
+MRYTLKDYQAQAVEQVLNRLHRARKNYQDDGVLSQFSLAAATGAGKTVMAAAIIEALFFG
+SDQYTEDIAPDPGATVLWFSDDPDLNDQSRARIHAASSELDGRLRTVENSFAETTFAPGQ
+VYFLNAQKLREGARLVRGAQDPTNAATPVMAAPDMAQRTIYDVIANTVATPGRTLYFILD
+EAHRGMKTTKKNDQERATIVQRLINGTALAPTMPIVLGISATVERFTQAMAHATDRDALS
+PVQVDPALVQASGLLKDDVVLTIPEEAGAFDTTLLREAVARTKASTRAWAAYAAEQGEPN
+PVVPLLVVQVADKPSDEHLSRILDVIHQEWPELRPQDIAHVFGTHTDRHLPGQIVNYIAP
+QRVQETTHIRVLLAMEAISTGWDCPRAEVLMSFRTYKDATYVHQLLGRMVRTPLARRIPG
+NEVLNSIDCFLPHFDKTTSTAIAQTLMRGQSDMDDTTSDPGKQAARRVLFDPVTLTPNPA
+VGEDVWAVFDALPSMNIPQGATKPLKRLDILANALSHDELLPGAVKTAAHTMCKLLDGCR
+VQYSEQIAAARQDVLTLSAQRLTGRLGTTTLSTTSLELLADDRAIEEAAAAAARTLTGWI
+AGAYIDHIVPEDEEDLDLREGDIIIASLARTSEVVADLEAKADKLVQDWLSQYRVQINGL
+TDERQAVYDRVREMARQPERVALTRPKLTQADQQERLPDGSERPLPTRTLHLMAAEDGTM
+PVDLNTWERQVLDSEAAEPSFRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFLFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGDAFGRIEAVAEIEGQLRVLDMKNDV
+VQAGVHAAQDAESLYKAAPAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002118.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ee01df79bc54df6855b0bedcff6e49d0a0f3520
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002118.fa
@@ -0,0 +1,4 @@
+>GCF_002008305.4_00164
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
+>GCF_003691675.1_00333
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002119.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f5c14f183505d8e4fb42b483d4e3d73169b864d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002119.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_00165
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYERIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
+>GCF_003691675.1_00351
+MNPELEQALRLATDPPGGVSLEALEDLVRDDPTTWWDISEAATHLNVTAHTLRYYGRIGM
+VSVPRDDAGHRRYDSPAIRRLVFITRMRTAGMPIADLQHYLALGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002121.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e50583d48265f50475b5a393dff7b758ca12c98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002121.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_00188
+MTAVPETYVFDTGPLRHFTLKGWLGVLKFLTAGHAVIPESVEQEIRDQQYQHPDLRQILD
+AEWIVVDRSEDLEFLAAFARYEEHLVAGGRNRGECGVLALGRTHGYRIVIDDNVPRVLAK
+REKLECTGTLGLLCEAIRKEQLTVPMVESLADDLIMGDYRLPFGPGGFKCWAEQQGLLG
+>GCF_005280335.1_00213
+MTHVFDTGPLRHFTLNGWLGVLKFLTGGRIVIPESVEREIKDQQHQHAALRQILDADWIT
+VDRSDDLEYLAAFARYEEHLVDGGRNRGECGVLALGRTRGHRIVVDDNVPRVLAKNEELD
+CTGTLGLLCEAIRADKLTVSMVESLADDLLASEY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002126.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09cf2ed535d5fa3ddb05818a943660e1651440f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002126.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_00402
+MTRREVESVEDRIREHLRRDDLNSAVELLRALSPGDALELLDRSEPRMVPVLFRLLDKST
+AVRVFAAMETGQQSDLVRQLQDGQVQDLFAELRVSGQARLLDEMPATVARKMLAGLDAGA
+RGEVGRLLGYPADSVGRRLRMAPVRLREDWTVAVALENLRDHGGREQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEESTEDAARAGGVEPLGRPYLATSVLALMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVIAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
+>GCF_023573625.1_00408
+MTRREVESVEDRIREHLRRDDLDSAVELLRALSPGDALDLLDRSEPRMAPMLFRLLDKTT
+AVQVFAAMETGQQSDLVRKLQDGQVQDLFAELRVSGQARLLDEMPANVARKMLAGLDAEA
+SGKAGRLLGYPADSVGRRLRMAPVRLREDWTVSTALENLREHGGQEQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEGSTEDSARAGGVEPLGRPYLATSVLSLMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVLAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002130.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bd08f5ea2aeb49b792558b94b4916816c10009d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002130.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00587
+MNVHSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRAPASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKNRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVEGESQAEIRSTLRDAVDDLDEVLKKIEEGTR
+>GCF_003691675.1_00321
+MNGYSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRALASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKGRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVDGQSQAEIRSTLRDAVDDLDEVLKKIEEGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002131.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c22e34b6bcc34a83b5ba646e5de5fa5d08432ffa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002131.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_00593
+MLNGINPDGLSGWSQISGWVVGTALVVLILAVGAGVALAVWGRALFSPGGMRKGWTMVAL
+AAVGATVLGAGTAGTSWGAGLGTSELMPAGARPQSVAIEKNAPKQTCNRQAVRDFDKEEP
+SPDRAERERVISTLLGGQPALDGYEWGKEPTGTESSYTVVTSVKWYATGEVNGSGEPDCS
+AQNEATAECSPVEVHVARQSLTNGAQTGRTLTLTRGQNCS
+>GCF_002008305.4_00594
+MSNLIHAATTVAAGVPDIAPRFDGPWMPTIQNVTGLALGTFLVVLIVAVGIGVLVWIFGK
+LSSSGRAQDVGISFVVWGIVAAALIAGAASLIGWGAGLPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002137.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7cd746d76054645e954c460120574102fab72ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002137.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_00835
+MVSMSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV
+FGLGPRQVPWWREVFGLIRIQGVVGV
+>GCF_003691675.1_00567
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGRTGGGACSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002138.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3bed68a140556e3ff3c3ca7657095ecc1768955
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002138.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_00883
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQVAEEVRGVFGIRWGDRPAHA
+RPADALGLAGGPARTRPGSASLTGRGAAAVGADPEAAARLERVLGLADTSRTERGGRAVG
+VVAAPDVRAALAAAGHRVVPLVPGTAAAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHQHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
+>GCF_003691675.1_00605
+MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQLAEEVRGVFGIRWGAPPAHA
+RPADALGLAGGQARARPGNASLTGRGAAAVGADPEAAARLERALGLADTSRTEQGGRAVG
+VVAAPDVRAALATAGHRVVPLVPGTAGAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL
+ELRGAVSAAAARGVTVWVLSRGRHRHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA
+PQGIADVLAACPEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002139.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..023d308af24eff713d987c945c67ce2eb54be108
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002139.fa
@@ -0,0 +1,18 @@
+>GCF_002008305.4_00887
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
+>GCF_003691675.1_00609
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002145.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a391a79b1b71e968767e223d3c8903a2a49a56a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002145.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_00951
+MFHPWRALRTLTHVVVVWARPHPTAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLADALPWSMSLDELADELWVTPLVLTDRLAGLTR
+TEREHLAALATEHSA
+>GCF_005280335.1_01935
+MFHPWRALRTLTHVVVVWARPHPAAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLSAALPWSMSLDELADELWVTPLVLTDRLAGLTR
+AEREHLAARIPEHRDTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002151.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86bb0816fb37f5e4116e70b02e85a1f39925eb8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002151.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_01388
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
+>GCF_003691675.1_01120
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002153.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6861aa43b209067f7dbb149dd7ca1975da61f9c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002153.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_01488
+MANTRAPNSKLAPGEHSIDRVKPTKQADGTYVLRWRVCLPDGTVKPGRSQGPTVAEVRRR
+AREKVGDLLATSADGSWKPSSSIVDYIDKVSIPAVDAARLAEASRRRYRVALNQWKTVLG
+SKTIAQTARVRTLEAALKRIAEEHGSESARHCKTVWGKYIAQQLVRDEVLSGNPLAGMSV
+DLSSSKPARPRAERTLTREELGAAIDWLLSLDPAAGVEKPARGRWSREDAVAKRRNVIDL
+ALLQAASGLRVQEANALTWNVFDRSADVRRTKTGKGRRVPLLFPDVVDHLAERRSLGGAY
+VIGAPTDPDKQWDRDACRKACATFYPEIGAAIDCEVFEHGRTHLWRGTLNSLLVAVPVEV
+RAAFLGHDEDTNRRYYTDVTDPAPMVEAAKALR
+>GCF_020097155.1_00216
+MPRPPLAVGTWGRISDPLEVAPGVFRAMAKVRDVDGVTRKVEARASSKERARRTLEARLR
+ARTAPPAGEVTPDTRVRDVARLWLAEVEARGRAANTVKRYRITVDLHVCKARGGVGELRV
+RECTTSRMEAFLRGIARDHGAPSAKVARTVMSGVLGLAARHDAIQGNPLREVSPISIPRK
+EVRALSPADVRVLRRRLAAWQSEPPVNGRRRRPDDLLDVVDVMLATGCRISEALALRWQD
+VDVDARKLAITGAVVVAGRGGAVRQDHPKSAGSVQTYTVDAHTADMLRGRWERSMDLGLV
+SPMVFPSSTGTVRDPSNYRKQWRTAREAIGFEWVTPHTFRKTVATRLADAEGLAAASAYL
+GHSGEAVTRTHYRAKAPEAADMTAALAGFWGDAEGGEGEVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002154.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afa321216f59f49a84cee908e507f60e0deaa9a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002154.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_01493
+MTTTTPKTARQLRAEWQAEIARREAEIVAAERAEARRIDEALRRAGRARVAAVETLYEML
+GIDEQTKTRTRRDGSVQTVRADLDEAERAERLVAAVAALLEGAAGTRSAPAGGAEAVPDE
+AAQMVPEEPSGALAPLPPAAGGESAEPDPEEDEAHASDDAEEPVSDEGDEAAREEDAYAE
+EPAYGTVSDDLHEAGWQA
+>GCF_005280335.1_02201
+MTTTKTARQLRAEWQAEIARREAEIAAAEREEDRRTDEALRRAGRARVAAVEILYELLGV
+DEQTTTRTRRDGSIQTVRVDRDETERAERLVDAVRALLAHCDGLRSAPAESAPTSAPLPS
+PAGLDATVSGREQTAHAESESTSDEGWAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002159.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42cd018bc1ff5f9d8cb0bc672f22596207268e94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002159.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_01509
+MTTPQFSVDRTRRPVATYRAISTKDAASTQRDGEAVLEVRELSSRSGQREAEVLFHDGQW
+QLCDPEHDLVPGFTFDAFPEHPFLAEAYGETWNGWDTPVVRREVLADILTALELSHRWEG
+DVTVLEVDDYEDRIVPRLDGLYDLQQAGWTVQQVELG
+>GCF_005280335.1_02214
+MTTTPPPVDRTRRPVATYRAISSRDASSTQRDGEAVLEVRRFAARDGHAEAEVLFGDGQW
+QLCDPERDLIPAFEFDAFPDHPFLAVEYGEDWNGWATPVVTRETLADVLAALELAHRWEG
+STAVLEIEDYEDRIEARADGLYDLAQAGWTVQQVEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002160.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ac6d15d466658deb83c4f880ae85a85238141c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002160.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01605
+MMHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHD
+AASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEG
+QTRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVD
+ATTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEG
+MTVADFRSSGVAIAAGEEATRARAEKLVELSRGRMA
+>GCF_003691675.1_01317
+MHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHDA
+ASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEGQ
+TRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVDA
+TTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEGM
+TVADFRSSGVAIAAGEEATRARAGKLVELSRGRMA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002162.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e215a8682e5e270288e71e47826e5b283b37049d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002162.fa
@@ -0,0 +1,10 @@
+>GCF_002008305.4_01607
+MFSASVIDDATGVNMGIGFLGVALAFGLTVVAMAYAVGHISGGHFNPAVTLGAALAGRLP
+WKLTVPYWIAQLVGGVAAGGVLLAIASGRPGYSLAENGLATNGYGELSPAGYSMGAVFLT
+EVLLTAVFLYVILGATDRRAPSGFAPLAIGLTLTLIHLISIPVSNTSVNPARSFGVALFA
+GGDALGQVWLFFVAPLLGAAVAGLSYRFVFPNTSRVTEELPEPAADGTRDAV
+>GCF_003691675.1_01319
+MAYAVGHVSGGHFNPAVTLGAALAGRLPWKLTVPYWIAQLVGGVAAGGVLLAIASGRPGY
+SLAENGLATNGYGELSPAGYSMGAVFLTEALLTAVFLYIILGATDRRAPSGFAPLAIGLT
+LTLIPLISIPVSNTSVNPARSFGVALFAGGDALGQVWLFFVAPLLGAAVAGLSYRFVFPN
+SSRMTEELPEPAADGTRDAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002165.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37c0243412063bd6163b611b587228c879b13566
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002165.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_01616
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRMDGDA
+>GCF_003691675.1_01326
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRLDGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002166.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3d6fe2c74a6de8556f180339b3797874a8445a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002166.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01788
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
+>GCF_005280335.1_01088
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002173.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6237bce60a5d0cfb930e753b711cef6b69e6122d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002173.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_01949
+MVPASSIHTAATARTGTTYSGPMPVSAQGPRVTVVGDSSALGSTSLMNLEMPGITVDAKE
+DRTFAEGLTRLGQLKAAGRLRDIVVLGLGVNTGGTAAAQARQAMDLVGPDRELVLVTASG
+PVAWRAFTEQAMRDLAARYPGRVAVTDWEAASRYVTDFRADRIHPRAQGLSVDAQLVRLA
+ADRATGARTVTVQAGQTLSGIAVAYAVPGGWSAISRATGVPLAQLPSLNGPTLSTVLHPG
+QVLRIRCPLT
+>GCF_023573625.1_00704
+MNRSTLGTRLGASVLVVAALVSAAPAAPAVTSASGTTTTTATTGLAPGTYLAQSGDTWAY
+IAPRVGVELADLLRANGATTSTAIRAGQPLVLPAVSKHLPATSRTGTPYSGPMAPSSAGR
+RVTVVGDSIALGAASLMNLEMPGLTIDAREGRTFAQGLTRLAELKQAGRLGDVVVLGLGV
+NDGGATATQVRRAMDLVGTGRTLVLVTASGPVAWETSTNTAMRNLAATYPSRVVVADWKR
+ASAYVTDFREDRIHPRGQGASVYARLVRLAVDTAPVLRSTTPRTVTVQAGDTLSLIATRY
+GVTGGWQALATLNKISDPHMIRVGQTLLLPATSTTTTPATYTVLPGQGWYAVSRATGVPV
+TQLLSLNGATLSTEIHPGQRLRLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002175.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1ed8fc8f41165338670be98c27ab96385669409
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002175.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_02002
+MTRLPGLRPPRFLDPWRRPLAPRLPWHVVLAASIAGALTIATLSLGEDLASVPLLVGAFG
+SSCVLVFLVPHGPHSHPANVLVGHVVSAACGIAVISVLPLAWYSLAAGMGLAMAVMAGLR
+VIHAPAGATALAVMLSNADWHYLVTPVLAGALVLTACALLYRRLMWRVIGPAE
+>GCF_005280335.1_00847
+MSRLSRAPGLRRPRLLDPWRRPLLPRLPWHVILAASLAGAATIATLSIGQDLTSVPLLVG
+AFGSSCVLVFLVPHGPHSHPANVLVGHVAAAACGIAVSSVLPLAWYSLAAGMGLAMAVMA
+GLRVIHAPAGATALSVMLVEAGWDYLLAPILSGALVLTACALLYRRLMWRVIGPPPPPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002184.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e214ecd700f375afb8c8eb09cf244b4daa2d482
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002184.fa
@@ -0,0 +1,16 @@
+>GCF_002008305.4_02237
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLRPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAKSVAGVEWNGQTIQLVGDPAILGAASTDDVEV
+>GCF_023573625.1_02169
+MSDFDTLSLEDLLAACAPGGSTSLLSETPLQPAGGPGAVIAPAKVIEGRGEPTYAYERRM
+ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE
+SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST
+RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA
+QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA
+LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS
+RALAPITDEVAVQVFEAALAHAESVAGVEWNGQTIQLVGDPAILGAASTDDAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002185.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6d5ad24e0700ffae7430700162dde99a8418185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002185.fa
@@ -0,0 +1,14 @@
+>GCF_002008305.4_02248
+MAATDHTLNPRAGANPSAAPNRLVRRRAVIGLLTGAPLLAACGGDPLSSDGGGQGSGGSG
+SGGDGGGTVRVGSANFPESEIIGELYAQVLEAKGLTVERKMQIGSREVYLGALKDGSIDL
+IGEYTGNLLAFYDKQAKAKTSEEVFAALQKALPDDLEVLAEAKAENKDAWCAAGDWAKQH
+GISSYADLKDYDGTLRVGGPPEMSQRDYGAGLARVESVYGVPADRMEFTPISDGGGPLTV
+KALKDGDVDLANIFSTTPAIEENGFVMLEDPEGMVTPQNIVPLMAKDRVTDQIREAVESV
+QKVLTTEDLMAMNAENSGEQKKQPREVAGEWLKEKGLV
+>GCF_020097155.1_00459
+MATSPRPSAPLSSALSRRAPRRAVLGLLAASPLLAACGGDPLAEGSSSPAPGSGGTDAGG
+AVTVGSANFAESEILGELYAQVLEAKGLQVERRMQIGAREVYLDALKDGSIDLIAEYTGN
+LLGYVDKEATATSSADVEAALKAALPDHLTTLAVAQAEDKDSYNVTKAFSEENGITSLAD
+LAAHPGTLRVGGLPELAQRDYGAGLAGLEEVYGVPQDKLEFTPISDGGGPLTVRALVDGD
+VDLANIFSTTPAIKDNGFVTLEDPKGMITAQNVVPLMAKDKVTDRIREAVEAVQAQLTTD
+DLLAMNAANAGEAKRQPRQVAADWLRQKGLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002188.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02dfead358ae5d883fd34599539e34bbe6ecfdc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002188.fa
@@ -0,0 +1,25 @@
+>GCF_002008305.4_02279
+MSTFQTPQYTIVELLQKARSGELQLPDFQRPYRWDDERIRSLLVTILRGHPMGVIMTLRT
+GGQNVRFKPRPITGVPAEGLKDPELLLLDGQQRTTSMVQALTGDGIVDTEDVRHHKLRRR
+YFVDVVKALGDVREQEDAVVSLPDTGIVTENIGRDVVLDVTTEEKQWELGLMPVTVLFDS
+ADCFAWMMKYQQALPERMEITQRFLSSVAQAVQTYKIPAIELDKDISKDAVATVFEKVNT
+GGLRLDVFELLTATFAGDRAYYEETGEDFRLAEDWALTEEVLRTYPVLTDMKSTDFLMAV
+SVLATLAKRREALAAGKTGQQVPQTSARREDILGMSLEDYRVWAPRLRKALPTVARHLRD
+LHIHDSRGAPYSSQVVSLLIITTLLGDRAEEHAVRARLNQWFWCGVLGELYGSTITTQLA
+KDAEQIPEWSLGKSAETPEAIIRASFSESRLGSLRTRLSAAYKGVYALIMAQQPPAKDWM
+LDQTLDFQSYDDLQVDIHHVFPRKWCDENGIEPWRRESIINKTPLAKKTNIRLRGDSPAV
+YTERLDDKGLTPQQVDAQISTHAIDPALLRAGDFDAFFNDRRRRLVSMIENAMCKPVVRD
+WEVDSESTDAPENFNDPAEMEADEPAGDEEAANVAD
+>GCF_003691675.1_02021
+MPDTFGHHPWTVQDLVSAVDSGHVRLPDIQRPFVWSNAKARDLMDSMYKGFPVGELMFWE
+NADPEHSRAIGTLEKSQSGSMQVIDGQQRLTSLYAVVKGKRVVREDYSQENIVIAFNPLT
+ERFDVPDNRIKRSSEWIQDIKTVFASPIDARSDYLDGLEKARGGERLSREDERRIEEAIN
+RLSRVLAYQFQVVQLKKEVSRETVADVFVRINSEGVKLSSADFILTWLSVFWEEGRQQLE
+DFARGSRFTPQELARMDETTVRWTPKNPYLTLDPGHVLRVVVAVGNRRAPLQDAYNALRG
+RDPRTREIVPANRERELAKLKDGQARALDPKNWDEFLKVIERAGMRTSAMVTAKNAVIYG
+YALWLIGRTEFGVPVDDLREVMARWYFMAQITGRFSGSAETRAQEDLNRLDGLERTPEAF
+TTAIDSLVSTTLTEDWWTVTLSEDLHTSNMSGPAYTGYVAALNILDADVLLSTLKVKDWI
+DPNRRPVKGVEKHHLFPKDYLKGALGLKSTRQINQVANQALVEWSDNIDISNEAPSAYWP
+AQVTEKAIQGERLAKQTWWHALPEGWTEMSYTDFLAARRKLIAGVTREGFRKLSDPNYQP
+SPPAHPVPASEPVLPTFEQLVLAGALPVGTHLLPTDGRTDSIAEVTPDGTILLDDQEYTS
+PGLAAKADGAEDEDGWLYWSADLAGQATILDEVRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002191.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3913f186d0377ac87cb509b07ed070fab7c0482a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002191.fa
@@ -0,0 +1,16 @@
+>GCF_003691675.1_00093
+MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV
+DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL
+RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI
+GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV
+LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP
+CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM
+QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR
+GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR
+AMAALNITGVADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHTAWS
+FLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLALRLHRVQSASR
+TG
+>GCF_020097155.1_00837
+MAFLGPGEHFRDLPGAFRTLENALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKDVTA
+RPLAPLRDLPPQRASALRETALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDW
+HTPPRSLDLHLALLSAARDDGGAPGAPPVRSQPRRRAEELRRPRSPAARC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002199.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aed18f59e7e04e49e544cdf34a4bb7a6331c5b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002199.fa
@@ -0,0 +1,11 @@
+>GCF_003691675.1_00325
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFVSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAHSAC
+LQYRRTGW
+>GCF_023573625.1_02006
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFLSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002204.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c000b15bc063ee28d827a9ea3d6e2b1ef782eb35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002204.fa
@@ -0,0 +1,11 @@
+>GCF_003691675.1_00686
+MQNTEQTPRDASTEAGGRLWRHRIVENDTLRMTVLSMLAAAVAIGLSTLLIATPLGDALG
+VGAARRASWMTGLMTLCLMWSIYSALDTVVLYRWLGRRDSTDLHALLRTRSRGPKESVDP
+VGWRALMLGASSTLGNTATFSVMAMLVVVISMWMPEVRSVPAMRLLAVATVLASWASIVL
+AQALRYARLAAQHDPKRSRPEGESPAPPIRFRGSDSPVFSDYVALSLTLSTMMGAQDVVL
+SGRAARTAVREHALVGFLFNSMIIAALASLLLTVA
+>GCF_020097155.1_01518
+MDSDDGRLWLATLPALAAGASGVLIGREAAAEFPSADWRVMFYGTLGVTQVVMYVVYLWL
+TLRRFHGLDARTLERDLRTVSRGPRPGSWAVRMGLPYGSTLGWMTSVSVVALVIVVVVML
+DPATAGQPLLRVLCALVVVSSWAVLWVSQALAYARMAAQHGGIEFTGEEPPVFEDYLTLS
+AFVSALFGTGDVTLTGRRTRRAMRSHVMVAFGFNSMLVASLATLLLSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002209.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6a26ca35d021a241782c24d55af366dfdd47fa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002209.fa
@@ -0,0 +1,20 @@
+>GCF_003691675.1_00770
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAEAVEREVAAGAVPMA
+VVATLGTTDRGAIDPLPAIADVAERHGMWVHADAAVGGILAASAATRHELPGLHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVVSLFAGARERTRQACGILRARPTFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAATHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEELVDVVEEAALRHV
+DAVRASRHRWRGVARTRPHGPSVAVSCTLPASAGPRPSAARVDEHGEQVCA
+>GCF_023573625.1_00998
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAAAVEREVAAGAVPMA
+VVATLGTTDRGAIDRLPAIADVAERHGMWVHADAAVGGILAASAATRHELPALHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVASLFAGARERTRQACGILRARPMFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAAMHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEALVDVVEEAALRHA
+DAVRAGRHRRRGAGRNRPHAPSASVSCTLPSSAGPRPSAARVVEHGEQVCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002211.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f75739ea17a13efb9fc1654c2c15b67ce3dfebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002211.fa
@@ -0,0 +1,10 @@
+>GCF_003691675.1_01621
+MRRDIKKKRAALSAAVVVAGLLTAAPSAGAAPTPAGEDTPSLDAYCAEEYWTNTSVTSNI
+FKQSHSSYSSVSGAPGVTLTIATGRTFGVSGDITGELSGDVSAILAGVSAKVGTRVGVNY
+SSTNTVSGSWKVPSTYTNGGKLAIGAKRAQGTWSRQMLNKSCNVVTLRSGSFYTPWQQFY
+FQHYRL
+>GCF_020097155.1_00867
+MRMNIKKKLAALASGTVVAASLMVAPAAGAATTPGDGEAVSPDAYCAEEYWTNTSVTSNT
+FKQSYSSYSSVSGAPGVTLTIATGRTFGVSGDITGEVSGDVSAILAGVSAKVGTRVGVSY
+SSTNTVSGTWKVPSTYTNGGKLAIGAKRAQGTWNRQMLNRACNVVTLRSGSFYTPWQQFY
+FQHYKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002213.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..318ee219ef517a9e032e9ff1085a0ae7ec672c3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002213.fa
@@ -0,0 +1,10 @@
+>GCF_003691675.1_01705
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
+>GCF_023573625.1_01933
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002215.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f84586df056b5cb31e8a138c14c8e5bbbe24aefe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002215.fa
@@ -0,0 +1,12 @@
+>GCF_003691675.1_01747
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
+>GCF_023573625.1_01975
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002224.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75bd496a88a46e7e95f19048b86b4a92c88d9da9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002224.fa
@@ -0,0 +1,23 @@
+>GCF_003691675.1_02172
+MSTAEAGAATSTPADPWSSWLGSRAAVRARRGLERRAEPPEPGAPSSDVVDLAANDYLGL
+AAHPDVRAAAARVATEGPVGARASRVVTGTHPAHADLESAAAALAGADAALAFSSGYTAN
+LGVLGALAGPGTAFLLDEHAHASLRDGTALAATARSGAFAPLPGASVTTVEHNSVPAFRA
+ALGRLRAEGRARRIVLVVESLYSVLGDEADLPALAALAAEHGALLVVDEAHSLGVVPGGS
+RTGALGLWAGQAPVVVTATCSKALGGQGGLALFGGPAARSWRDHVLNTARTFVFDTALAP
+VLAASAAAACRIAATGEPAARLARARETAVDVFTRRTELAGHVEVGAGAVHSIRMPGPEQ
+AVAAAAELRAHGVLVGCFRPPSVPDGIARLRVSVTTAVPEPRLRAALEAVASVAARAWGA
+STGCPFAHGDPRPEAVRGDHLRISDPADLRRVLTDPGTFASDNALTAVVPLSGPARRILA
+AARFRLPPVLASAGGEEHRAVRRVVAPFFSPAKVREARGRILATTRTALTAALADTGRAG
+GAVDLATTVAAAVPARVMSALTGVPNPPEAQLHRWSADSLELFWGWPDEDRQLRLARSAA
+DFHRWLRGAVVEARGDDAQPGNLFAALHEAGVDDERIVSLGYFLVIAGQETTRLLISTAL
+TRALADPARWAALGAGADGGAGADAAEAAAAELVAECLRTSSSVPTWRRLATADVRVGEH
+EVRAGDELLLHLSGEQHDDARLAFGFGLHRCLGAGLAELETALVVREVARLLPDARLTGP
+PATWLRLLSFQAPQHVLVTPGPWHGGEDIRIEQSGVDTCASRS
+>GCF_005280335.1_02386
+MYAFKDQLAAELDELRESGLYKRERAITTPQSAHVKATAAGAEDGEAREVLNFCANNYLG
+LADDSRLIDSAKRALDERGFGMASVRFICGTQDRHLELERRVSRFLGTDDTILFSSCFDA
+NAAVFEPFFGREDAIISDALNHASIIDGVRLSKAHRFRYANRDMADLRAQLEATKELNDG
+AGARRTVIVTDGVFSMDGYLAPLAEICDLADEYGALVMVDDSHAVGFMGDTGAGTPEHAG
+VSDRVDVYTGTFGKALGGASGGYVAARQEIVDVLRQRGRPYLFSNSIAPSIVEATITALD
+LVEDSASLRAQLFENAALFRRRMTEEGFELLEGEHAIIPVMLHDAALAARMADAMLDQGV
+YVTAFSYPVVPKGQARIRVQLSAAHSAEDVEAAVAAFVAAREAVQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002225.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8b0967be30c9cca3f478eab17a70ea5fb8afce6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002225.fa
@@ -0,0 +1,10 @@
+>GCF_003691675.1_02187
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLAGGG
+RGLQVPAISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLAAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDAAGARAGVLALHDFLARSALDYAARRADHGSAEPPAPWAEGR
+>GCF_020097155.1_00156
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLVGGG
+RGLQVPPISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLPAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDSAGARAGVLALHDFLARSALDYAARRAAHGSAEPPAPWAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002226.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6c9423b4df9d37361ba6d5c693d570650d2cec2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002226.fa
@@ -0,0 +1,6 @@
+>GCF_003691675.1_02215
+MGDYYQDNAARVLAHIGAHHDADPGPLADTGRAHHGDMHAGVVVGQDGTIHAHTRRDASG
+TYRVHLPGEDVPVDLWAARERRVIGPTVHVPLWRIFSGQGVP
+>GCF_005280335.1_00048
+MAGYYTTNAARVLAQVGAHHDADPGPLADAGRAHHGDMHAGVILGMDGTIHAHTIRDARG
+THRVHETGAEWAADLWAARNARRIGPTVHVPLWRVFSGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002227.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e99e4464fecb246453654095497eb1b593ba089a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002227.fa
@@ -0,0 +1,6 @@
+>GCF_003691675.1_02224
+MYSVYAQHWQRDTEAAASARVYQVSRLRHDAAPAPGVSIFRHGRPVLTLTPDDARRIADG
+LHDAAERAERVPTTPTRKEHHS
+>GCF_005280335.1_00042
+MTRRTFITNRDRWTRDLTTATKSRANAILREHPDGGTVPGVMIFRDRLPVLTMTPDQART
+LADQLHDAADTCLEAANG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002232.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..985066351b76be5e1825dec29860c3776a167441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002232.fa
@@ -0,0 +1,8 @@
+>GCF_003691675.1_02301
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
+>GCF_023573625.1_00285
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002233.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a730a4be9e3b67182ffd8a1ad962e94d3d9dc9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002233.fa
@@ -0,0 +1,12 @@
+>GCF_003691675.1_02302
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA
+>GCF_023573625.1_00286
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002237.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51ba02b1b3bb5cc41e54cf8012e7f4f8fe84d3b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002237.fa
@@ -0,0 +1,14 @@
+>GCF_005280335.1_00078
+MRLAAVNPIPGLFTIAPADRDHEVGLRVGVTVLVPLLVLLAAGRMDLAVYAVFGAFTGIY
+GRNLRHGPRLQAQLRGGGLMLAVLAAATLAGRLGVSEQADPWGLVLWTTVVAGVAGVVAT
+LLAAPAGVHHNYWAMVAAVVPLVGHSTRYRVSRGLQRVIGTFLGLVLTAGIILLDPPVIV
+LVLIIAVLQVAAELYIARQYVIAQTVVTPLALLSTMLVGVTAGGAGSLMAAGGLQHLADR
+GVETVIGAAVGIVCVLFPWAWRRWVWGSPDPARAIPVVRGPGS
+>GCF_020097155.1_00062
+MTTQAPGIPLTMGRIRARRPRRKDPRPVRLADVNPFPAMFTIGPPDRGHEVGLRVGVTIL
+VPLLLLLALDRMDLASYATFAAFTGIYGRNEPHGVRLRTQLRAGLLMLGVLTAATVAGRF
+GISEAHDPWGLVLWTTVIAGAATVATGWWNLRPAGSLFHIFAFAAAASVPVKPPVVEGML
+MAVAVVVWAIAVGLSSRVLPSHRTPLTWPPSDRPDRGRRRLILLEAMWYVIAAGVAGSVA
+TLVAAPQGVRHNYWAMVAAVVPLAGHSTRYRVNRGLQRVLGTVLGLGLTALIVLLDPPAV
+GIVLVIAVLQVLAEVYIARQYVIAQTVVTPLALLSTMLVAVTVGGAGSLAEAGAFRNLQD
+RAVETVIGAVVGIVCVLYPWAWRKWVRRSPDPTREIPIVRPEQIQRPVGGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002238.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83fef8e12b608905cc725ac985d696c1bb0ec13b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002238.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_00081
+MLLLDADTLIQAKNTYYAFDFAPGFWDWLDRGHAAGLLASVEAVGQELKRGHDELADWAS
+ARPSFFVQPGTAVPGSIAQLAAWVHGQAQYTAAARQEFLAGAGDLFLIAQAHGGSHTVVT
+SELSRPESKKRVMIPDACQAVGVPCVDLFGALRATGGLMLVLSPAS
+>GCF_023573625.1_01541
+MYLIDANAFIEASRHYYSFNLAPRYWSWLYEQSVAGTVGSIKAVYDEIADGDDDLSAWVR
+DNTPEEFWLEEDDDSVAAIIDLATWATGPTRQFTQAAIDEFMASADLRLVAQARALGATV
+ITREVPNAESKKRVKLPDAAAAVGVSCVQPFQAYERLGLRFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002242.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535494ecdf62713621fc7272915a75664f363db8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002242.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_00104
+MTTALPDALRLTDEARERLHADCRHLHRHPELSMQEHATAAWIEEQLDEIGVERFRCGGT
+GVVGVMRHPGGAEGPVVAFRADTDGLPIEEDTGLEYASTARGTLPDGREVPVMHGCGHDT
+HVVSALAAARLLAAAPDTWGGTIVWVFQPAEETGAGAAAMLEDGLWDRAPRPEVVLGQHV
+MPLAAGKVQLIPGMAMALADSQAITFHGRQAHGSQPQDSIDPILMAAHAVTRLQGVVSRE
+TDPRDPAVVTVGTFHAGLKENIIPDSAEIALNVRTFSAASRDTVLGAIERIVRAEAQASG
+APEPSFRTIARFPRCHNDDEQSARVAAALRAELGEDHVLDGRPLMGSEDVGALADAIDVP
+LVYWFFGGFEGEDPAAFPGNHSPHFGPAMAPALDAGHRAALAGLLAYVGR
+>GCF_020097155.1_00074
+MAAVAAELGEENVMEIGPLMGSEDVGALTDAIDVPLVSWFVGGFEGEDFGDNPANHTPQF
+GPVMEPTLTTGVHAALAGLLHYVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002243.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ea9d980bd17516693c61b60ae4fcf09beb052d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002243.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_00115
+MTPTSALSSRAPGLAACLALGLAALGTATAVRPWAPALSPLLLAILAGLAWRNLAPVSER
+LAPGVAFAATSVLRAGIVLLGLQLLLSDVLALGPGVIALVVGVVGVTFAATLALGRVLRL
+PWDLTVLVASGFSICGAAAVAAADSVVRARREMVATAIGLVVLFGTLMIPVMPLLTGALG
+FEEQAAGLWIGAATHEVAQVVAAGGLVGGTALSVAVTAKLARVVMLAPVMTGLAWWQRHR
+DALEPATLDDGAPTAVERPPLVPWFVVGFLLAVLVRATGWLPAGVLDAAALVQQLLLATA
+MAALGLGVHLRSIAAVGPRPLVLGAASTAVVVVVGGFGATLLA
+>GCF_020097155.1_00083
+MPARLEPGIAVAAKPVLRAGIVLLGLQLLLSDVLALGWGAVGLVVGVVALTFAAALALGR
+ALRLPWDLTALVASGFSICGAAAVAAADGVVRARREMAATAIGLVVLFGTLMIPLLPALT
+GALGLGERAAGLWIGASTHEVAQVVAAGGPRPLVLGAGSTAVALAAGRAGAALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002245.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efe4ce284cf7b0a73681883ccfe60da4731f13ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002245.fa
@@ -0,0 +1,14 @@
+>GCF_005280335.1_00148
+MTAQTPATAPADDAPLEVPVLDLSGMRRPDGSFDPDFLARLRHAAHHVGFFQIVDYGAAP
+GQVDDLFRVTAEFFARPEAEKLALHNQDSPHWRGYSAVAAERTQGRPDSREQLDFSPDRA
+PVPAERIGEGEEYWHLQGPNRWPADMPELERSAMAWTALMDRVGEDLLKALSVAIGLEED
+HFAEAFDGDRAWMAKLAHYVGGVAEAGTQGVGLHADYGFITLLLQDEVGGLEVRPHGQDA
+WLPVEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFYSPRLDAVIEQ
+VELSAELAADARGASDDPDNPMLASFGSNMLKGFVRAHPKVTERFHPELLDR
+>GCF_020097155.1_00106
+MTAPSPDSATPARVVPVLDLSIMRRPDGSFDPDFLDALRHAAHHVGFFQIVDYGAAPGQV
+DELFRATAEFFALPEEQKQALHNQNSPHYRGWSAIAAERTQGRPDSREQLDFSPDREPVP
+VERIGEGQEYWHLQGRNQWPAQMPELERIAMDWTALMDRVGEDLLKALSVSIGLDEDHFS
+AAFDGDRAWMAKLAHYVGGVAEAGAQGVGLHADYGFITLLLQDQVGGLEVRPYGQDEWLP
+VEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFFSPRLDAVIEEVTL
+PDEYAAEARGVSDDPTNPMLASFGSNMLKGFARAHPTVTKKFHPELLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002246.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0214d1d51399d08a910c31c4d9c369122d4243de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002246.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_00170
+MSTKQTRISPISGGRRPVSPLGPALLAAAAGVVLAGVRRMRARSRRREEVAARVAADRRA
+GR
+>GCF_020097155.1_00121
+MILARIPRRSARRAVPVVEATQPPVRDRSREVSPLGPALAVALGGVVAAAARGLRARTRR
+AEAADRARVARDADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002248.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cc8ec10dd2a6eb64143046bc695c20b5b22684e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002248.fa
@@ -0,0 +1,10 @@
+>GCF_005280335.1_00249
+MRHFDDPVLQAMASRRSVSQVGPSTPTDKELAGLLAAVTPVADHKALRPWRLILLRGEDR
+RRLGEALDAAAGTERERGEVNPKPYRAELLIAVVASHRPHPGVPGWEQDATAAGAAHLLE
+LALWQAGWGVMWRSGLYTDAPAVRAAHGLGDRERLLGWLYVGDVDPAFRARLEASKKPAL
+DPAPFLGRMPQG
+>GCF_020097155.1_00183
+MVCMKHFDDPVLQAMASRRSVSKVGPTTPSDEELARLLVAVTPVADHKALRPWRLITLRG
+EDRAVLGAALDAAAGVERAEGERNEKPYRAELLIAVVARHVPHPGVPEWEQHATAAGAAH
+LLELALWQAGWGVMWRSGLHANAPQVRAAHGLADDELLMGWLYVGDVDPEHRVKLAASRK
+PALDPAPFLGTMPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002252.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14e2b2e0addf2fa5ac01412550f949e4d63bec5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002252.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_00345
+MAALTAVVVLGVAGCTGPEGRTGTTTDGPGTSTSPPPVVQQSEAAAHPADNLPLGGEPWA
+VVTLTRGGEALDPGPWRQVRIVTSEPFILAAPELCPQPRFGITAVTESAWEATPDVAQPA
+IGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEMRLRRADVELVLSEEG
+>GCF_020097155.1_00283
+MRPSAPPRRPRVTRMAAMTAVVVLGVAGCAGPEGRTGTTTTDGPGTSTSPPPVVQQSEAA
+AHPADNLPLGDEAWAVVSLTRGGEALDPGPWRQVRIDTSEPFILAMPELCPQPRFGITAV
+TESAWEATPDVAQPAIGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEVRLRRADVEL
+VLSEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002253.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..103f387523ad7d7781e9e843ada880038d61356a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002253.fa
@@ -0,0 +1,17 @@
+>GCF_005280335.1_00347
+MGDDNARMIRRFRSSSTRRPLHRSLTRRGTRPRRRLHTDDRVSLPPSSVAGLFVVPFLAT
+HLFAWGLFASVYLIAHPGGDSVFTASMWRLTTDVAVNAGLAMEDSLLALTSTGVAVTVAL
+YIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPASMIPELLL
+QGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIQGKFGGDFTLP
+PMRQWAKAARTLTFRRILRLLIWFFGYLLAGAFLGALTFACTSLTLEREWDARTLALGAL
+IGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLTTGLVLLSASPSQGSASLGTAV
+LGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPRPLLGTTC
+RTSPLRDAAR
+>GCF_020097155.1_00285
+MVPFLATHLFAWGLFASVYLIAHPGGDSVFTASMWRFTTDVAVNAGLAMEDSLLALTSTG
+VTVTVALYIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPAS
+MIPELLLQGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIRGKL
+GGDFTLPPTRQWAKAARTLTLRRILRLLIWVFGYLLAGAFLGALTFACTSLTLEREWDAR
+TLALGALIGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLATGLVLLSASPSQGS
+ASLGTAVLGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPR
+PLLGTTCRTSPLRDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002255.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91097bb8ec2aac804b66c65ea8bee2a1eb24cacb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002255.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_00368
+MVRVTEVDPATSIDELSDRAELIVRGAPGEVDAPGDGRTRITVDASETLAGEGRSASSST
+CSASPTRAPPTARRARSCSGS
+>GCF_005280335.1_01750
+MVLIARSARPVVALATALALALTGCAAEAAGPVDGDSAAAPAPTSTGASPSAEEAFWARY
+QATMVSEVDPALSFDDLTEKSTVIVRGPVMAAAGVREVDGRVVVAPADGDQTSSLLTVRV
+EERITGEAGDTVRVWVAGPAPTAEPPTESYLWYLMPADTPDALFTVSRSGVIGPDAGGTL
+STVMVPGDGEFILPDGAVTLADVQRRTEELLER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002257.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da726fb747b22d2301c8b9f7a014d237ae65a0b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002257.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_00395
+MIAFIDEHRDQFGVEAICRTLRATECGFITST
+>GCF_020097155.1_00664
+MIAFIDEHRERFGVEAICRVLSATECGFITST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002267.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1df696495ccea0af9fc2222ca24e625bbcfeb657
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002267.fa
@@ -0,0 +1,10 @@
+>GCF_005280335.1_00517
+MTSVLFVVSAADAWTLKDGTTHPTGFWAEELATPHRLFREAGWDIVFATPGGVPPTVDRA
+SLGEAAGSEEERAALTAHLESIRAELDAPLRLEDVDDREFDVVFYPGGHGPMEDLAADPV
+SGALLSRRVTAGDPVALLCHAPAAALAAKDADGANVFAGRRMTAFSDEEERAGGLAEQAP
+WLLETELKEAGVVYEKADEPMAPKVVVDGAVYTGQNPASSAELAERLIADLG
+>GCF_020097155.1_00466
+MTKVLFVVSAADQWTLKDGTVHPTGFWAEEFVVPHQTFTEAGWHVDIATPGGRVPTVDQL
+SLGMMAGSPAKREQLRAALDRLRPALERPLVLADVDDSAYDLVFYPGGHGPMEDLAYDPV
+SGALIARRLLDEAPLALLCHAPAAVFAAKRADGTIVAEGRRMTAFSDLEEKLNPFARKAK
+WTLEAQLKHGGVQYEKARFPMQSHVVADGALYTGQNPQSSAALAERLVHDLSARVER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002268.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3ffd27da081f370f8f1889a2bdc02159293b9a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002268.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_00521
+MVVIAGLAVRLAFDGAWTGPVGDALYAVLVFLGVAWAEAFPPARLVFGTTFTAADLGLYA
+VGVAAATAADALASRARHGSGLARGPAGS
+>GCF_020097155.1_00476
+MSAPAAPGPTTTTPRRRSRLALAAAATVAAGLLVRVGLRGVPGAAAWTGPLGDALYAVLV
+FLLLAWIAPRARTLPLAAAAFGVCAAIELFQLTGIPAALGRAFPPARLVLGTGFLWSDLL
+LYLAGVLAAAAVDAALRRRAALSPRGSGPRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002269.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cff92cb9819e467c4d88a4c58cbb483347e58599
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002269.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_00523
+MSLFETADDRVSVDVWSDVMCPFCLIGDRLLGQAADRAGHPVQVRYHSYQLQPDLPADRT
+RPVLDMLVDAKRMPREQVEEMDRQITARGAEVGVEFRQDIALAVNTRDAHRLSHVAAEQG
+LQHAMVQALFRAYFTQGRNVADHEVLADLAAEVGLDRQAALDALASDAHADTVDADVEAA
+RRLGIGGVPFFVVDGKYAISGAQPLEVFERALAAAWADKADGAPPAG
+>GCF_020097155.1_00072
+MKVTVYSDVACPWCYIGKRRFETALAGFEHAEQVEVEWRSYQLDPTLPERSDLTEVEYLT
+RMKGLAEPQVRRMLDHVVMQAAGEGLTYDMDAIVVANSFPAHRVIQRARAVSAEAASALE
+EALFAAHFERGQDIGDAAVLAELGAAAGLSAEQVEEALTDERWAEAVRADLAEARAVGVT
+GVPFFVLDGKYAVSGAQPPELFAQALAQTWAERAPLRAFTPAAAADDDDAPLIGQACGPD
+GCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002272.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c640be8a84af1b204f73755fe5db1b241c8f0de0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002272.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_00571
+MSQYLISVWHAPGVHAAGTAYESEDQMRLAFERVAAFNARLEESDSLVGAGGLTPPEEAV
+VVDASAAQGPEEVAAQRRIAEGTASPEGAQLGGFWIVEAPDEATARTLAGEASYACGQPV
+ELRRLQG
+>GCF_020097155.1_00498
+MSQYMITVWHAPGVHAAGTAYESEEDMQAAFARVDDFNRMLMGSGAFVAAGGLTPPGEAR
+VVDAVAASDAGQAAAQAEVREGTLAQGDMALGGYWIVEAADDAAARGLAAQGSYACGQPV
+EVRRLQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002273.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a126b8df3c572075c82e0f2360c9d9bd5ed530bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002273.fa
@@ -0,0 +1,15 @@
+>GCF_005280335.1_00581
+MNKDAQPSTELLSSIPEGHVEFGLHTFGDVTLDAEGRRLSHPEVLRDVVAEGVLADQAGV
+DVIGIGEHHRPDYAVSNPEMVLAAIGARTERIKLISAVTVLSSDDPVRVYQAFATLDGVT
+GGRAEVSLGRGSFIESFPLFGHDLKDYERLYEEKLDLFMKLRTEEPVSWTGTVRAPLERQ
+SVFPTTAHEHGLPAWVAVGGSPQSVVRAASHGAGLELAIIGGAPRRFAPYADLFRREVAE
+RGLEPRRVAVHVHGFVADTDEEAMELYYPHWEAAFTKLARERGGPLPTPEQFRQEAVHGA
+QHIGSPETVARRVADTVRAIGASRFGLKYSNATLPHGPMMRSIELYGSRVIPLVRDMLSE
+G
+>GCF_020097155.1_00799
+MDVKFHIDTFGDRTSTLDGELESHAQGVRHVVELAETAEQAGVDGITIGEHHRDDYTVSA
+PDMVLATIAGRTERLTLGTGVTVLSSDDPVRVYERFATLDALSSGRAEAIVGRGSFTESF
+PLFGYELSDYEELFEEKLALFAELRAEQPNPVSWTGKLTQNLEDVVLYPPLEGAEPLKAW
+VAVGGSPQSVIRAAGHDLPLMLAIIGGPSARFAPFAKLYRDAREKFGHAGETQVGFHMIG
+HIAETDEAALEQFAPHYLEHHKRLGAERGWGSMGMEGLMHEVRHSLMGVGSPETVAKKIA
+RGIADLDATRVNFKVQHGPIPHEYNRRSVELFGEKVIPLVKDMLAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002274.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..538a7709c7fd2a6d99ffc21dba14fd8af00f6921
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002274.fa
@@ -0,0 +1,15 @@
+>GCF_005280335.1_00592
+MPTPSSATPDPASARSASGARPADALPDDGAPVRVRLGVLVARPADPAVLDTAALAAQLD
+AAYPGLTWDVTVRQEELGDEDDDALDLLEITRDRMLDEDWDIAVGVTGEPLQQGRHTLTE
+QVSPVHAAGVLSLAHLEEAPVDAVARVVGEVLGIDPDDDAPSAADRRAAAGWARQLADDV
+EHRDREAPAAYALRVAVRNARMLLGTVRANKPWTLAVSLTRSMSTALATGALTLITTDLW
+MLSAEYNGVQTAVLGAVSVLAVTLSLIVGAHLWERPRRRAEREQVMLFNMATVLTVLIGV
+VVLHVMLMLAALAGALLLVDPDVFHVVTGEPGEFVQYVKFAWFVGGLATIGSALGAGLED
+DDAVRAAIFTRGASR
+>GCF_020097155.1_00515
+MSPARPHSPSAAAYPGLAWDVVVSAEEVGDADDDSLDLLEITRDRMLDEDWDVAVGLTGH
+ALVQGPHTLRSQVSPVHAAGVVSLDLADGGAREAVEDVVARVLGLDPDDGAPSAGERTAA
+VARARQRAEDVEARADESGASFTWRVLRANARLLLGTVRGNRPWLLAVSLTRSMSTALAA
+GALTLLTTDLWMLSAAYDGVQMSLLGLLAVAAVSLSLVVGAKLWERPRRAAEREQVAVFN
+LATVLTVVIGVLVLHALLMLAALAGALLLVDGDVFTEVTGEPASPWQYAKLAWFVGGLAT
+IGAGLGAGLEDDDDVREAIFTRGATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002275.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1820f52d92a1e2189d8b8e2d1824f2d58c0cf4c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002275.fa
@@ -0,0 +1,15 @@
+>GCF_005280335.1_00618
+MTEQRRHEVTLRFLAAPTDQGHTGTVDAGRVLEWVDKAAFAAATAWAGSYCVTAYVGNIH
+FRQPVLVGQMVEVTGTVLHTGRSSMHINTVVSAGDPKTGELTEAARCLVIFVAVEEGKPV
+PVPEFVPRTLEQELAAEYAVSRIAVRDEIQAAMEGQRYTDAGTADRTVLRFLAAPTDVNW
+GGKVHGGIVMEWIDTAAYLCSTRWAGRETVAVFSGGVRFYRPLHIGDLVEVEARLIYTGE
+KGMHVAVHVRSGDPKTAQLELTTYCLTVMVARDDDGDAVPVPAWEPVSQEDKALWQHARD
+LLEIRGRAPGNRLPNHLLAERGED
+>GCF_020097155.1_00543
+MTDDAARTPASTDAARPSPGPVPAPASPTEPATPVVERRREVTLRFLAAPTDLGHSGTVD
+AGRVLEWVDKAAFAAATAWAGRYCVTVYVGNIHFRQAVEVGQMVEVTASVLHTGSSSMHI
+STTVRSGDPKTGELTEAARCLVVFVAVGEDGRPVPVPEFVPRSLEQELARDWAISRIAVR
+NEISAAMKTQRHTDAGTAERVVLRFLAAPTDVNWGGKVHGGTVMEWIDTAAYLCSSRWAG
+RDTVAVFSGGIRFLKPLHIGDLVEVEARLIYTGNKGMHVAVDVRSGDPKTDDLQLTTNCL
+TVMVARDEHGDAVPVPAWKPVTDEDRALWAHARTLLEIRAKAPGNRLPDHLLRERGEGPD
+RGEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002278.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21fd3c249015c355c10284cffe1df75ad68bbdbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002278.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_00645
+MTAPHAIPPSGLPSAAEVRRVLSALVQRCFSRETHARLLDADVSEGVLTVVAWQAGPSPV
+VPGRVIGHRTDLGMRLAECEGDLEAVLLDVLQFQEFEPSAPGRAASGAEPAWLLERYPEA
+TWYAQGASGT
+>GCF_020097155.1_01292
+MPSTEAVLSILRRLERRHFSRDAYARLLDADVTGEVLTVVAWQGGPSPSDPERVIAHRTD
+LRQRLTECRGDLEAVLMDALQFGVYEPSSPGRPPAGDEPARLLEKYPEATWYE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002283.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad14976ec974e6c79c9b3863e06f33e61b233b00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002283.fa
@@ -0,0 +1,10 @@
+>GCF_005280335.1_00754
+MSSAKNSDQRRQDRAAVLQAHWAAEAKAARKQKVLWGAGGVTAVALVGALVTVAVVTDPP
+PPTRQDIEIAGLETFEDLDAMHVNSPVDYEQDPPVGGDHASTWLNCGVYTEKVPKENAVH
+SLEHGAVWAAYDPSALSEEEITALQEALPDTHAVVSPYEGLESPITLSAWGAQVAVETPD
+DERIEEFVAKYWQSPEAPEPGAACTGGLDGPGRVA
+>GCF_020097155.1_02190
+MSTKLMADPEAKAERRRKVLVGAGALTAIAVVGGLVTLAVIQNPPPQAREDIEIAGLQTF
+EGLSANHVSTPVDYEQSPPVGGDHASAWLNCGVYTEPVPNENAVHALEHGAAWVAYDSEA
+LSQEQVDALRTALPAAYVVLAPYEGLDSPIVLSAWQAQVAVDSPEDERIEQFVAEYWQSP
+DAPEPGAACTGGLDAPGRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002284.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f823865e1255ba734ecf8e38cef67bcd757ec01e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002284.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_00759
+MPVRLRPAVLDDAKALTALARSQREHLAPWEPERPARWFTEAGQREALEQADCDRAAGRS
+YAFVITDDAGHLLGRLTLASVVRGAGQFCSIGYWVALEATGRGVATAAVEQALQIAFGEL
+GLHRVQAEILPHNHASRRVLEHHRFQRYGLGHV
+>GCF_020097155.1_01982
+MEITLRPASPGDAEELAALTLAQREHLAPWEPERGPGWFTVDGQRHALRAADADRAADRA
+HAFVIVGASGAIVGRLTLASVVRGAAQFCSIGYWVAHEATGRGIAGEAVRRGVALAFGPL
+RLHRVQAEVLPHNHASIRVLEKAGFLSYGRAPEYLRIAGRWQDHLLYQRVNPDWRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002288.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a681394325c59e054860701ad706adba67805a02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002288.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_00861
+MNDILTVGLVGVGRLGSAVGQLVAEAGHRLLVADRPGSRVFRSVVETLLPGADAVPLADV
+VERADVVILALPQPALADLDLARARGVLLDATNAWEYTDGPDSIHRMDPLAWTERVPGVP
+VVKSLNHAGYGELLMDARPAGAPGRRAFAVAGDDGAAVDLVASLVDSMGFDAVPTSAADA
+PLLEPDGAVFGRRFDEAGLREALPHAAARVG
+>GCF_020097155.1_00800
+MNDTMTVGLIGLGKLGSAIGRLTAEAGHRILVADRPDDPVFGLVLESVLPEARAVPLAEL
+LQEADVVVLAVPQPALAGLDLTAARGIVVDATNAWEYTDGPDSEHRMDADVWAARAPGVR
+VVKSLNHAAYAELLADAREHGAAGRRALAVVGSDDDAVARASAYVDSLGFDPVPGPSAAA
+PLLEPDGPDSEHRMDADVWAARAPGVRVVKSLNHAAYAELLADAREHGAAGRRALAVVGS
+DDDAVARASAYVDSLGFDPVPGPSAAAPLLEPDGPVFGVRLDADGMRAALAEGLEADSAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002290.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9ff3edeacc06cd7848167e0d2288b4364847fb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002290.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_00897
+MTSTPTRAKRKQTARELAERFGVSPRTIRRTVAQERADYLADAAARHERIRALRAEGLSM
+RAIAAKEGVTVGTVHYAIHKDD
+>GCF_005280335.1_01315
+MTSTPTRAKRSQTARELAERFGVSPRTIQRTVAQSREDYLNEAAQRRARIRALRAEGLSM
+RAIAEREGVTVGTVHYALHKEDQQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002296.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c47e933900b1bce8a5f7f7a229b8e8be430fdc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002296.fa
@@ -0,0 +1,10 @@
+>GCF_005280335.1_00947
+MTPADHRPEPDTAPEPEAFPALEDPYRRSLLTNEQRNAWAALSAASLGLVSQMESDLHRD
+AGLTPFEFHLLYVLGAEEVSREAEGTMPMSRAAQLVDSSLSRLSHVVRRIEERGWVERRP
+SAEDARVTLVGLTPEGRRRMEAAVPVYDRMVCRVFVDHVAEEDLAEVTRLSMRLLAGLRE
+GHWLLDAMDPHGSRRAGVAGADAGADAGAVTGATGESEEDSEGRPAS
+>GCF_020097155.1_00887
+MTKDAHHEKDANAHPPLPPLPPVWLKDAGCSGADLAAWIALLQAASALQARVESDMHRGA
+GVTPFEAHFLAVLKEAGGEPLAMSRAAHLVDSSLSRLSHVVRRLEARGWVERLPSPEDAR
+VTLVRLMDEGRRRIDAAAGPHRALMEDVFVTALDAADRQEAARLSLKLLGVLRPGHWLFT
+EPTGPDEGADPDAASHVGEPLTSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002299.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd88450e0c1c6fdee900d569220a03237bf7a4a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002299.fa
@@ -0,0 +1,10 @@
+>GCF_005280335.1_01005
+MDPVSTPTDPHRHPAPDARVRVQAGDAVVADGPLWARAALFAVPAVWLGLLIGISLIEAP
+LKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGPGRLWLG
+GLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVALIVAVA
+RHLLVRTTAA
+>GCF_020097155.1_00949
+MSVPPHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGISLIEA
+PLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGPGRLWL
+GGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIALIVLA
+ARHLLPASPGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002301.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ef6826120992cb95583e2568570a5eb7b633dc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002301.fa
@@ -0,0 +1,12 @@
+>GCF_005280335.1_01012
+MKIPAAITGGVAAVLVLGLTSCGASEVRPDHGVTARLDRENGQVVLPIEDYAASQADEAV
+MTQARLAILRSCLQKSGHNGVKPPTSNAERAVEERPYGVWIVDRARAYGFDLPPAAETVE
+PAAPPGGWSDEADPAFNEAYEACSSEVMEQMLAVSSPATSPGTTSVIADVTARARGLAAQ
+DPVWDEARDEWQQCLRDNGLTPVAEEGAVLSAESENLSDTRDAQGQTHSVKAEEIRLATI
+EATCNEQTRLTQRLGDLEAGYQAALIKKHEAALVEEKLVTAEHLEAARAYLARHQ
+>GCF_020097155.1_00955
+MRPDPRPFRLAVIAGIALSASACAQSGAPDVPPDTSATAHLDREHGQVVLPVDEYSLDHD
+SEQLIGQARHVIMRTCLNSKGVNGLAPTATSSPAEERPYGLWRTASAAQNGYTMPRPAST
+EAPPLGGQWSEESDPAFNTAYDACNEIVRDDLDSVTPPETERTTAIDIRDDAFTLASATP
+EWKEARKQWHDCLTSRGLTPRTDDNAWSSEQGFGILTTADPQNPSPAAKQEEIRIAVIEA
+TCNEQTQLTQRLGDLEAGYQAALFKGKEAQLAQEKADNQKFVDAARAYLASHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002302.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e79a30c24067193b43ae03f6ba2a86371e4e3186
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002302.fa
@@ -0,0 +1,14 @@
+>GCF_005280335.1_01023
+MSPREPAPLPAAFSDLPFGAADLRRAGVSVERTRRADLRRVSQGLHRAREAERGEWADLG
+YPVDPLPWVPEEAAAVVPLTGGVVSHLSALLLHRLTVPPWVRPDGRLHVSRRHGRGVCDR
+SGVATHGRSVPQEDVVALHGIAVTSVERTWLDLASLMPRGPVDPLVIAGDALVNRPWIAG
+DGRRGEPVTSVESLRAALRRAGRFKGVRAARAALDLVRVGADSPPETELRLALVDAGLPE
+PELQVSGDPGDRFAPVADLGYRDWRLALQYDGGHHRSREQQARDARRDGWFHDRGWRSLR
+LTADDRLDGFRRAIAWVRRHRP
+>GCF_020097155.1_00964
+MAPRAPLPLPAHLADRPFTRVDLTTAGWSIERARRGDLVRVVHGVHRSWEAETGDWADLG
+FPVDPVPWPPVDAAAVVRRARGVLSHQSAALVHGLVVPAWVRPDGRLHLSRPHDRGLSGL
+PRVQTHARSVPPVDVTSIHGIPCTSLERTWVDLASLMPRGPVDPLVIAGDALVNHPWAGE
+GQARGAARTTVVSLRAALERAGRFKGVRAARLALDLVRVGADSPPETELRLALLAAGLPE
+PELQARIDPADPWAPAVDLAYRPWRLSLQYDGAHHRTREQQGRDARRDGLVQDAGWRSLR
+LTAEDRHDGFRRAVEWVRRHGSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002304.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89db609d250176d3adffcd552b73f49a6de5bc03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002304.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_01138
+MTARRGPLTPFFDSVRTTGFRRTRPRLVGGVAAGIASGTGVNVWLVRLALVLAGLLPVLG
+VGAYLAVWALTPWEDGTVPAERALGGR
+>GCF_020097155.1_01067
+MTPVSRPRPGGARRTPLTPVFDGIRALGFRRTRPRLVGGIAAGLAANTGVDVWLMRLVLV
+LVGLLPVLGLGAYLVVWALTPWEDGVIPAERALSGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002309.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a09789626f84e3dfa02be1b400df66af1c58116
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002309.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_01296
+MSADIDAYQDQLVAWRRHLHQHPEASFEEHETVRYIRAELEPRLPGATFENLTPTSLVVT
+LDTGRPGPTLGLRADIDGLAMTEDRPDLDFASTTPGRMHGCGHDGHTATIMSALVWAHDH
+RDELTGTVLGIFQHAEETPPGGAKEMVETGRFADVDYFFGFHYWSTLPTGTVDIKPGPAS
+ANSDRFEVHLRGEGAHASTPEDAVDVVTAASSLVQQLLLIPSRRVAGLDPCVVSTTWMDA
+GRQSALNVYPPEAHIGGVVRTHDDDVRDTVEAAMRDMVRGLETANPGLSCELDYLRGYDM
+VWNDPARTAVVHELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDA
+GHHNPRFGLDEDAFPIALRLVVEVLRNGPRLAAG
+>GCF_020097155.1_01205
+MVQELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDAGHHNPRFGL
+DEDAFPIALRLAVEVLRNGPRLTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002311.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a48113ab73635eb23c27a0d7ae4c4bc8961f4efe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002311.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_01319
+MDNVGIAVRDLEEAVAFFEDLGLTVLGRDEVSGEFAETAVGLEGNHAKIALLATPDGHGK
+VELMQYLNPEPVEAEPTRPNEIGMHRIAFAVDDLDAALAAAVRHGCRPLRGVARYEDAFL
+LTYVRGPSGILVMLAQELKAGE
+>GCF_020097155.1_01227
+MGIRFENVGIAVEDLEEAVDFFQGLGLVVVGRDEVQGEWADTAVGLDGNHARIALLTAPD
+GGPGVELFEYLHPEALPTPDTLPHMIGMHRVAFRVDDLDAALAACDRRGYAPLRGVADYE
+GVFRLTYVRGPSGIVVMLAQATGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002312.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4b2d666ae25b76af40c9b9b9aabc844d0510d48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002312.fa
@@ -0,0 +1,37 @@
+>GCF_005280335.1_01502
+MKNSTASGSGFQFDASQPYQLDAIASVVDLFDGQPKDAEKLVTTLRSAAVLPESDQAALD
+IDLTQEVGAVGNSLVLDRDLILANLQRVQDRNGLEVAPALAGDALDFDIEMETGTGKTYV
+YLRTIFDLAVRYNFTKFVILVPSVAIREGVSTSIRLMREHFENLYKPQGVTFDASIYSGK
+SAEEVQSFATSTNVQILIMTIDSIRGNANTRIIHQTRDKLNGLRPIDYLKATHPVVIMDE
+PQNMESQLSQSAVGELDPVFTLRYSATHKKQRNVVYRLDPVDAHDLGLVKQIVVAEVAQQ
+GADATPYIKLVEVRREPSWSARLELSCRKADGSLERRIVSVKQHQELSDARLTNNPIYEG
+WRINEMSIEPAYVDLTLHGFLYEGESIGASAGAIYREMIRETVREHLRKESMLRAKGIKV
+LSLFFVDKVASYLGDGTNNDDANGDFVQWFDEVFVEERAKNARYQELLPQAPSKLRRAYF
+AQIKGKKGAPNAFVDSDERRQGAREDDAYELIMQQKERLLDENEPVRFIFSHSALREGWD
+NPNVFQICTLREMGAETERRQTLGRGLRLPVAKTEDGYTRVADRGVATLTVVANESYTKF
+ADALQREYKEAGVEIGRVRRAEFSKIPLQDENGALTDDQFGYQRSVLVWEHLKDKGFIDK
+DGAVTSKFQPNQLGFDLGLPVDFAWAESIIIELVERANIGKYVKPVSKRQPRMLNKQLYS
+NPEFEEFWETISQKTTYRVRVGRDQLIENAVRAIREAPQIDALRIQVTRAGVKVLRGGAK
+GEELGTRSADLKGSYDLPDIITELQEVTSLTRKTIVDILIGSGRLGEFIGNPNDFIAMTK
+RALQSELAKIVVDGIQYERIAGSVYELRELQRDGAEEKERFLDQMYKVQHTQKTDFDYVV
+FDSDVERQFAELLDSREDIKLFMKLPAKFKIDTPVGPYNPDWAIIKQEDGEDRIYMIRET
+KSTLDDSKLRPTELAKIKSAKRHFEAIGIDDYARAVPGKWNL
+>GCF_020097155.1_00290
+MKLQFSTKQYQTDAVASVVDVFSGQPRDPGPQYQIDPGRRASTGEDAAVALTGYRNAEIA
+LSLSALLEGIQRVQRAQNLPVSTRLATSAAAPGRPNLDVEMETGTGKTYVYIKTMMEMHR
+RYGWTKFIVVVPSVAIREGVKKTFDITAQHFQQEYGTRPQTFVYDSSRLHEIEAFSSNGG
+VQVMIINIQAFNSSSKDNRRIYDVLDDFQSRRPIDVISANRPIVIIDEPQKIGAAKSLSS
+LANFNALMVLRYSATHEVDHDKVHRLDALDAFNQKLVKRIEVRGLTVRGLSGTTAYLHVS
+DIEVRQGKNPRARVETEMQSAAGTIRRKLAWVTKGTSLHDLSGGLEAYQGLTVVDVDARR
+NVVELSNGDLIESGQLADHDVTEDTKRRIQIREVISAHFHREREMFRRGIKVLSLFFIDE
+VAKYRDYDREDTLGDYARMFEEEYVEARDAVLGELETEDDAAYRDYLRRDEVSAVHEGYF
+SVDNKSRRMVDGKVAGRGDEKGQSTDTDAYDLILRDKERLLSLKEPVRFVFSHSALREGW
+DNPNVFTMGMLKRSDNEVSRRQEIGRGLRLAVDQHGVRMDDPATVHEINRLTVVTDESYT
+DFVTGLQTEIAKSLKGRPRKASVAYLTGKTLTTHEGEILTLNKEMAELLHRHLIRNGYVD
+DDDLLTQQYLNEREAGTLAMPSNEKLLGVVDFCWPLLDALHTGVDIVEPSRAMKRLPVNR
+HNLERQEFQRLWERINRKAVYRVQFDSEELVQKAVTALDEKLRVTGLTYTVETGVQGEDL
+EAEHFRSGQGFTSSAITTQKESATSGSRVRYDLLGEIAERTTLTRRTVSAILRGIRPDTF
+AAFPKNPEQFLTEAGKLINEQKAAMVIEHLAYSPLEDTYDISVFSENQTSQDFTLASEKL
+EKHVYDYVVTDSDVEKRFVTQLDASTEVAVYAKLPGGFTIPTPVGDYNPDWAIAFDEEDT
+HVRHVYFVAETKGTSSSFELRGMEDAKIRCARKFFDALNRKNAGDVRYDVVTDYNGLMDL
+VKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002313.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7f8290fc4386550651f1eefd9e6564fcf833504
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002313.fa
@@ -0,0 +1,18 @@
+>GCF_005280335.1_01644
+MSAPHPRPLLLRGARLTTVETADVLVAEGRIAALGAEAAAQAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPKLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSQLHVC
+HVSTAGSVRLIRWAKEQGVRVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+EALADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQHAMVDTGLMDWAGVA
+RVMSVTPASIAGLEDQGQADERGVPRVGAVANLVLVDPEARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPAQPYRHPAVAEAGGRA
+>GCF_020097155.1_01541
+MSTTVPPALLFRGAALASGRVADVLVSDGRVAAVGEVPAVDAEGASVVEAAGTVLLPGLV
+DLHTHLRQPGKEDAETVETGTRAAARGGFTAVHAMANSTPTADTAGVVEQVWRLGREAGW
+CDVHPVGAVTVGLAGEALADIGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKSFGGF
+VAQHAQEPRLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVCHVST
+AGSVELIRWAKAQGVQVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVHALRAALA
+DGTIDTVGTDHAPHTAESKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWSGVARAMS
+TEPARIAGLQDQGQADESGEPLVGAVANLVLWDPAVRRAVDPETHATRSRNSPYRGMELP
+GAVVHTVYRGRRVVADGELTQPVVHADAPEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002316.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d7fc82769eb2c08c4a407fc65533fd744d3c954
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002316.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_01924
+MTDLAAEHPRTDAVDSVSTRTHDEPFAVVGPWKDDPAAAGTAEKVKVTDEMLELVEAVRP
+TLLADGMFLVGLDIVGDKLMEVNVFSPGGLGSCQSLYGVDFAPAIIEDLERKVSVRKHYK
+GQIGNANLATI
+>GCF_020097155.1_01875
+MKIGFVVNDVATEKPVYTTTRLAMAALQAGHEAYLVGAGDVAYEPDGSLSVLAHGTQKKH
+RSLERLLEEVQDPANAAQMPVDELDVVMLRNDPADDATERPWAPTAAVSFGQLIAAAGVL
+VVNDPHTLANALSKAYFQHFPELVRPTTLISRDEALISEFIDERGGKAVLKPLQGSGGSG
+VFLVDRKESPNLSQIVEAIARDGYVVAQEYLPEAKNGDVRMFVMNGRPLEVDGRIAAFRR
+RSSSDDVRSNMSAGGTAEKVDVTDEMLALVEAVRPKLLADGMFLVGLDIVGDKLMEVNVF
+SPGGLGSCQSLYGVDFAPAIIQDLERKVATKDHYLGRIDNTRLAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002321.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47a5e2ed781c5192cca73c8cea93adc0ac2b67f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002321.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_02345
+MRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLALEHALLSTGASRGREGLVHHS
+DRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWESVEEV
+ELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>GCF_020097155.1_00308
+MYSRRIVGWAVSGSLHTAGLPLLALEHALVSTGASRGRQGLVHHSDRGSQYVSLAYSDAL
+ITAGVTASVGTVGDSYDNALAESVNGLYKAELIHSKRIWESVQAVELATMGWVHWWNTQR
+LHEALGYRPPAEVEAAYTHDQDPAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002322.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a02cc18679b7e78b6e2be488731b9024f7321a72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002322.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_02361
+MDENPSTAWTGTCGFRMLPTDDFAQGPSTARLTEVAGGAALALDYTWVHPEQGEQAGHLV
+LGRPDDGGRVTVAFTDSFHQSPEVRVLEGTAARTEGGGDAGRDRGAGAAPHPIDGDGVAV
+TMEYSGWGWTVAVRRQGGRLAMMMQNVVPAGVEGAEPGPYDVMRAAWTPAGA
+>GCF_020097155.1_02252
+MSLPSATDWTGTCGFRLYPTDEFSSGPSAARLTPVAGGAALALDYTWVHPDQGEQAGHLV
+IGRPDDAGRVTAALTDSFHQAPEIRVLEGASSSPEGDAHPVEGEGVAVSMEYSGWGWTVA
+VRLQGGTLAMVMQNVIPEGVEGAEPGAYDVMRAAWTRTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002323.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..689a628c00e2ca8dfdfb817466bc12e41c7e6d12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002323.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_02554
+MFGGGMMRDLMVGSGWLGLLACMVLGGIARLPLAAAGTRRAEGRPWAVQGVLGFGLLGLA
+LLAALPADPSPAWYPREDGDERRG
+>GCF_020097155.1_02424
+MFGGDSMMQDLMVGSGWLGLLGCMILGVLASVVLGTAGRRRVQGRPWAVPGVVGGLLLAA
+AVASALSSFGTFFGFMGIAFAVFMGIGAWNAFTTPARAAERLREQEAHAERLGAAYARGA
+ATGPPAPHSPDAAEPGQAPAHDPDWYPATPGGGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002324.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48e6c41cf587a2e84666ac0267a1a2e9792ab5ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002324.fa
@@ -0,0 +1,13 @@
+>GCF_005280335.1_02638
+MSDTLRVVASRRYGTLSPLRYPGGKAALAGFFGDIIDALRVERARYIEPYAGGVGAGIAL
+LREGIVEELVINDIDPAVYAFWKSAVGDNASFVEMVASVPLTIAEWQKQREIYRSRDERD
+ALRLGFAFFFLNRTNRSGILNAGVIGGQRQEGRYKIDARFNRETLIERLTAIGGLADQIT
+VSDLDGRTVIQRYAQDDRAFMYIDPPYVQAGSQLYLNAFDGRDHTALAAIVNTVEKAHWL
+MTYDTAPLIEKLYREHFQCRLELTYSARYPGQAEELLVASPAVAGVVKALQGQTVMADAT
+SA
+>GCF_020097155.1_01769
+MTALVMDSPLQVRASGRNAAFSPLRYPGGKAALANFFGDVIERLGISNARYVEPYAGGVG
+AGIALLRQDRVQELVINDIDPAVHSFWRAVVEYPDKFADLVVNTPLNVDEWRNQKHVYRE
+ANESNYLALGFAFFYLNRTNRSGILNAGPIGGMDQSGNYKIDARYNRQQLAERISRIGEL
+SSRITVISLDGASVARQYAGDPSSFTYIDPPYVEAGGSLYLNSFTYRDHAQLAKSLDRCP
+DGNWIVTYDPSDFIRRIYAKHDVREYELNYSANRTGKARELLIASRPVARVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002327.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c93fa4ca725f459e527bc32dc3d43039ce23f98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002327.fa
@@ -0,0 +1,5 @@
+>GCF_005280335.1_02670
+MCRAVTCKTCGKTTWAGCGQHIAEVKRTVPAGQWCPGHDKEKEKAAATSGFFARLFGR
+>GCF_020097155.1_00542
+MCRPATCDVCGKTTWAGCGQHVDSVKASVPAGQWCDGRHTPAEQAAARKDAPARGGLLAT
+LFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002329.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60bc2ece49c7a8c2c9d7d000ad3aa7a2bd146eec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002329.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00003
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHATTNHMLSNPKAYSHPAGTTTGTIH
+>GCF_020097155.1_01380
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHVATNHMLSNPKAYSHPAGTTTGTIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002333.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ceda80e0057b7c5e2b6d4538cad2afe06af34daf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002333.fa
@@ -0,0 +1,10 @@
+>GCF_020097155.1_00306
+MSDQNAVLVEYVDPDAVSLPLRVRARSEVWLPAFVVAVVLWVLFVMILLGLPPVLFEDPS
+AMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEAIWLNP
+THGLAPDKKTQVGFAVHERAWTDELRRGNRWDSGFPFGLGGMKPRDGMIMTQFATEPPIQ
+SLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
+>GCF_020097155.1_00334
+MTVSDQNAVLVEYVDPDAVSLPLRVRARSEVWWPAFVVAVVLWVLFVMILLGLPPVLFED
+PSAMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEEIWL
+NPTHGEAPDKKTQVGFMVHERAWTDELRRGNRWDSGFPFGLGGMKPRHRVIQTQFATDPP
+IQSLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002338.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8895624408f5ad83b7768a48b1cff8f79422c1e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002338.fa
@@ -0,0 +1,6 @@
+>GCF_020097155.1_00332
+MGAIDQSTDNDADYDVIEQTWLDAGQTVKELVDRARTLMEENDDIAAGAHQKAGNHMGLV
+HV
+>GCF_020097155.1_00337
+MTIQYDSAAAAAYEDEVLRIASRIETILGDREQQKRFVADNYQSTDNDADYDVIEQTWLE
+AGQTVKELVDRARTLMEENDEIAAGAHQKAGNHIAGMRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002343.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cc20a3ccc1a52e1aeb4f84bdddb5d7ccd02242d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002343.fa
@@ -0,0 +1,13 @@
+>GCF_020097155.1_00633
+MSTLLPIRPRPAPEEALDSYLERVATANGVTTSGFVRQLTTEARAPLRFTNIAPPPPILD
+VLASWTGTDRGLLQDCLLTRYPVIPFIDSQNRHGTRSVVAHGWVLLNRSQACPWCLAETG
+VWKITWRLAWVTACLDHDRLLATDCPGCQKPLRTTHHGALRPAGPGARCGNPRPQGQGKR
+CPFDLSRISPLSAPPPVLQQQRRVERALRGAEVEVAAIALEGTTYLRQLQALTSAAMGLS
+APTTAVQPEYSEGVPAEISTLSGRARPAPRPADIRAAAYVRRDRTIFAPP
+>GCF_023573625.1_02215
+MITPLPVRVTPGPNEAMDSYIERVAAANVLAITPFTHHLKRLSGSTLRFLNAAPSPELVA
+TLARLTDTPESALHELTLSRYEVVPEIHNHHRYAARAASAKGWFSLIRTQACPACVGEGQ
+PWASYWRLPWVTACLKHGCLLITRCPGCRVKLRSTRLQGLRAGGFTPLCGNPRATGRVPQ
+CEDDLGTTALTLAGQPVLVQQQVVLAALRGSTVFCHGEPVTGTEYLRRVRSIAVLLFHTV
+AISTATGLPAWAQKLRAEAQARTKERGPRWGVSAPDCPQSRAAVFLIAHQILTGPVGAGR
+GSLDVWLDLVPPSNEGTRAWAEDHTTTPDAISYLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002344.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fe67dbd200d6c6789f35e65173cd3530c5d3bb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002344.fa
@@ -0,0 +1,20 @@
+>GCF_020097155.1_00634
+MTDQEHPPSALAPIVGESLSGYVRRFNATGLTPPLALPPRYADADLPPGLTDAVHRSTGL
+DAGQIRRMTMAGWPLILRGRGLHHRRGWALHRHDVWLCPSCTPLTGYRALRWRLALAPVC
+LRCHTLLTHERTFTPTRAATTEELARLRRLDELTTRALQGSKASRSHLSVLRRICAAGDA
+HEPDGDVLPRPPLGGTSRPAGNQRGTHPPGEPGIVMKQLATLDPALLNESRARAHLQQLQ
+HQDSLPSSFVVAPAPFQPESPTALALARARRRALLRQLTDLCAATGLRPQHIPTVVDPWR
+STRWSRLRDLEDQAFEALALHTLLLEALGEDATGSAVFVAHGIPAVVNQHDLLTRVRTRG
+TLTPGECDRLLARAQALVDDGLVDYAYRRGTLLAVPSLPRIPAVHLPRHPFWPARTLVPA
+WAWVEYARGLPDSGPAPDLSLESVDRFHADLDPEARLRLLEAFDTHVRGEDWAAIASAAG
+SSFPTFASAHQRSA
+>GCF_023573625.1_02216
+MSRPVHMPPLPGESLTGYLQRYRQSGMAPIRLDVTGVFDNASAPASVVVPVHTATGLAPE
+QIKAMTMDRWVPSIRGYRVQRRHGWKLHPHQWWICPQCTVKTGYQSLRWRLALQPVCLRC
+HTYLVDPENPQIPRPVPEATLKIVQSYDRILDDALSGSLSARQRLSGLRKTCKGMAQAMA
+HDQQPASAGAQPSTLTWWGAYPCGDPVTVGHLMTLTRAMVTRGPARRRTVPRRDRPLQSK
+RAVSGATVTAMSRARLRATVSKLAEWSQSTGLSPRHVPTIAQPSLYGTARRPSMVAQAGT
+TLALHMLLDEATGIPVSSARTRAAHGLSGEPLEHRLLHSVITRGGLEEDQQRLLLRTAED
+LITDGLIDFRLRRTVFRSQPHLPRLPTPAHWIPAGEEFSAETMTRAWIWMHVARGHPQHG
+PVASVRLDEIDDFDHLLDPETRMHLHESAAAQIDGPDLADILTTTTTHNRRARQQDLREH
+AG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002345.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e11a1ee64e3e903d60b59e40cdef19eb6ca446e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002345.fa
@@ -0,0 +1,28 @@
+>GCF_020097155.1_00636
+MNFSVDLNIGDRVLTDAGPARVKSMWALGVELETINEPAKLVPWTDLIIRPTIDGQAQAV
+DAALHPWWDQLPEKVQQDAIFKMECVLEILTGFRSGLASLAQPHEPVVPFGPFSQASVSA
+QCEAMARLVSFEKSADRELMRRVQDGELDSPGVTPRAVHHWVRRWQASGLRGLVDGRALR
+SAQGFGALDPRFLKIAEQEFARFDGSASATNRQEIHRRIQVRMHAEGITDAHLPQRLVSD
+YLSHRFAQLGKTTRAHRSRRHRKISSTASAALHHLGHCATDVTRADNLVYDEFTGKPMSV
+EIATIMSVPARVIVAVRVFPKSVSATEVALLLYDAMRPQSMLIDQDGASDWRWCGVPTSL
+QLPEQASPLANDPASGLGEHAIPAMTPTHLRMDNGSIFRSEQLRRLALHWSITLSHSRGT
+RPTDNPHIERFHETLQRFYQQLPGYKGRNVSERGSWTGVVAEAPLLTAADLERRLRQFIA
+LDYHRRPHTGLTLPGAPEVNISPLEMFDWILATTGRIHVPQHPDLIYQFLPTRWLTPGHA
+GVEYKNMTYDAAVLDEFRSKIPGRFRDEDAKVPFHYDPRDATRLWFRHPDTDRIHEIPWR
+NRHLLHAPLTDVVRDEARRRIRARGGPKALTGALIDRQLIEEIGHLAHTRADETWTTTMA
+ASRMRFDQARRDHDEAALAHRLTTPEAPTDLEHGGRHLRLVPPDAMPDRTATNGLAGLFE
+PWPDYAQEI
+>GCF_023573625.1_02218
+MRAQMSAPIQAGDSILTEHGPVEVIAPQSTGLLVRAPGGQETLITHAQVIPRRFQNGTIA
+GVMASLYPLWDQLDQAVRDDALFKLECVNEVNTGYRRGVASLALEGEPFYPFGPGWGVSL
+RARYQAMARLVSLEKRVDRVLMRRVYDGEVQRPEIGLRTLQSWGESFEEHGLRGLIDGRA
+LRKVQDFGVIDVRYRQAADEVFGQFDGEISAVNQQEIQRRIYALLRQRGQSDVQVPDRLE
+SDFLRHYYRRLGKGTRAHRSRSLRKIATTSSAALHHPGYCASDVTRADNLVTDEYTGKPI
+SVEICTIISVPTRVVVALRVFPRSVTSFELGLVLYDAMRPFSMVAADGAIDDWRWCGVPT
+GLQMSAPQCPRHVKEDEGPLGVHYIPAVTPVEMHTDHGSTYISDQFRTLLQQFGITLSLT
+RGGRPTDNPHIERFHETLQRAYQQLPGYKGRNVSERGSVVGVQADEPLLTARQLEAYLRA
+FVAVDYHRRPHTGLIWPGTEEQALTPLEMFDAMLASTGRLHYPQHPDLIYQFLPIRWLTI
+RHAGVEYKNMAYDAEVLDEFRDCRAGAFRDKDAAAPFHYDPRDTTRLWFRHPETDRIHEI
+PWRGRHLLYAPMVEIVRDQALAQIRRRAGRRHSAKVSMLELIDEIGQLATAPRDETWAHK
+LSAARMRWDQGQRDHDEVAHARALQQAHVPKPRTSRAGRDHLLSLPGGRTEDTPPAGFGL
+ADLSEPWPDYPEEHDELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002352.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08d138abd163e734e059cf1bae3f876f9f2e0daf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002352.fa
@@ -0,0 +1,13 @@
+>GCF_020097155.1_00673
+MTRMSVLEAWTWINEYGSAIGAVAGVVAALVAIIALISAALDSKARSQPMIAAEFRPAVD
+SDSSIDFIITNLGPTPARDITVTFNPPIVIPDDSDRLLAPYLVKRYERPIPVLNPGQILS
+NTWWAGRAGTGNELTNHEPTPDEVNVTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDM
+IRTERCIEEHLVLHGGHVDHAHGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMI
+LIGMPGIEKQFTHYPQLYSRLGFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQA
+IAAVERITRGNFRLLERLLPQIQRVLKINELDVITNDVVEAARSTLVIGTT
+>GCF_020097155.1_00677
+MTSQFIVTKEHRRFAEFADAVRKQNTIGVCFGPAGVGKTLSARRYAHWDSIGPFIARWAA
+RSEDDTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDMIRTERCIEEHLVLHGGHVDHA
+HGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMILIGMPGIEKQFTHYPQLYSRL
+GFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQAIAAVERITRGNFRLLERLLPQ
+IQRVLKINELDVITNDVVEAARSTLVIGTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002354.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a1ddf369a7e7f1f2910435166bb6cfafa9e3e35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002354.fa
@@ -0,0 +1,9 @@
+>GCF_020097155.1_00736
+MTKSLISSAVVVLLILLVTVLTDASTWLVGLLSGLACLAGAWCAPLFQSGSPYGGTFFGG
+WQSRWDGPKAVQLLAAGAAVAVSVVLNLFGGGVPAVVGIIVALLVGALIPVPGDPAGGGH
+GADPEDARPA
+>GCF_020097155.1_00738
+MRMTPARVASAAVLAVLTLVCLLLMLDTWSFMGALLVSLIGAVLFVAGAWFAPLARSGDA
+LGGTPLRPWQAGFDGPKTTQVAGGGLVALLVALVTGGAPLVGPILGVVAAVIGGRFLRIP
+SHAQVVAAVGPEVAEASEHLPGEHHDAAPADSVADPDTDPVPVPATEAADSEKPRHEHAA
+DVSPETAPVPVIHPADAEHPHGSHAAMAHPDPVDDVPGDGEPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002360.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd50dcdaf659fb695d282c531114c0927ac4c39c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002360.fa
@@ -0,0 +1,16 @@
+>GCF_020097155.1_01197
+MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS
+ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI
+PD
+>GCF_023573625.1_01532
+MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS
+ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI
+PD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002366.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bae2eea9dcc62609214f3334bb48c75285ef450a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002366.fa
@@ -0,0 +1,12 @@
+>GCF_020097155.1_01889
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRPLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAIPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
+>GCF_023573625.1_00896
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRSLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAMPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002369.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89264cc0bc1b68ffaeec07d6e5b3319631741166
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002369.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_02318
+MEIAFASTRHFGQGEVLRHVSADYVLKDFMEMNKVPSAAMFRRSRWAEVGGYLESMRWGM
+EDYEFWVRVLRDGGIARPVPTAYYHYRSRENSRLSTLGTHAARDTHQAIVEANPEHHAIL
+LQAAFLRLEEMHDLHLEYRSYVHKWQDRFRPLIRARDFAKRAVRKMS
+>GCF_023573625.1_00519
+MDMNKVPSAAMFRRNRWEAVDGFQEGLDGQEDYAFWVRMLRDGGMARPVPAAQLHYRLRA
+TSRAATAGSEYWEATRKAIISGNADHHEALLRAAFERLDELRADLAEQKRYVQNWQRRAR
+PLIAVRNRIRSLLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002371.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4666d511ad88c1a6bb220dd55b9a6f59b11cac47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002371.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_00036
+MTGQWEWTTLREVLVPQPNKKPLQQGWSPKCIPSPSPDSETWGVLKTTAIQPGRFDETQN
+KELPATLAPRPAIEVQQGDLLMTCAGPRSRCGIPALVRSTRPRLMMSGKMYRFRPVEGVD
+SAFLEKWLLSAEAQARIDAMKTGISDSGLNLTQDRFLALPVPMPGMEEQRRIVDIVEEHF
+ARLDVAEGSLDVADKRLEGLVESAIQLCLDWGSVRQVELRSLLAEPLANGRSVPTREDGF
+PVIRLTAIRDGWVDPLQRKGGDWSRNDAKKWLIRPGDFLLSRGNGSLGLVGRGGLVLDDP
+GEVAFPDTIVRLRPNREKIDLDYLSMLWNSRLVRRQIESRVRTTAGIYKINQEALKSIEI
+PVPSLEVQGRLASSIGGVRLAGRRIAGVVEAERRRTAALRRAILTAAFAGRLSGRSTDTE
+VIEELVASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002373.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32422d1dd78cc6180e4c9217806377556d1cc1e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002373.fa
@@ -0,0 +1,3 @@
+>GCF_002008305.4_00173
+MSSSRDAVLVVRAAGGRWKVENFFAAHPKTSETESLWDFTVPALLEAADRAGVHIEATAM
+NEKLARHYKRKIPDLRRLGVVCTGQVKLLRVPRPHPTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002375.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2347e59cd51e0553b7c61e07bc2afdff547b966
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002375.fa
@@ -0,0 +1,11 @@
+>GCF_002008305.4_00407
+MEVEGWTHVSPSLGEYRYLSGGEGQRVTAFDVTVPDSAAHLVLQGHAWKPEFPVRVNGAP
+MVLRHVHPLDTPVAPFSPDTRVRVWDFVQHVPVSPGTASIEGVVHASLPTEKSTALLTVG
+FLDEAGRPLPGPSDLPQNPTFGPFVQLRGAAEGPLETQFQIAVPSQARWVRIQGRRGWGN
+SDVMMQAEVDVTEVRSSAAEIDAFLAEIPEGDTLLVIDTTAPPLGHETLSLRPNNLARAF
+ERAGVWVVFLPFSSLQEFPARVSDRILQVARKDFGRLVRGLTTRRRSMGDTYICSSFPSI
+GAVALGTQLKTLGWQVVYECRDDMEEFNRVGYSKWYSPALERQMLIVADKVVSVSTALDA
+KLVSMWPALRDHAVIPNAVNRHVIDQSEGLRTEESFDRREHLRVAGYVGHLTPSWFDWPL
+IAEAARRMPETVFEIIGHGAPQGMSLPSNVHLLGPRSHEQLADIVTGWKAGLIPFLDIPL
+TRSVDPNKIYEYFAWGLRCVTAPMGSVETYPSTWVHRGVDEFVEKLDEALSTPWAPGERE
+AMESFVQSSDWDDRAERLLSYYGITTEGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002377.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a1effa1faf1487dee9a72e2c4753e2f104af242
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002377.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_00409
+MDYFDRIQNRLEGREAGVPGWLGAKNATRQFAAQIGIRTPEQLFKGPLSDLERFDFPERC
+IVKPGFASTSIGVHLLERRGAELWDLVKDEPVTVPGLIETLREIEGRYDLSPDDGEFLVE
+ELLSDRRGVTPPADVRCYMFQGECGFVLVEDHIAGPAAASYFNGDFSPMTDVHDRFGVHP
+GVTHLESIVDAAEPPAGAEELLAVARRVSTAVPSAFCRVDLYDTPAGPVLGEITFYPGTF
+FYKNRKVMAPEEAARLGKMWDAAEKRLAGSLLIDAPKRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002379.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68726e34d39d16cf4ffb4e899ea984ff5db7d259
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002379.fa
@@ -0,0 +1,8 @@
+>GCF_002008305.4_00518
+MKILVYGAVHQQPNIGVSALAAGAEAVLSRAFPDADIRFRSTGPLGDGPMNLSHTAPLLK
+EMVVNRRGLRGWTRSFDLLCDIRGGDSFTDIYTSKMFFKLSAFPLYAQALRVPVVMLPQT
+IGPFENRASRILAKRFMRGCRLVMARDPRSSDFAAELGRPVDLTATDVVFAIERPEPSLK
+HRDVVLNTSGLLWHAGNRHVDSDAYRAGIRGVIDILLAEGRQITLLAHVVGRTDTGADND
+RAALAALREDYGDRLEYVVPSGLDEVRSLMASANVVVGARMHACLNALSIGVPAVPMAYS
+RKFAPLLDQLGWHHTVDLNASGEQIATAVLEEIHAVEGEDLTPVLRTARARIDAAVEALR
+QLSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002381.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22865b42b86c24da756d52e3770bfed5649f0f40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002381.fa
@@ -0,0 +1,3 @@
+>GCF_002008305.4_00520
+MPNLNDFHRPALDDVTTVDPRTPLLPFLRQLARAELVVGSSLHGVILAERLGVPARVIRS
+DAEPSFKYEDYYEGTGRANVRLAADIHHALDLGGVDSGSTVDATLAAAFPRDLWER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002383.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60f609f023ca969aeab99636226a386924a1e2d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002383.fa
@@ -0,0 +1,7 @@
+>GCF_002008305.4_00590
+MSIEAMKWAQKVAETGQLNTGQAFVLLLLGDHADEAWSCHPSQELLARRSAQTVRSVERH
+IARLRDLGLVDTESRYGDGRGRIGLRYYLREEALNDLVQDAETRMNTRPDNLSGKSETRT
+KTRPDNLSGKSETRTKTRPDNLSGKSETRMNTRPDNLSGESTHPTISADSPDNHDFADYK
+DRARTNPQEPSSVRPSVRQSGAVRAETTTDDGRRTDQVIDGGEGVGLVHRGVVLADLVQR
+VPAAADLGDGQLRSIVDVVLARASGPVRKPTAFVARSLASEFEELVTVTRPRPVAVTQAP
+AASGQVRELRTGEPCQDPDVHIPAYGQAVLADCPHCRLERRAMPRALMEAVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002384.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9478c01da0234648edfa78b593975c40b7031750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002384.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_00591
+MTGQADRVAPAGMVLVTGDELAEAVASVRGTVVAVLGPSGNGDVVEDVLQSTWESAWHSR
+ERFDPDRGSLRTWVGTIARNRAVDHLRAVGRSRAGQEALEASAVAREKTAVSTVMEDPAE
+AVVEALAAHREVAEVMRVVESVMESSEMTARALAVVLAFGDDVVAASEAMGVSVTALRQA
+RRELVRCARVVRAAQEVARSGQAVTMRVLISCLPDDGDAGDWARQVALACAQAGGRMEAV
+TVEDVMQATGFSHSTSRQYLAETRHLLRVATTVIRNERAEK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002387.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..585dee3e2549891a087a53fc41fffdcf0b2a3538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002387.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_00605
+MTESRLWLLCDARAAHRQGRAGLDRRRHERLVEMVSFARARSPFYRRLYQHLPEQLTDPV
+LLPVTGKAELMRHFDDWVTDRAVTLSAARAFVEDPALVGEKFLGRYTVGTTSGTTGTRGI
+FLWDERSLAVTTALLARLLGTWLTPADVLRMLARGGRIAMVNATGGHYASAAAAAALRKN
+RWGSDRIGVFGVHTPMAQLVAGLNDFRPAILAPYATMGALLAAEQRAGRLHINPALVVLS
+AEALPEGEYDRIAATFNAKVRQGYAATECPFLTYSCQHGWLHVNSDWVLLESVDADHRPV
+PPGQPSHTTLLSNLANKVQPILRYDLGDAVFVRPDPCPCGDPLPAIRVRGRTADLLTFHT
+PAGEPVVLTSLTVTAWVDRVPGVELVQLVHTAPTHLEVRMQFSAGTDPERLWQAVHTEIR
+RLLVDHGLGHVTVARGDGPPQPTPGGKFRAVIPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002388.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50e835871e708663040c633bc14f2f995e423e53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002388.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_00606
+MPGATPIGDEAEVPTLGAVDHLRVLTRVLLGPVVKGPIVRRPAAVGLAERLDADAAGVAE
+MQRLRSRYGAGPVQLRIPGRRIALLLDPADVRRVLNDSPTPFSPATLEKRGALNHFEPAG
+SLVSTPQQRLSRRPFNEQILETPRPVHSHAEAMKAVITEEVSTLGGHVDFTGTLDWESFA
+VMWARMVRRIVLGASARDDDQVTDDLRRLRARGNFSYLMPQNRRLRERFLRRLQHYIELA
+EPGSLAALVAQTPAPDEAVPHQQVPQWLFAFDAEAWATFRALALLTNHPGATGTARSEVA
+HAPDLPFLRATVLESLRLWPTTPLILRDSTATTHWRNGTLPPDTALVIYAPFFHRDDQTL
+PQAHRFSPELWLQERDDNAWPLVPFSAGPGMCPGRNVVLLTSSLVLGELLRQHDFTAQEP
+LDTGQLPGTLSPFSSHFTVRHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002394.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e4035b1e92223141c2c2a75525c7a6a1e3fdfd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002394.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_00701
+MILADAGATGVARVRSRGGVYDVVVPDSGTDYIQGHLQREGSPYEEEMLDRMAAALLPGD
+LVIDVGANIGNHTLNLACVADARVVAIEPDSHLADALRRSVELNGAVDRVEVYECAAGAQ
+PGFGRLILHDPANLGTQSLSFEEGDAGQDVAFYTLDDLIQRQSVRMVKIDVEGFELEVLQ
+GGMEMITRDRPLIWVECLDYEAYEAVSSLLSPLGYRVVDVVNASPTLLFSPGGKQNDAGE
+RTGINAVMHRLYTERRIAESLRSKFQTITNDLEDPEARKLVTHLGALAELEIGQSAAEAE
+LKGALTDARRRIAELEARERLHLEDFRAIRGFVETVEDRLWSTRTVQAENEAAAERLRYL
+EDALELVTTEKEMALAEAGEMRATLRRIRSSRTFRAGRALSEAQSVSGASRALPRLLAII
+REEKKGRDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002397.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..427236ed0eee73c0911570c762c94f3d617872ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002397.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_00840
+MKRPERPISSDWLDLRRPADERARAGSAPLLDALAEHFTETGADSPVDVIDVGAGTGANP
+AWLAPRLRFSQQWTLLDHDADLLELVPSQLQDARVRHVRRVTAGIEDLGSLDEAEQDRCL
+ITCSAVLDLLTMDQLAGFCDFLAERRMPALLSLSVTGDVVLDPGHWADAQITRAFNQHQR
+RGSLAGPDAVGYAAGRLRADGMRVEVAESPWKLGPADDVLLRRYLHDRAQAVIEGAPDMG
+DVVDSWLAEHLGQSDEGRLHVEVRHRELLCLPPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002402.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc7fb86f9712857ede8a836df44dd051518a2fa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002402.fa
@@ -0,0 +1,4 @@
+>GCF_002008305.4_00899
+MADALSLSEKVSQRALFGAMARIWPEVMAVPLGNNSWAFEHDGPDPDWSGPHHAARTAPL
+PTVEPVPRTGPRRVGEFSGRTLLALCRGLMDSPHPDVLQDHLSEPILTAVVESALHGTVS
+PPEGMERRVFARHLWRIALADQWYGWEWMPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002404.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9c50d0c84539d756cefbdaf6bed1e4918f7f4f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002404.fa
@@ -0,0 +1,5 @@
+>GCF_002008305.4_00952
+MAKTTKYTAEVSEGRDELLDGKTIARLRTIAVKNQRGETVRELKAADNDEDVRAKLRAAG
+YTLKDWAGGTTPATLERGRNPLVAGCLWPLVAVMALLAWAIFSAFNNASPDEPEEWDAKI
+ACQTLVKEKLRAPSTAKFSRETASGGPKAWTVTGAVEAENALGGTVGHRYSCSVTFTGDD
+EYRGTATITDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002408.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7a637883c6a3b590661c6919cd4e6927ca7b4bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002408.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_01498
+MTAEPLRPNDAIAPLPTVEGGFKTVMADPPWRFQNRTGKVAPEHRRLDRYSTLSLDDICA
+LPVQDVVADDAHLYLWVPNALLPDGMRVMQEWGFRYVSNIVWAKRRKDGGPDGRGVGFYF
+RNVTELILFGVRGRMRTLPPARSQVNMIETRKREHSRKPDEQYGLIEACSPGPYLEMFAR
+KAQPGWTAWGDESGADSAPRGQVHKGYAGGAIEAPFVEPHVRLDEAVADALAEDLKTKYE
+AGASVQELVESTGYTTTRVRGLLKKANTQMRPRGRKTKQAEALFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002409.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3cb19fd12199db5174172642b09f71ecd0e81db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002409.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01499
+MSPFPSPGRISFTKFTSPEGITDVLAGVVPGVTTAAEVLQDLAAAKLADPLWDDLLSYDP
+PFEPGKSRAAGSQVAVDNELLRACREGREDRFLLLWAQLILADPRLDAIVREVFTDSTGK
+LVPEMVNASKLGAALTARHAADPDEPHDTKAVSNLLSLLERCRLVEPVKHGKTIVGVERV
+LPTAHAVPAVVRLIGERLAERGFGAQPGRELDLALALGANAWLNLTASEFRDAFDGKTPP
+AAQPQSVPGALPEDLKVIATLLRRKGQVLLQGPPGAGKTYVARRYVDWVSAGRRADSRLQ
+SIVEALPDDRRTVPAIADEIVSRGLSAVWDIVQFHPGYEYTDFVRALVAQPHGQGVTFVA
+QHRIFSLVCAVGAELARRGYELEMVLILDELNRGDIPSIFGELLYALEYREEPVASPYTV
+DGTPSLTVPHNVRVIGTMNTADRSIAVIDYALRRRFTPIDLEASDSPIRGYTGFDDETAR
+EAALYLYERTRDALSEASQGLQVGPSYFLAEPDGEDGSIAVLATRFVYEVLPLLDEYTLE
+GEVDASRVESLRQELGLGQRAKQWDQGAALAAHLVAGQPWKPAAADPEVGEPEEALSVDL
+GGPLADGGDAPASGEDTRDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002410.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16847caf382be8788a6e3dff251056777dfa364e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002410.fa
@@ -0,0 +1,9 @@
+>GCF_002008305.4_01500
+MPAEFWKAAGCRLTKSAGESSWMLEAGDLVGVSRVSTALGDVTLQVLPKLATADVFFLAD
+YAYDQRHEPLRLLPFEQVELDALRRDPAACLLVWHARAIHRFATRWLRRDYRRVDQVLNG
+KIKGKPLISRYVSQHLAVGDPARIPCRVKERTQDTPNNRLLKAGLHYILSRSHELELPAA
+RRVAVREAKAALPLFSQVSDIRTEPVSQRDLTATTHRGAMSHYRSILLSTEALLRGEIMG
+PEVGAGVSTASFMWDMPTLFQEALRGVIDSAPGLALSVEGIGRARVHAHDGKQVRSSKVD
+PDLVLETAAGGQLVIDTKYKDVLPSDHGVDDEDVTLVADRRRIKVTRADIYQVVAYTAHD
+KWRGATGALLYPVVLAEGDTLPRPMQIRGFGPPVWMLFVDVGQQAKGNLPAFLDSVRELA
+DRSAAGAVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002412.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42efefbe7279f5141077a9459d7a4813467f933c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002412.fa
@@ -0,0 +1,3 @@
+>GCF_002008305.4_01508
+MSTIYRTQEWSGHGKQNYFWNEYRLEGDTVVKYRCNRFKFFDGDENVWEHTEDAQESWAK
+GDPNMPDWLLQYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002413.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66ca383930e7ec0543575ebba432961134b601b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002413.fa
@@ -0,0 +1,6 @@
+>GCF_002008305.4_01510
+MGTLGNPHGTFRLDDPDHWIGSYLRRQDLPEILGVGDDALADLPFVKTEEGEVVDENKVH
+RALGEGRIPGALPPGSRKISLNELVLTAVLRRTFPDCEIQRQVKVKNPRTGRANTVDLRL
+DVPGQEPILIEYDGPSHFIRQYRAEIPHPLARKTELEPSAGMEIVIWPYWMHICSASAQA
+LFDPTVHGVPALWSSNKFFGDFATPDAACVIEEITGRFNAVGEEGYGTVYEAGVDGMHKP
+AHPIIESILDGRAAKETLVPNGAENPNRWLPISVRDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002422.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1151c4da22e4d81363669fa55ef60794c0a03853
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002422.fa
@@ -0,0 +1,12 @@
+>GCF_002008305.4_01960
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+MDPRKARLTTMRVVLHDEFNKSAALDLERYLIQMLSGDGAREVLNRNAGLTESDYYDRTR
+YQEMFADIFERLRAEKVFSRSREQILNSTLFKLSPFKVLTPEQEASLRHIVQLLVADDDV
+DRGPLVIEGGPGTGKTVVGVFLAKLLVDLANLTEEDVEVDLSSDHDFFDLFTHANRNALL
+RGTKGRGLRIGIVVPQQSLRQSLKRVFRRTPGLHPSMVLSVWNVGDAEERYDILIVDEAH
+RLGLRSAQSNGALNTKYTAINQRLFGDDDVSHTQLDWITQQARDVVLLVDPRQTVRPADL
+DAATMDALLARAHAEHRHHALVSQLRVKASDSYVDFFGKLLRGEHPPAPDLGEYDLRMFT
+DFGAMREAIRARDTEFTLARLAAGFAWKWQSKGFRKDPSKPDWDIELDGVRMPWNVADTD
+WVDSPGSLDEIGSIHTLQGYDLNYAGVVIGRDLQWDDTAQRVVFSRADYADTGGKKNNGY
+LSRTYSDEDLREYVINIYNVLLTRGIRGTYLYVVDAGLREQFARWFPGISGPDVTSAPFG
+VPPGGRPGEVLRTVDVGHTAEAEFILSTDDLEQARRRAEELRRSRKRTRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002425.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c9a139834604f5777e494db6754968c82faa1fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002425.fa
@@ -0,0 +1,3 @@
+>GCF_002008305.4_02067
+MRRTTYLRILAGLLLMVLLVWFWGRYALFPMEMTTGNARFIGWGLALLAGYGSYRLWMKA
+AELSEDGHDTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002427.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81ffbadafc2e59a162fd51083311eaa5866bca6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002427.fa
@@ -0,0 +1,3 @@
+>GCF_002008305.4_02223
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+LEAHNDQDGFLYRAIAVHPPHGGLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002428.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c735195a784d986708da0ac8a83651bb2c059a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002428.fa
@@ -0,0 +1,4 @@
+>GCF_002008305.4_02233
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+EAQTMRGIDVRDPSLGVHGRVDRVERLPSGRLRVVEHKATPVKRAARISDANRLQLVLQT
+MALESQGNTVEDAEVYFTTHHRRVPVELSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002434.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1642bd163fda4d4d637b907c2ea9d6e2eab23ea0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002434.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_00089
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002442.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c464ce1efc40ce5dfb87739541a7b7e0f4e85c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002442.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_00356
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002448.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f778b898970ee3c38eef589b7afe10c5977c3977
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002448.fa
@@ -0,0 +1,5 @@
+>GCF_003691675.1_00500
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002451.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59fe53aed67f573b83153cede5bfd486b62663fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002451.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_01108
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+AAAKKSGLPLVAAGPARPVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002453.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e84609cf19f28cbe2fbd0c6129581fb6cf16b003
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002453.fa
@@ -0,0 +1,8 @@
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+VDAGHLASYAGIAPVTRRSGTSIRGEHVARGGNKRLKRALFLSAFASLSHPPSRAYYDRK
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002463.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8f239827cc982ef837fd8655a1ddf51d3c01d51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002463.fa
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002466.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab034ff5cbe792b8cc4a1cbde2402afc412e43f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002466.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_02018
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002467.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..917c9dbce35a51432069058a98a881cbb2b9e9d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002467.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_02027
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+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002476.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43287dd7b15c4cbc562b499839e6998474d891a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002476.fa
@@ -0,0 +1,3 @@
+>GCF_003691675.1_02220
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002478.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ff3d37d825b6b34865a4c84df30b0d38307d949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002478.fa
@@ -0,0 +1,4 @@
+>GCF_003691675.1_02222
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002487.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002487.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b86fbd566e0ca64fd56d67f22355503a5adea65f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002487.fa
@@ -0,0 +1,2 @@
+>GCF_005280335.1_00041
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002488.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..400af01e0fc30dcab7eaab9619fbfe8728689804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002488.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_00043
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+HDARESVAAYFNRAAEEFVDVHREHFSAGPLLAHHVLGTTAAGHWGELVDAAERMSLAAA
+VLDVVDGVEDEAPASRYGRNLLHPAAADHSPIVGGPSMLRADGDLVRVGENITAFAGGWE
+WLGSPEVAPLRPWIDLATADARPGERVAIAYDPDAERADAATFAAMAADHGNVQSSQYDV
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002489.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a67fd8ed5a99061e90f7c13b9031ee54c96653da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002489.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00045
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002494.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f19fe8367243890eac0fe9749ae70fa1256b0812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002494.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00077
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002507.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b9acffbe138977a03d387be018d520f7ac8de46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002507.fa
@@ -0,0 +1,6 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002508.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..120fcbb5f7d07db938aea923ae994146b514ce45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002508.fa
@@ -0,0 +1,5 @@
+>GCF_005280335.1_00177
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002512.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cd6229ad085a1af92f2bc5f4d7c4935f9f39df1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002512.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_00192
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002517.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e494aaed9b4c78f5a45bc4140c805f2a0318eeb1
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@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002518.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c1daf22d482cb2d5a1594c3091a1543fd2c9474
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002518.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_00310
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002520.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b42e1ed0a7dcc98f1f1d5b61716d32a0d4f71d6
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002520.fa
@@ -0,0 +1,6 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002522.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c73d8657ecbcfc14a3f52a9f091f8c850ee84d3
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@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002523.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc5a49ff0bcf8805578a599c6e190d5456fb91aa
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@@ -0,0 +1,6 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002526.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d3249b5c52f51e0b73addb3dd8508acf9107d08
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@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002528.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db680d9e344726080c0c0611ee4463d7ab480a22
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@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002535.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47b2dddffa51679e79948be7cbf9c2a2a6b7b8f0
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@@ -0,0 +1,5 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002536.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..975d3c0c1039431da52a2d62d3512bef577dff68
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@@ -0,0 +1,3 @@
+>GCF_005280335.1_00467
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002537.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3c0650e1a6dbfdeca66212d5a7d488c19d4cb6b
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@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002538.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0770f588d08ca28ae73678e5d58a24d3884d2ab1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002538.fa
@@ -0,0 +1,9 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002542.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60a74f55d94c087be85fa5c342fa378983561078
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002542.fa
@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002547.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dfc0a3fbcc81d96802d35ded0c5c12c71847fd5
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002547.fa
@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002548.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..167a0c5ac66cc7b929ef83350fb18813e5e39554
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002548.fa
@@ -0,0 +1,7 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002560.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f484875b657b74358bd47810d536d61d454ca5ef
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002560.fa
@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002563.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b37672678751adcb2e464cbe338951ccb8a2a03
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@@ -0,0 +1,8 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002566.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8be753b12e602a493f858a88dfff55254221af4a
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002566.fa
@@ -0,0 +1,2 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002570.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bd7acbe91b75e0a24ccd28ab516969ec2a4c0b9
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@@ -0,0 +1,6 @@
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+EDIPDASADRRAALVRQRELVAARIDELTRLGRALDAALGRPGDETEEDTMQNEDTRRRP
+GTRPDLDLTDADLRELFGDEYAEEFDGYQAEAEQRWGETDAWAESARRTKRYSKQDWERI
+KADQEAATGLAAAALRAGEPASSVAAMDAAEAARAHITRWFYEVSPGMHRGLGDMYAADP
+RFAKTYDDVEPGLAAYLRDAIHANADRLERDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002571.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9704e657d64aacbb3e7aa1a44e015c0fa09d615f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002571.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00623
+MPKKFSPELRERAVRMVLERQATQGGPRSHSIRAVAPQLDVSEETLRMWCQRHGHEIAQA
+PVSETPAEEIRRLKRELAEARRANEILKAASAFFAAELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002579.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d2f466222d75abadf3ae7be7ca6b54c961e2709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002579.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_00708
+MVSRSSHPDTETAPGRVRIRTDDGVVLLRCARGAQGEPPRLGLEDSGSTFGLALHAERCA
+APVPGVRVEVTRSGLFAERSPAGTVLLPDDGGEPLWLSAPERSAAGQILLGVVEALRAEV
+LPGHVSVPPVPAPRARVERIARWDEVLAPNGLAGGLAPGERPSQAQQALGGAWRLVLDAA
+PDLPVEARLWLAHREQVAGEKVVRLTATWHGPGADVPWHVELHVSHRLGEGQTEFLVIDG
+STQEEWTIADAVHVPGVPLTWRVHPAPRPDTAGRTGEGLYALIDALAHACPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002580.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb799e398fe0064730dc849722a2f384a121055e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002580.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00709
+MAGFTLSRGGSTFLRMELFPGNNTYRAGTGKARGWSLHKDTAGHANKAWKLKDRSGSIRA
+SIYADGKFACDRYSQCAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002584.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb8a739df69b402f41d4efbaa7d28f01948bdb47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002584.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00732
+MPKKYTPELRERAVRMGLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002585.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56d1f2f74e176d9427b0f326f82fa3d057c2763d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002585.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_00738
+MADTTGADTDGLPVVVIGAGPVGLAAAAHLAERGLTPLVLEAGPVVGAAIREWGHTRLFS
+PWRYNVDAAAARLLETRGWTAPDPEALSTGAELVEQYLQPLAATEALAPGSAPGPGSSRC
+PGPGWTRPAPPAGPRPRFWSESPTRTAPWRTFTPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002588.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaebed9266133bcc1ac8c38cde139d537c29f760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002588.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00751
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002594.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2eb60e5880d19c699172e3fdd9b539fe345d9aac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002594.fa
@@ -0,0 +1,12 @@
+>GCF_005280335.1_00790
+MPRRPPSSSASGAPRPARLAPLDARQRLQRGGEGRVLLLERRRGLDQRFVPGRGVVDGTV
+RDGGLLGLDLRQQPVPQPRRGDAVVPVVVLDVGADRPRDLGVPGLHRGDVPVVLGDAVRR
+RRDAVLRPVLRPHVERLQLLDGVARHTGPQGGADRGVEVHEQARAEPVVQLALAHPVAHR
+EPLERRDLVRGVVVDPHPRVGRAPRLHERHELLERRPLLAAGVRPQPREPEVPEGRAGGV
+PARGLHPAPQVLQPLHLTGGGGPQRVALEVEEHVPLAGLGQPEDRHRVHDGERRGPVRPP
+GRQLGRGLVPQRPPRALRHPRGGRGGVRQLLDGLDPGLPQPRALQAGGPGGEQHVPVRLH
+RLRTGLARPADRQGVVAPAGGLPGGHVCPQQALQPGPLVPIHRDDLGEVRPVPGAVAQPE
+AAVPGARHAHPVQQVRVGGDLQQRRHAGVPGQLGVHHLVGALGVLLVPAQHQEVGEAAER
+AVVQHRLEDDGGPPRQRLRGPLARGRHGGRGVRARPLQPHHLLLAMLGHQAPEGALLVGV
+AEPGHALQHGVLDGEPRRPPQRRIHLHAQPPVGARGGGRDVRGAEGDERAVGRDADHGHT
+LGVTPDTARPHRSAPAVVIRCHEVGGAPVRLDAGHIDGVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002595.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a11d8f117063db60fdeb5b9ffa8a667d5c66373a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002595.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_00800
+MRAVEHWRSAVANFNMTDIRTQLDFNLFTEFDADGLAPRERRAEEFTGLMEQLIIAARRI
+AAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002603.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e07c2a13aff0d8664f4c9d660998bb362f42646
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002603.fa
@@ -0,0 +1,5 @@
+>GCF_005280335.1_00820
+MPKVVDHDSRRSELVEAAWRVIARRGLTGATMRQIAEQAGYAHGALKPYFPAKTDLLDAT
+YAHVFGRTQARIDDALVGVRGLEALRRLCLEVLPVDEDLLVEARLVISFWDQAARHEAEA
+RVSAATLEAWRTRLDAALGEADDDGTLRPDLDRRALVDLILTWLFGAQVTAVVDADRHDR
+AALEAQLALLTAAIRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002605.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12dc5ba61581ca742c1ab71c68d633711d5fb6ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002605.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_00828
+MGGVRDVAPALTYGEVGATLGELPPGYRHLDERRTVGHGRADFDRLAAQLLAWRLQRAAG
+FAVHPSTPTLDVGTQVRLAPGPGLVPGGGLLGRLVGGWQCRVVAVVAEPDRAGFAYGTLP
+GHPESGEELFLLTLEPRTGEVVLRIRAFSRPGTWWSRALDPLARAAQRRITRRYLRALE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002608.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c4b6039ee92fad8069e621515f0d8cb677e6c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002608.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_00886
+MTDAAAVLGAFFVAENARDWETYRSFLHPDVEWVLGDRVIRGIDRYVEAMQAAYGDDVRF
+RCEWSHVSESGSLVAALLVDDAGRRSLDVFEFKDGLVWKEHEFLLGRTASEAEPRSLPTQ
+GEPRSTEATEHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002612.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9f4483b773ccb89e746e30f99b03cf27cc0f5c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002612.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_00965
+MGGVHVRAGREGRGGEHLAGGLAQGEQHVRGGVLVRGAGRRQHGVHEPLDAAAGGGALGR
+ALPRVRLHEGRVQQGLDRHGGALAGVGHAGGEPAAGGVEVADRPARLAQRARDAHRGGPG
+LRRRGGLRRGVGAADGGRGGQRTAVGADGRAQGLEVGGGGRRGGGGGGPADQEGALRLAE
+GEVAVDRRVVGAGGGLAGGRVGRGLAHGASFRDGGCGARPTAAGRGLDSTSGPRRDTVGA
+GVRRPRRGGLSGPAGGAGVWWCPRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002616.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92cc408def2c73ce3d4c87452bf09bf11be98aa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002616.fa
@@ -0,0 +1,5 @@
+>GCF_005280335.1_01050
+MSAAELVRRWESAAQPAPTVVDVGSVLADHYRARPLDNAVFACGHLQSDDELRPDTDKML
+WTITDPVTLLRCARHAFGSLDAYLSHLESEQQEEDEAIQAEDGIERADVAYWSALEGRIP
+EEDHPYGLALTQHALGQRVTAILEVEDGAVTGFKVEGVLGRMVDEHLEGLVGYPAPGSGY
+DEAVPLMRRGDPGDEMFLQHLRQAARFGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002617.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7976b4ce562eadb4869e71be166f9e5bab31b99f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002617.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01055
+MNRYQQSRYFQDQEKTRANTASNIEFTGIGGAYSANVKAQNRQSGDQYAEQKGLGRNKIY
+NIPNATPTGQMTRLIVTNDTWTTVTVSINGWYRTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002618.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4a2348ec2410fb9d1d5c5ea7f0698c5d571249d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002618.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01056
+MVDGSYPLYAAAGRSSAGFVVLSALWAGLHAGLIALMSALTALLIRNRVLALLAPAVLLV
+GASIGLELTVGPAAAPLITWVHPGGLLPSNLIAAAIPGLTLGLACGAMAVVLLRRAPQMD
+RFS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002623.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16cd2e853ae2a4f2f424e483301fb612b1df27a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002623.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_01217
+MTFLQRVRRKAVGDGRLLRQVLTVLSGTTMAQLITIVGMIPLARLYSPTDFGLFAIAQSI
+VLAGTMVAALRYDIAIVLPESQSAARTVHRLASRIILLTCVVLAVILLLAHRVVSEHYGN
+PSFGIWLTVTALIVYAMAQIMNTQNWLIRMKQFGLISQNRVLAAALMLTAQLVCAPLVGG
+FEGLLIGMLVGQVLTLIVLNRRVPELRTSHPVDAPAIREMAVRYKKMPLLNAPNVLVDAV
+RDAGINILIGNIALGSLGQYSLANKATNAPVYLIRGAIAQVFLPLMARARPGELTPLVTR
+LLIRIGLVATPVFLVFYWLAPWLFPLLLGDQWGQAGLIAQALMPWLFMNTFTSPLANVYV
+TTERQGWLFGFAVVYAAAPLIFLTTSTLPLLPRVQVMAWIMAAALMCMLVMTLIITRQFD
+RRGQPAEVTPDMARPTKEPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002625.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..027270410986e2a0db19b46004ffb5315e8f0ba1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002625.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_01269
+MLAVLRNPTYARLFSAQIIALLGTGLLTVALGLLAYDIAGSDAGAVMGTVMAIKMVAYVL
+VSPVTTALVSRLPARRVLIGADLVRAGVAVSLPFVTEAWQTYVLIFLLQSASATFTPTFQ
+AVIPSVLPDEREYTRALSLSRLAYDLESLVSPLLAAALLTVMAYNNLFFGTVIGFLVSAA
+LVALARFPAIQAPEPAPFLDRLTRGTRAYWARLELRGLLGVNLVVATTTSMVIVNTVVLV
+QADLGRPQQDVALLLAAYGGGSMVVALGLPRVLDAVPDRRVMLAGAAALPVLLLAAVGAM
+SGLDAGAQWAGLLVLWALMGAATAAVLTPSARLLRRNSTERTRPSVFAAQFSLSHACFLL
+TYPLAGLLGARIGLPAVGVVLVGIGAAGLALTVLAWRRAEGQPPVDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002626.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..564f3a3e41435dfe53151dd21f957ddaada18080
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002626.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01270
+MPYYLRMHADTKISGTPEPFPDHVEMAAEVLRLLSDATRIRLVLALHRDEELPVNALAEA
+VDRKPAAVSQHLAKMRMARMVTTRHEGTRVLYRLTDEHAVTLVLEAIRQAEHSAGPGQPL
+RHTHAPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002637.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002637.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9993da25a5891fe4850375b3cc55f4384784c389
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002637.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01323
+MAYEQKTTVTDVPVEEYLATVEPARRQEQGFALLRMFREETGAEAVMWGPSMIGFGHVRF
+TYPTGHSGEMFQVGFSPRKSALSLYGLTTYGSHADLLARLGKHKVGKGCLYINKLEDVDE
+AVLREMIRVGWGDDESFVDSHDGTVIERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002641.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c019dc271731f3d445fc0dea8813e0f102c4428d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002641.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01329
+MDPDRSGQRGPKDFHRRIVRAEDPAHPATEVLRTITEPGSRGSRIRAVEGRAGEQAGPTL
+EH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002644.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8db61a5ff0b7dc37d411b13bbfa506c5d60ee428
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002644.fa
@@ -0,0 +1,2 @@
+>GCF_005280335.1_01347
+MLDAVVAALSAAWAAGGAARGPAPGRQRELAAAEGWIWLPETDGAGRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002657.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2edce18a5f517b810b2798b78bca7a8c8972654b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002657.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_01509
+MHLPIRAQGTTLADEQAKILDDEFFLSNPLSHFSSRVSMLLETARSSYEASPENEPEFFN
+ALGLDSADTALKFDTQHRSVQVAIDALSLRHQAAEALTRFIYARVAATPRKGDAKSTYLA
+IADCPNPMIKVIEANKAAHDADPHRFLQLLFPPGIVVEGPVVGAAETAVEWANHAVWLLT
+SDELSINAAHNKLKHGLATSARGDVRIELITTPPNEDGTIPTSAFGEGKSLPLFDRPMLT
+YLSRPPKDLRQGLEAVSLRVDLPVVLAQTWMMANVYAAMFHIAAREHYGKSLPEGVAPFP
+TRVVGRLPEHVIGGRPLGYRSAATLPPDGTTAPRPSGVAFFKQFWPMTVDFESKTQGVVV
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002662.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f9638f25543a6ceba17d6d22e4bb2364cc7581d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002662.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_01631
+MSTGSTPSDPSEQRDQSNRTAPSDHPSSRGGGPHAAAAALARLAESPARVGLVRDVRPWG
+GPRVDLRLQDGRVAAVVPHDPAAHAAPIAPHASETDDGLVVEGHGALCVPTLADAHAHLD
+SVRLGLPFRPHTGRPGVWGMMSNDRENWRHAEAPIGERVETALGMMIARGTTHVRTYAQV
+DVDAGLERLEAVLAARERFADAADVEVVAFPQAGLLLEAGSADVLAAAMDAGADVVGGID
+PCQLDRDPVRHLDAVFGLAERYGAPVDVHLHEQGSLGAFSLELIAERVRALGMQGRVTVA
+HAFALGTLPDARRDALLATLAELDVALTTIAPAGAGTLPLDRILQAGVRLGLGEDGQRDY
+WSPYGNADLLDRAWQLAFTQGFRADDDVARCLEVAAVGGRSVRDPAAPRVSADRPASART
+IAAGDAADLLLVPAETLASAVMDRPAERTVIHRGRLVAAGEPHAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002664.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2873c626cf6419d06283281454c2c6033dcc5c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002664.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01735
+MTGPAVTVTGPDEPAPGMTAAQEEDAHWEHLAALAQAAGVMIRAGALRALPLETEASASL
+EALAARGRDRAEALTVLLGLPEESLGTGPPEDALSAEAVVGLQWALAERVGVDPDAWSTP
+RPWARAWAARSSRSRSGGTSPPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002667.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ed914ae5704707ba5b28a27e3f5fba1efdbaa53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002667.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_01802
+MLLTSLLLTLLPVAAAVPISRRLGRDAGWVLALPLLVAAGVLAAAWRGGVEAEHHPWIPA
+IGVDLDLRLNGLALVFSMIVLVIGAAILAYSSRYLGRDPAVHRHGTFYLLMTAFAASMLL
+LVLADNLVVLFVAWEFTSFASFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVATMVAT
+TGTASLSGVLDSGIWQDPTLSTVLAVLLAVAAFTKSAQFPFQSWLPDSMVAISPVSAYLH
+AAAMVKAGVFLLLVFSPVLAGHAVWSALLLISGLTTAVFGAVAAVRRHDLKGLLAYSTMS
+QLGLLTAVIGIGTPAALTAAIVHTVAHALFKSSLFMLIGVVDHEAGTRDLRVLAGRRVRL
+PVTGAALAVAALSMAGIPPLLGFVSKEGLLAAALGTPGPAWAGPAVTAAIALASVFTVAY
+SGRLVLGALGLWGAEPRRRARALGVRPRRGGPRGAGVVLGDARAGRGGRRRAGPGPARAR
+RPCLRRRPRGRRRGAPRPPGPVARGESGPAGLRRRDRHGGRAGAAAPARRAGRRPSGPAR
+LGPRRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002669.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e91ca85540e34239378b6add79c548014d69d20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002669.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01838
+MAEDPAAAMAAAWRELTPAAGRLAVLMDNPRSDTSMPRCLEQHRDDPAACAYGKAEGIEE
+SGAPALQAAAASAAADPQWGLVDVNHLVCPGEDACAPVIGEALVLFDTNHFTATFARTLA
+PELGEQIEALLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002670.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9af386696372d7f75e02a8b13bb467398d2456c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002670.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_01843
+MIAEDVDRAREAVEQALAAVAAPRWQDVPGGALLPDLLVQAETLSRTVAALQTALAGHLA
+EAYEHEADRQEVLGIPPGKGPHRDAADCLRDTVRIDRRTAQRRLRRAAATRPRRDFVTAP
+LADPALPEVAAVLSEGAADEAACDAVIETLTRARTDLALAAVPQDEADALLAAGESLLAA
+QLHHADLDGMRRLCARWRQHLDAVVLPDSGIPTEAELRAAQGLFHRGRRRGLHRWDLHLT
+DTQHEVLQTVAAAATNPRARGAGPSGQVDAPAGSPDLDPRTRGQRQADTLVSALQAALAL
+ATPGVLPATAGHRPQVLVTIDHETLLRRVRTASGTAAVLSEAEFTGPIDPREIRRIACDA
+EIIPAVLGGEGEILALGRSRRLFTRAQRRAVTARDGGCAAPGCTLPASWCEIHHIGHWED
+GGRTDVDNGVLLCSHHHHAVHAGWWTVAVVAGIPWFTPARHLDPRPDAPGGTGTTGSTAR
+RRPRAPGERHRRRRRRRRNRQGQWNRRTRRDGQDGQVGQVGQGQTEPVRPGPAAPPRPPV
+RRLPPPWTVLSPPWRPPGRRRPRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002672.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69e777febbdc8f420c7fab2e2ab7b86316f2d710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002672.fa
@@ -0,0 +1,2 @@
+>GCF_005280335.1_01856
+MMMSFRSTGKGRRGACGAVAGFVLVVAAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002673.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a45393853bc04d3c728a6c09a1da7ad9ed37342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002673.fa
@@ -0,0 +1,2 @@
+>GCF_005280335.1_01857
+MPCPTWLDVVEARLPAAKDMLKKLDEGVDFIGVMPEAMKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002676.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0b760fd5a3d5b8f91c41b67f4ae16e4e258a4bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002676.fa
@@ -0,0 +1,2 @@
+>GCF_005280335.1_01881
+MAHGGVIRAAVGLLLRHEGEAFAALERIDNARAAVLQGAFATDTGAEGWGDWTLEGYGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002677.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58d4b8603f80187c651ffd09a4894afe620e23fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002677.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01909
+MGAVFAAAMLAVGGTALATPPPAEAVTTVVITNGNFHNCTSRMNSEMKLFRMEGYTVRIA
+YKCKWFADARRWEGTFYASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002684.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5efe33649e8ff5e642b71f750ba8e3ce8690205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002684.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01943
+MTAAVAQTVEVPAVLTTSDLAARWQVSEEWVQDAAKAGRIPGFKVGRAWRFRVDAVLAHE
+EAEQAALSPANVFALAPGAVARRARRATA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002685.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ed7e14a3c3d6747b5a5bf787f366c52f107478a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002685.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01944
+MSVHPIRLQIPFADTSLVFGFDADAERDVRLLLRFARARASHGAGGFWLEYGWDTGESQM
+VWIDPAHMPTARFDVTATPVADQGREDDMSRHLARTHHVYLTAKGWQSDTHELAVDN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002687.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bc35a1400f31bff0533445553618c3d4a521635
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002687.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01946
+MSARIAEWPPIEAWITAPDPNGRGRIVESVVLRDGRVVPAETDPADLYPWWAPAAGTRAH
+AVQRVARAVTAALVPVLAGLVFAAVVLLAPAGEWAAEQLIRGWGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002690.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0fb930d8810569317cd1923581fdca7fcb592ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002690.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01950
+MNDPKAKAAYHGVPCDGRCCRQNRHLGVCPHGRVCAYHLNEDARQAREERERDQIADLER
+AARMTRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002692.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..372b61f2f07ef12ce41129d6e31c919d6b5cf8f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002692.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01952
+MSYHHINEDGTAVVCTAQESAWCRSRPNCDTEEWNEHGCAEHDREHALTPGHECWQARNV
+NAWGGPYPDDQPDLRPGAPVTLTYEGEGIVTWDYVNGARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002695.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd57cd618f2f25b4d0d7873e06003fe077fb19ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002695.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_01955
+MKLFVEIADLRRALQALTPHMDPKDELGVFGRIRGHATDGNLFLMATDRYTAAMAVVSLW
+DKDDLTGSIRDDALEFSAQDVKEVLTLFRAPRRKDEPEGDLLIETSPGSSDPARRLVDVS
+GLFPGKEFRLPGADVDEKFPNLARVMSRRPAPTRTVRSNLTFAGEHLKKFLAASKAYEEP
+ITLQPVAEGSNMMLVAVGESFRGMIAGWRWPEDKTPDFEGWDMQWRLWSEELLGMAPDLR
+RPEGHEEAPADGEERDWSAALEQWAKDLADRLAKEQDDSEDEGDAPEQEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002696.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5e1c3f9082a381618fb934ba25de88ce8cee1f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002696.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_01956
+MPWLKVSDASAMHPIALAAMEAEDADERLVNELFGYVARCAVMSAQHEQDYVVTLATARV
+TAGGDARFKVLAAAAERAGYWTRTTVKDASGAERPAFRLVEEKDLFHMLLKKERAWETQR
+RADVANPELTVPVRLRDGDGCRWCGKSVAWRDRKSGRGATYDHVKPGQGAASPEDLVVAC
+RACNGARKDEENTSFSRTLMAPPFRPLYGPDTLAFLAEHDVVPEQQDTATAAERQSQRET
+APTPTTAAPATAAGSTARTATAAPRQGVRETADGQERRRGAQVRDVDGQAADAAAAHAQR
+EADARRAEAERERRLDAWLADHGISVAPAPATALSPLDVEEADWAPSEGDAGPPGGPDLQ
+IPADRQAEGSGFPGTGRDGSGREGPGLDVSGTGGARDGSGLDGGSAGSGRRRRRRGRRGG
+RGRGGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002697.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a5309707727c9c9fc53b798c5a4253fbd19ed1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002697.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01957
+MRQDEYVRMMAAGMSEDQLQRGVERLARSLGWLAYHTHDSRRSSPGFPDLVLVRGDRVLF
+RELKTEKGRATPAQKTWLAALTAAGMDAGLWRPVQWFDRTIERELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002698.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19a00ea1b8fb32430c07df4ae1e8958689e2f598
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002698.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01958
+MTNWDDADQVNDELLGRMERPDGCTCDLEYTTDYKGRILHIYWSLELTCHHHYPRTAAQL
+ERLNSCPKQEGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002699.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d251c3f1d788328b633413c7217193ca95bf142
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002699.fa
@@ -0,0 +1,5 @@
+>GCF_005280335.1_01959
+MSELMELVDRLTVETRQILHTDAGPAVVRAAPLLEQLQDAVHPSGEGGGGSSGSVGSGAP
+LDVTALALLCQVKDEAIHLSWLARSTPGVLTLRPGLGGFTLAERIRWTASALDGRAAEAE
+MLATVRGWTASIERLFDPPRVVALRGAECPACGIARTPVLNRDLDEFVDVPALTIVQGQT
+PRASCAECGAQWHGPEVVDLAVQLGAPPSVAHLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002700.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3c8c0e3462484e51ee23c4be19d97255d018487
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002700.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01960
+MATSRTGTSEYKRWRSYVLREAERSGQHRCPYCGVTLDYRTGRLPHSAEPDHVTAWSAGG
+TNTVDNGRAICRRCNQSKGARAAPRPRAVQAAAPLRVSRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002705.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee5fcf54707a6513627dea2b7863d190460410d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002705.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_01965
+MAVLNTQEETLFLRMRDQVRRHQPTNRHRENLFNARKQLQKIGFSVPESMRSFAATVGWP
+EKAVMVPARRLKPTGFVSSREEELADELNAHLDSGYAAAVEQYAIEASVRHGCSFVFATP
+GDQTAGDPDVVLSARSALEASAIVDRRTLRTIAGLEATDEAGVWLMHVPGEVLLVDTRTG
+EHVVRERYRAAPGEVGVVPYVWDRSLDRPFGRSRITNPVIDLSGQAVRIMLRQEVQAEHF
+SSPQRVLSGAREEAFTDETGQRRPMWQVATGAIWGIPDFFDEEIGEWRRAELTQMAAASM
+QPHTDHLRTVAMMFAGETSIPISQLGIVHDNPSSADAIRQHESAMVDLVQAQIPSYMASR
+KALGRLVLAVAHRGLSPATNTALAHVHARFADPGTITRAALADRAQKFAAAYPELRGSSV
+ALRAWGFDDVEVRELQDHLQRAESAGLVRQLLEAGPGVGMSGHAEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002706.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ceb27f57eb435cb569275ad78f90db1cc2f5d7ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002706.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_01966
+MPSREQLEAFNRDQALLHDLVMGALDGMARRLGRFATPDQVLTALLEAMPELVGQFGHAS
+ATLAAEWLEEVYGIRAVLGETYPLEAVTQTLRRHAGQLWQGAGPEAVVAAMRDDVARWVK
+AAGRGTLRDSATANGLRWARVPSGPITCAFCLMLASRDAVYLTRNRALRTKSGEDRYHND
+CDCIPTPIRGPQDYPTGYDPDELYSVYSEATSAVGSRANTTAILENIRRAHPGRVRDGVH
+TTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002708.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f53766b9f6dd8e5cd81357b3f5a6e018f1a6e03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002708.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01968
+MPMLHRQNIGSGRKNWLGSAHGVNHAQTATLDVSTFTAAADHPEGRIPSGTPVNAADRTA
+VVKWDPAAGGGALGFLIDDVDVVDGEAVPCAVLLHGAVVVEELPVEFTVPTAPTAFIFE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002709.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d8ee73e95c94b252c18832d83a785daa0dfc458
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002709.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_01969
+MENLNDLISAVELTAEARMAAEAYEGEGQSFARYLPSVTTDGISIELTQTGSGGLVEEAA
+YRAFSAEPEIAGGELGDIVTLRLPALGQKRPLTEWAQLMDRNAGEEVQRAAFRRTARLAG
+AAIAATAERQRVSVAVTGAATIAGRRFQSTDDFGRAASHTQTAPQLWTDAAVSRTDYLRS
+LVDVYVGTNGVPPGAIVMGSKVYRALLRGSEFTETLANGATRPMGRDAVFAVLDDLDIPV
+IERYDLRTSAGPILPENVVLLMPPAGPTVAEEPTALGAMYWGRTLTSGMEQYGILEAEQP
+GIIVGAFRETGIPHTAWVESDAIALPALANPNLTLAATVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002710.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4a695f7d4b43453198e11300034cb88b0d1b8fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002710.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01970
+MIVTHTTTVLRDGEPVVLLAGQHVPAWAEDLVGAHLLAESAAPAEPVEGAEPAEPVEGAE
+PAEPVEGAEPGPADAGEPKPPVAVAVVDAEAEKPAPRRRAPRKKPAEDLEPDFTRPPTEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002713.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f14530e9898a3c372c9144711d4921fa844c4022
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002713.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_01973
+MTTAGLRRVPGVRRYRALADGVRGLGTSSVVAEASLSAAERIAARARSTGEGEYQAYPTS
+VRAGWANEERAGARVVETRRVPSDARQRVLVTALRGSTTGGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002725.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e97c783ad560ddd34c1be1218c0a4b39595ec01c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002725.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_01985
+MPDRILRTSAGVLGGLIIILGLTYAWLGITWLISPTPTRLAGIEWAPIGAHTVGIWWIAG
+GLVALIGGAWSARPVAAGVGAFAAILTPAVVAGLFLVSVWHGNDRGLITAGSYLPYALLA
+AWVTWRSGRGSEDTARDMAATRHDSQEGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002727.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d0ae92bf423ae4e4aae84c05e27b6e8e3a7112e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002727.fa
@@ -0,0 +1,7 @@
+>GCF_005280335.1_01987
+MPTPFLTGLGRVLTTAGVTWEGVPGWETRTGFASGYRDVYGATVHTTETHDATFAKGGDA
+PTLEWVVDADGSRRGAHTYALLIGRSGKVYLIAAGPGWQAGHGSWPSKLGPNPGIPDDQA
+NFHTVGVSMDANESQYPPTEAQLVSLVKVLAALRAEWAPDRFDVMMHGEWSPARRTDPTR
+VPGGWDAIRKAVAAGAWPVQPKPTPPTPAATSSRPAPATGTYTVRPGDTLGGIAKAHGTT
+WQALAKLNALADPHLIEVGQRLRVPALPTHTVAKGEGLWGIARQHGLTVDQLANLNGLTR
+TSTIHPGQTLRLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002734.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ca22fcabc040f7c1a34f0b68454e037ac790953
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002734.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02048
+MKPGPSLEKALYVGCLAAMSIIGVAVAVLGLLGQFRLVVILLGLGAVVASVLIPVHARRM
+RRFMGVAIRRAGGRGRAAAPTSSPGPAASVEVGRETMAALTRINRQLVSLREETMGGQLR
+PVSGAGSTDAADDRSDSSMAVAEALVGVRHELSVLRAEVAHLAEAPRGGRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002738.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6545f29300b5beed702ef470804017f4cbdae6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002738.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_02102
+MADRGHYELPHSGHNGIELVGTFAYEDAILRALPRLPADGASVEAQFTVDLVPEPDNPHD
+RRAVSVRHRGEVLGYLSRDLAADYHLPVKRILASGARLQTGARVFAYLSWDDKPEVRVYV
+GLPAPDALTPLNDGYPATTAVLPYGRTYQVTKEDQHFEHLFDYVPRSGQGPVILTLHKSE
+AMLRNGTVRRTVEVRLDAEKAGELTAATSAHYLPVIEHAEALGRVVGVWGTITGSGLAAE
+LTIKGAKSSELTDEWLREMPIFPHLVPEAHSYEVPDAYQGEPKTKGRSRAMGGHSAARLR
+EQLDQRFVSTSPAELDTTPSPSTPSPEKKPGKPQPPANPTPVPLNRDVTRLGIGTGPRTP
+IYYTVKGKEVFVDDRDRSSAGKHPRRTAWLLIAGLAVLGLILSGVPGIGPFLTLLTLLLV
+LISGPDQLRKAKVLDIDPHGTGHPSRDWRDRERGDVGEENQDHDTEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002739.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e82b5d6dd0959c8b2abc5745ecda1cfd4464a5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002739.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02105
+MFHPWRALRALTHVVVVWVRPHPAAPAATNGIDVVWLDPRLTQVERRWVLAHELVHLEHS
+HRGCQPAAVEHAVRAEAARRLITLDALLASIPWSEHLAVLADELWVTEQVLLDRIAGLTP
+TERQAIAARAEVHHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002741.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..513369c9e2f820fe518e3c0d7b3a82c42b686621
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002741.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02166
+MHSESLDPSPVPDRHGSDPDRPDPLVVVDGAEGRVVPAPTAAPSSTHDAGGDPASGGEGV
+DPAAAEPPTLVSVGVLADWLGLSPTEPLPEVPEAPAYAQPGRCRPRRLVLLDVRFRATGG
+GADHEAYLRGHLPGAVYVSPAQPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002748.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c951f8cf1d789f803f925d20768dd4d1ddbb68af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002748.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_02213
+MAQLNWTYEEVVLAADLVARNGWKGLRSADPRVAELSRLLRAATIHPLEGRPHNFRSPSS
+VQRKTFDIATRHPDYQGTPTRGGKHEAAVIGAFLDRPEQMHDLARYLHASLGGADPAAGV
+AEPAGVVADPEEEALAAWEGMTRAVRHLRRERDPKLRAAKITSMVAAGGRIACEICGFDF
+EQTYGAVGQGYIEVHHVRPLHDSGPVLTRLEDLALLCSNCHRMIHRARPWLTPGELAARI
+ADRGLVRGSRPDHAARLCDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002750.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcb4dea35abc1ec8cdb1bf90815355fc7b4fc883
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002750.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_02216
+MPVLPGFIADPLWEQFQALLPERNINHPLGCHRPRIPDRVVFDKLLARLVLGGTYQQHAD
+ETCSATTMRARRDEWIRADVFEQLHHLALEAYDQAVGLDLNNLVVDGCIVKAPCGGDNTG
+HSPVDRGKSGLKRSVLVDGGGIPVGWVLAGANRNDSPLLRPTLETLAVLGFRLPEVITVH
+LDAGYDSARTRDLLSELGCTPNITPKGAFLPISHTRRWVVERTNSWHNRGFSALARVTDR
+QGCVQNAWVALASAIIIIRRLVRQSWKRYRWDSRPARCP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002752.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c2dbbf653d9ad55c61311e9f90e6a1563665ef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002752.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02224
+MKIRHKLAAATAAFGLAVAAAAPAQASSIPRTYDARTNTYYSYSDSANQVCYQKGTNRTA
+QARLSVQIKINGRWYTRISALYSDTRLHCFTLRSQNGFYEGRSVRLIVSDNRGSSTTRYF
+YR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002759.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c0da18e9edf079ce18cf62ff9afef76aae1fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002759.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_02298
+MATGDTVAVGQELAVVEAMKMEHPVTAAVAGVVTVHVAEGDSVAAQALIAAVAPAGADES
+AEPAPHEASAQNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002769.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..436d271bbe11aea969ae7d0ecf91b3cd7a1e589b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002769.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_02460
+MPVEPRICITSGGDEIRLRSYINHAIYAREHGLDYRLETGIDPQIVTKFDYKVAILRRLL
+PRYDWLVWMDDDAFFTDFEADNLRRLISEAERDDISLVIAEGPTEPNGFWSRINTGVMLL
+RNDETAHSIVESTSTADLATVRAWWDDDRDGLFTHGDQDQMWWAIQTGGHADRVRIVGHR
+ELNSRGHYYEDSLTDAFVMHFTGYPDKELGIARFADRFDIGQEIVPEPLLDKYHVRVRSP
+LRGARRAWRERSVDTLAAVKYRLRPHKDRIRHVAGFLPPAVRRRWPLGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002778.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9a69d50f2086449c7d3ce67421a98162bc4cb8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002778.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_02579
+MSTIAQFADAAALPYGAKADMAAEPTLATIATTATTALTCITAAFGHHDSERLDVMSTVE
+ADASVDTMVAARRDALQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002783.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13a07f35bebace940ee8006e81822e5768e29f2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002783.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02618
+MTEKLLASAQARTRECTRAVLATVKELEASQSAITLKGVAARAGVSRNFIYTTPDVLAAV
+QKAAERQRPKLPSEPAPTAPSSDASLRTRLAAALAHNECLQQEIDRLTATNQALVEEVIE
+LQNPAPKNVTSIRKRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002784.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f92e7cff603f705de85e2ba6af1559332ae80052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002784.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_02619
+MKQSAYFGKFLADRVNLDDTRLGHLDSRVKAIVAELMKDVQLGQHVRRWEKQGSWAQRTI
+IRPRKNDEFDADILLHLNEVPGWEPKDYLRHTRGALRRSQRYREMVRKKNRCVRIGYAND
+CHVDVVPTIKLSDGRQVIVNWKDNAFEDTNPQGFTDWLKQQDDITRGNLRKCVRLLKFIR
+DSKDSFDIPSVILTLLLGKQVTKEGADERYADVPTTLVTLLTDLHLYLQRLPDDGTMPPI
+HLPKCPGPSLNHRWDDPTKIRNFRLVVGRYAAWASTAHAAADSKAILDGWQTLFGKDFSP
+DGQLEPRQVSAAAFAKTSGTRHNREVPQEEFIEHKFTFAPTHDAEIIARVLPRTGFRHGL
+LAVLGFVPKGSRIEFEFRSDAPGPYRVYWKVRNFGSEVGNQWRGHLMEGGYSPHHQEPSA
+ITGKHWIQAYAVQDGKVIAWAHCAVPIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002785.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53051d85b6af382b0c7a6b261de7e6f6d81d0abd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002785.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_02620
+MSSGRVSVSREEELKVYVRAGGRCCFCQAYLVEGQIAGAPMKIGEMAHIVGAKISKRSPR
+GEDPLPQQERDKAENLMLVCRGEHKEIDRVGASDWATVDKLRRIKADHEGWIRRVTGLDR
+SRHTTVLRFVGDVRGNAVDITKAAAAGAVLLSGDRYPKFPLSADDFGFEIDIRAFDETSP
+DYWQRAAAHIDRIIDHKLRDEVTAGRVDHVSVFAFALLPLLVHLGSKLDDTFATDVYDNH
+RVTRSWEWPDSEAAARFETSFPADPSSADEAVFVLNVSGSISDAEVPAALADLPQWTLAL
+AGATPGPGPLRSAADLAAFSAASRGLLAEVERRAKHTRRLHVLAALPLSAAIELGRVHDA
+HVHPRLAVYHRADGGYKQALELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002790.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca4943fa095218507cebd3f86fc092cd6013f13b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002790.fa
@@ -0,0 +1,9 @@
+>GCF_005280335.1_02649
+MRLRRFAAASAIAAVAALTLASCSSGGATTESATAVVPELAADQQVEIVFESYNLAQAGV
+WTDTINQLIGEFEDANPNIKVTGQAPQGSSSAINTIDTVGSVQKQLLAGNPPDVAQLTFD
+TLDFTATELGAKPLSDIVTPEELAEAFEGEHPMHPNARVLADWDGKTVGMPYVFSTPVLF
+YNATALEEAGVTDPDFSTWDSVEQIAAQVTAHTGKPSIDVSCVIKGGNWCMQGLFKSNGA
+QVLSDDRSTIEFGSEAAIETVERFREMYDAGVLRNTDTNGTYEGLPKGDVSMILISSALQ
+GGFMQAAEAGGWKLDAAPMPAFDGQEAVPTNSGSALFVLSDDPAKQRAGWELIKFMTSDR
+AYELISSQIGYPPLRTGLIEEGGVLYDWAQANPLIQPNIEQLDRMQPWLSYPGNSYSQVD
+TLLAEAIEEAVFYGKSAADTLPDAAERAQALIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002793.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6cace588ad043778e6b4ebd0f44710a242091cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002793.fa
@@ -0,0 +1,11 @@
+>GCF_005280335.1_02656
+MPVAGVAGLAMDAAFPALGWWPLAFVSVTLSLVTLIGRRSWGALLVGTVFGAAFWFPHVS
+WSAQFLGEHPLSWVPWVALAGALTIYTAVLTVPIALAYRWLPRRRNAFAMRLLALPLLVA
+GAWTIRELIMGSWPYGGFPWGRVAMSQSESPIAPVASWVGVSGLGFLMVAVCAAAIEAVR
+WIVRAQPARGNATEHPRTPLASWAASIPVLGLAAVMVLVPQFPTSHAGTIRVGAVQGNGP
+AAYVDEHEPGAVLESQLAASAPLEDEQVDIVLWPEGGVDSDPLADEATAHALDDAAARYD
+APILLNAAAADGHLVYNTSFLWTSNGPTAAHAKRHPVPFGEYVPDRWFYGALVPSLVDLL
+EREYAAGVDTPAIEVDGVEVGLAICFDVAFDDVIHEGAHSGAQVLMFQTNNADFRDTDEH
+LQQLAFARMRAIETGRSVVNLSTTGTSQVLAPNGATLAALAADEPGLMIADLELRDGLTA
+AVMLAQSINTLIVSGTLAGFLVLAFLLLRDRASSRHHRVLDSSQRSSIGLHECADAHRRE
+RL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002796.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78645031697ee7f897599d378fd4bce8cee24490
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002796.fa
@@ -0,0 +1,8 @@
+>GCF_005280335.1_02661
+MTPRRGRSSLALAAVAALLVTGCGASEPEPVRDPYPVDGSLPVVDTSGLQLPTPFEELEV
+VDPGWDITPQYADGVYLAAGERDGVLEFTAVDVYGDVLWAAQRPASCTGFVVTTDAHGRA
+LAILGDLQITADALAATTATAYDLTTGEQVWGPVEVPGPYQGPGLVFAAPPDGFMGETGP
+RVALDPTTGDVAADESSPEGIRIIGEYHGIVLLTHEDALIARDTADDHELWRIPLAEHGW
+TAASISASLRPEPGDGLALIATSETTGALLNLDQGSIVSSTARDAAVDPTTGTLVTLDDT
+GLHGYDADDRPLWSLPVAAETTIAAIGGVFLYLREDGAIRVHNVLTGDVAQAYEPDGQGP
+IIVPTHITINGAALLLQERRHLVATIAESPLNESFPTSSHAGMSIVGARVADST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002798.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4847243d0132cad2f94afec37054f7714bf64306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002798.fa
@@ -0,0 +1,6 @@
+>GCF_005280335.1_02663
+MPTETTNRPKPSNRSRSSLIVPVAVLTLAAVLIAVIVAVKWSGTTAEEGGSPSDSGAPTE
+VQNPEQPDLSAAETRDEADLLAAGPVDAPVVLVVFSDYQCPFCARWSEQTLPSMMEHVDA
+GDLRIEWRDINVFGPASERAARASYAAALQGALWEYHDALFEDGERRSESELSEEALVAL
+AGELGLDTEQFAADLGSEETAQVIAANQQFGFDLGATSTPIFILGGQPIVGAQPTEVFQE
+AFQSALDAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002800.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7746679666a6bc62086091276a3433391abb8fac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002800.fa
@@ -0,0 +1,4 @@
+>GCF_005280335.1_02665
+MKAADGRSGDLLRLGALEAQVMDVLWDHGPATVREVIEHLPSDPAYTTIATVLTNLDRKR
+LVTITRQNRSTRYGAKITRHEHAAGLMEQVLEASRDRAASILQFVDSMPENDLDLLRDYL
+ERRDRGDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002804.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c36a6f7868062a31c7f0f1fa8e0ea2a54f2f18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002804.fa
@@ -0,0 +1,3 @@
+>GCF_005280335.1_02677
+MAIVVRIDVELARRKMPVGEFAERVGITPANVAVLKNGRAKAVRLSTLERMCEVLGCQPG
+DLLEWVPDAAAAPGPGAAPANDDDGRPGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002807.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20a20c426a0acdde8a6a331a6817471dceaf9f59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002807.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_00052
+MMSRMSENSEPGSEADARDSGSGSVGNLELFFDLVFVYAMAQLTELVRDDVSWRGFGHGV
+LGLLAVWWAWVCYTWLTNTFTTHRVVFRCLVIAAMAAMLLAASALPTAFSTGALVFGLAL
+LAIRVIHLVMFVVDASHDDEHLRAGLLRLVPSLLIAPVLIAVAAAFPAPYRELLWIGAAI
+IDFGGPLVAGVEVFRVVPSYFVERHGLIIIIALGEAVVGLGTGASEHLQQPVVLAAAVLG
+VLIAASLWWTYFGLTAGAEQRLEDADGPERARLARDAYSYLHLPLVAGVTFFGFGASVAL
+EHVSDPLPLLPAIALSGGVGLFYAADVAYRWRDHHQLVPDRLLAAAACLLIIPPALSMPA
+WSVLAALTAVGALRLTWELVRRPRIGPATAGQVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002808.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8de587ee1a21007c6a2f7b223c51f3dc25cacad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002808.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00054
+MLIVLRGNAASGKSTVALLLQDRLDRPAAILSQDHFRRSIYAECEQDSLAHADLLEAAAL
+HCLGRGHHVILDGIFHAGRYGPMLERVAAASDDARFYAFDLTFAETVRRHAMRPRAAEFS
+ADEMASWYHGWQALPFVDEHRITATEAPEQIVTRILHGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002809.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9691cc2f3b77ef949c39f8a5575d44c34fbffd1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002809.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_00055
+MDFHRPSLEELRAAAALPSHTAAGLTHEVILTEIAAGRMKPEWSCIATNDDGDVIGRAMW
+WGRDSQEPIALDLWDVAPGTSEPGEVLTGLLTHGGVLVEAPDRRALLPHTLRVPVGWGDQ
+PEVAENVRLKMQVASANGLGRVNERLQFQWDWGETVPPNPARLRFTPASDEVFMRLFADA
+AAGSLDVMTARELEQTTAADLARDEIAYYLSCPGDRSWWRVAQTHDGEIIGLAIPSATPT
+NRNVGYLAVLPQHRGHGYVDEILAYITRFQIEDRARRITATTDAVNTPMVAAFTRAGYTL
+VEVRIDLEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002811.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f3e7832110539f3ec058c8a125947ce0b051c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002811.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00078
+MKRLNVTARLAAAVLLAAGLSATPASAASPLPVSDGVVAEAGLAPVRDGGVDSGVRDGFC
+TVFPFMCDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002813.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e46922f48c0fa82df13ef266ad1bdd2f6a8d203a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002813.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00086
+MSALITLLALSLTTGLCCGVPYATMTEPMPAHVHSTGIAIGYDVSVAVFGGSAPPASPVP
+TSSCERASALSGAAAARRSGRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002826.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e34e210cf18e54eaebde2552cbb3a9fbdf7bc63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002826.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00214
+MSATPTPAAALSLTHLTPQDLAARVGVPVATVYNWRTTGYGPRGFRVGKYLRYRLADVEA
+WEAEQIAAEDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002831.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8daf9c673dcfcb371b2f622d8fe325aa8c1cc0ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002831.fa
@@ -0,0 +1,9 @@
+>GCF_020097155.1_00269
+MERLPAWLLETPLLAPWTVPVCVAVGVLLVLGLWVGRTRRRPWWVQALVVGVPAALALAS
+WWWVNVVWAPIPDGVAGPVFAWAALPVVVLAQAAVGPWRPRPLRWGLGGVVAVLAAVLCA
+TLGVNAHYSAYESLAVMTGRNVTWTDWDAVDTAPARQVVPVDRWTAPAGLPEHGTVSRVG
+IPATDARLAPRDAVVYLPPAYFAEERPALPVMILMAGVPGEPPDWFSAGHAAETMDAYAA
+AHHGLAPIVLSVDANGGGALTNRLCWDGPDARVETYLTQDVPAWIGRELQTDRDRTHWAI
+GGLSNGATCALQTVARTPDGFGTVLVFSGELHPSLGTEERTIAEGFGGVRAAYAANDPLS
+LFAAAQRGEGPGADGAYRGVAGVVSVGRSDAYVGMPVPQELVDAGRAAGMDLTLREYPGG
+HTWTVWSRAFADQLPWAAGRMGLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002838.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a8259346ab15a69fae459f69d46b4f0ea8281cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002838.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00313
+MHASGQSPYWQNGVEMLIRHSNGQCTHYAHLDRALYRAGASVPQGRVVAWSGNTGASSGP
+HLHYQAIDCNTRVGIASTLQGTKPGTGSLPVSTNVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002839.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002839.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b37287ddb7c1576129371a846490e586fec98339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002839.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00318
+MPPSATRATVEGHLSRVATPIFEGVAAGVEMADRIMRTVPNRDNYPAFRSMATRIGAREH
+WINQGLGPGWHIAGNPAMQAQTLLVNPAAGIEMRFLRERRRSYPGGVPVAGHNAARREAW
+SQSPLPFTLSGDPSTQEAIDEIILLLLWDMTTDGDIQVRVVHPLEPGVYGRAVPVDMEFQ
+VQPGGTLFSRLSYEGDDQNENLFAHIDRADNEGDGMNGLFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002842.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..429096093c15f65f18289e623debf267fad379c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002842.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00328
+MFTHGSGFVKPPAPNGRPESHLFASRKPDSHNSSDTRNEACAECLSACPEYPTCSTCNQS
+TFHAHVDNPSSEIVKCRGNNAPITYTGKQSTINGNPTHINALKIDPTGVVPVESKNNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002844.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ff800b52025a253f0140cc0eec0811dfada392
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002844.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00336
+MTFALNEPEYVAVIDSVDGDLGTVELKARAVTTEVDELLGICLDSDVTSALTQFRDDALD
+KALRALTESARAVVDSGRAVATSYREFDAEVAKRATAAELGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002849.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92eeeed9e448d03586a5f9ac8cf32c398fe2b3d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002849.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00348
+MAEKFGWRPNDYLENPRAFGKEDTSPAWRETWFDGTVIQDDPRHHDRQIAAKIQHLVAIE
+VTRAARLRDETLADVSKHTRMGADQFRRLMRGEGPMQVVDFATFRRVYHVDFGINPDPGL
+ANIRETKF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002856.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6bb4ef563cdce60357ccf27a7f70e055cb7850d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002856.fa
@@ -0,0 +1,6 @@
+>GCF_020097155.1_00411
+MTVDAGVLVGENGRVRGIRASSWTPERQRRVERLLRVVEAAALLLFGVCAAVLLLTEPRL
+SGTIRSVSVEGVGARLSRYGLLFAAAVITYVPRRWKWALPGYAVSALFVVGMVKMLEGAP
+SEGFPGLQVFRTDLPWLIGLLLVPQVAGVARRAGLSVRRRYASALAWTAFVEGAGAGRND
+CGCVKNRVVQNGAQETRVLLQRFDGTRRSGQVWGVVEPSECIEVDAARAVVARTDWRNAL
+SWAALDRWGRRLPGREEAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002857.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d034b983927ce1d29164dab6dac29995418a767f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002857.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00414
+MSQRPACPYLPLPRATTLRDALVYTRASMSRLPDVVHGSLPLRRLMEAARPVLTAATSLL
+PLQDVLAAAAGAVLALSALLWAVLFLHRLLLCRGWHGHLVYTTDGRTAFLTIRSTSQGWE
+LSDHVATRSAKGDGRGLREALAPALRNAADAAGAPILVTAANRTLADLYRQEEPELREVG
+TTLLGRVRLVRPPRRAILPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002865.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d9606a0fea469fa56bf2383b5ec0293bf8378f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002865.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00460
+MAAAEGAGLIRSRVGGAWAPAPGPHDPRLPLRKAGFRHAGDAARWVRSLTPLGAPVPQGA
+ELTRRILQARPELPVDAAQALTLLAEGAGPGEDAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002866.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96b278443a5a85652765b8c0aa925a650fc304d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002866.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00470
+MKKTATGLTLAAALSLTAFAAAPAQADEPIFENCAEARAAGYGNFTSEHATFRHLNDIDN
+DGVVCEGPNSPYGPNGPAVAKPSPKPAARPQASLPSHVTQPDAIDNQYTYPDCKDVFAAG
+LANLPKSSKYYHADLDADLDGIGCEVNGDDAWVPAAIKAKYAPATAARAEESAAAEAPQV
+TVVPEGTPKTGPEGVALAPFALGAVALAGVAGAGVVARRRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002867.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5ff9996216cf04165f9afc0f9c1ed67ef3ed9f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002867.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00471
+MPDDVLPASRPTRVRVPSLGIDSSLIELGLQDDRTVEVPPTAPGSPAGWYENSPTPGSRG
+PAVLLGHVSDTEDGTGVFGHLRDIQPGALVEVDRADGTTAVFRVDRAVSYDRGGFPKDEV
+YGNTDDAQLRLITCDSYNAWTGHWDNNFVAFATLVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002869.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b17d511bb61f05c91baa17f044926aa0a839fd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002869.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00525
+MTTTTAPRPAARLRSTLVAVAVLPALMIGAPAASAAPAVSPLGHDMRISDPGTASPDFYR
+YICRRVPIIPC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002871.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95160c3388953f560c84fae4865257f7d0e86270
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002871.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00529
+MTAALERGRPLEGAPARPATPHRRARCTPPWPRPGVLALAAVLAALLALAGAAVGHSAAG
+SLPAGLLGGPHTSDADWTLTGILGRNLGAALLVFGGVVTGGALTAVTLPLVGVWVGATLR
+LALDAAGWEGAVGATVLYAPLEFAGVLLAAVAGLVPLAAALLRPRDADVVPGPLSRYLGA
+LPSACLLIGCALLLITAAGVVEHLVVSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002874.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..884f8c4017becd86df0ec9b0808a44424cb88138
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002874.fa
@@ -0,0 +1,11 @@
+>GCF_020097155.1_00532
+MSPTLAAPVGTGHHAVPRPVPAPDAGWSRAAPAPTPRRRLSLLADLRCAELLTSLGLRMS
+LRSARLLLTVAAVAGPVLLVLAAFAGARFTALVLPPGGTLEALSVTVLPLLCGLSLGGVI
+LAEAVGRQRETVSGHPNIPYFRALDVPATLVHAVYALPRLLTAGTVWTCVGAGVLVACLS
+TTSDASPWWAAGTALLVLLPVALTAVASAVSLAVASRPPRAGGPGVLAVGVGAAALGAFA
+GAGLGRLAAGAASRPGRRPGEVSPVTAVPGQEHGVVLLAGGVLLLVLALVGVAAGRRRLR
+ARSFPLAAADPVRLRRRSAPGGGALSWAWMLWRQRRGSTRWAAERRVLWGLALVAGAAAG
+ARAVGVGRLDASLAGLPHSPLLEGDPVGAVHTVLVLGLTMVGVALGETAHGDLGRHRFGR
+HLRQAVELGAPLGVTVRGWMLALLGPALLGGVCAGVAAVLVWPPVGVLAPALVLGGVGAT
+VLADHLLPPPRTADGGVGEGMLTALLALVLASGPAALLLAGAGPLATAAGVALLLVGAAA
+CLARRLCVLTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002879.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01ce6e28bbbff6a8411b5833768b485bc42477ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002879.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_00618
+MTEARRPTSARSPVLRILARILTAALLLALAVLAVAVFTPHSELGQRLTTRLFLAQALAF
+AEPAGAGLTLLGLGVLALHRGAGTRRRTAVGGVAAMLLGLGVGLLAWPDAPPWAAGPATA
+TGNTGRHVRVTVFNSLDTLTAADARRLIDETDPDVLVLPEAAPSRVREALAGTGLAGGVH
+EGADSGFSRGRPAGVAPTTIAMHPRLGAYHQTAPTPTTFGAIRLEPADGADGPVVVGVHT
+GPPLPRLMDDWRGDLDRLSAVDHAAAQGPMVVAGDLNATLRHGPLADRVHLADTALRCPD
+DVGGTWPSDAPGRLRSPIDHVLVTGDVEVLSCTTLRVGASDHLAYAAELRLPGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002882.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf9462892ed4a0be7627b0d4a3897eea1c9a4ff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002882.fa
@@ -0,0 +1,6 @@
+>GCF_020097155.1_00624
+MNTDRDACAYLEEILREVTPDEEARKKAASHRASLEDWLKKDLDIIRMRETGSWHHGTAI
+SRHSDVDYFVTMRGSRPSASWSALEELRSSLALGVSSAIVRTDRPAVNLMYFDSGPSVEI
+TPAYFRDTDDYDIPDPGGTGWIQSNPAVHLDYVNDAQKKTSSRAKSLIRLVKTWKARNSV
+PLSSFYLEMRVAKYALSNPTIIYDWDLRSFFKSLEGDGLREMNDPTNYGRRISTGASSLV
+DTIAAKYDIEQAVRSSSLALKAAQDGNPSLGVAHWRRLFGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002883.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaff325a07871e34d69669fbd88cc4e1a6af14f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002883.fa
@@ -0,0 +1,13 @@
+>GCF_020097155.1_00629
+MAHTTTPPSPRGGKRLTIADVPHMRERYAASNPLPPEEVAAGSNKKFTWSCKAGPDHTWE
+AQANSIRMSKRGGCPFCAGKRPSVTNRLDVLFPDLAAEWDQELNEGPPAVVAGSEKKVWW
+RCRAADHAWQANIRNRTVLRAGCPRCAAEKSSKTRSVPLPGRELTAVAPDVAASWHPTRN
+GTLQPDEVAAFSNVPRWWQCPAGHEWEISPAGRLSKGGAGCPYCSGRLATAETSLEVQRP
+DLTLEWHPTKNAPRTPRDVKPGTSATVWWICSAGHEYESRIANRAYLGRGCPYCSGQKIG
+YGNDLATKAPLVAAEWDHERNGSLTPADVTTGVQRRFWWSCTQGHSWRTTVASRVALGTG
+CPECGAGWRRSRPEIALQFELAHLLPAAVVGDGHVQTADKDFRVDVLCPELKIAVEYDGN
+HWHMDTFERDLAKTQALVEAGWVTVRVRQNPLPLTGRHDVPCENGDPAVYPMTVRLMTSL
+LEEAAAAPTDHPIHAHLDELRLRLETYVDGGTARAVEEAERETRAHHVDRPKRDPFAPPP
+RPKPGRSLAELNPAIAAEWHPSKNGGLTPADVANARNASAWWLCSLCGAEWEAVVGQRTR
+RQTLGCPDCGKARAGAARSRPQPGLSLADLRPDLAAQWHPTRNAPLTPHDVRPGSHKRVW
+WRSPGGQEWESSVYNRTSKRPSSEVHGDAGPDSPDSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002884.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8ba0f5895e8d7e5ce0c67743e5df5c8f929cf60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002884.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00632
+MTHQPPAEPAIIPSDTTHDQTADRKRARQWLKTLNVSPNPELVEGLIPLVSLYPKKSVLG
+FYAGRLLKKGKLPTEEAVLKLLWGQLEQIIYSIKALESRTGRDPFITPEQETEILQWVDN
+FWAQHGEGPLWSELAENFHWSRTQQNRLIHYLAARGLVTFSFAPRSLKTVRGATTIPSLE
+GPGSGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002888.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..182277c0bd76483ee2a6e77a1c8a0f52c9b4a3c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002888.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00653
+MSTRTTQQTVEDFFSAFGAGDLDTVKNLFAPTINFTVHGSPAVPWAGTRHTRDELDTFFP
+AFAALGPATEYTIHQIVVDGDHAVALGHNEFPVLATGKSFSNDFALHFTVQDGQITGYQM
+YEDTYAVDQAFTPTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002890.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0e6423437c963af8c537714cfa612cd7fd70147
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002890.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00658
+MAVGDKNALLVQVFDTMVADEHAQRAGATPQSTGDAPDTCVKRLGVLVQPFVAMFTGSPE
+LARSYASILVSGTHSSSLFTELHARLVEEFATAITKQGCTPAADAPAKAQALYAAYVGTL
+FTWSARGLVDPSAITNGLRTSFAAISICKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002892.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2477acebb1e3db93544570a3171f1d291194dda5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002892.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00680
+MSTPDELADEVADVRSLNALAEAWRTAPDGSRRFVPNFDPRSGGTSSRVLVLMQSPGPQT
+IAAAHTAICSEDNPGPTAAAFRAARIESGLARNDYLRWNLIPWEILGRVRPVDIDEGRHA
+LETLLKVLPVLDAIVTYGTAALNGVMRHLTLDEHPRLVPVIAAPHPSPANGRHRAEQQRR
+SVQALRLAALTHRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002897.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e2323a721dd120794ee69bc8e690ccb793122d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002897.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00691
+MAVFYSFHYDRDVHRVQLIEQMGALEGQPILNHQEWETVKSGGDTAIKEWISDKMKWKSA
+VIVLIGKETASREWVHYEIQKAWDDKKPLLGIRIHGLSSMGSVDSSGPNPFDKISSVSGV
+PIFDPTQTDWTGKIDSKATYNHLKDHLTTWATQGKTRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002900.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afd6bc54144005da38973888a2b390b405b420ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002900.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00704
+MPRTISVANTGEWLTRIAVGDAIGITAEATTHNHRAPEVVYLPIEDAPPVTVALTWPGQR
+RSHPQVGVVATCAQDYFTRLIDIGSPPRLLSTGADGQLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002901.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..375dcafad6ffd24f887b005c099c6503a0dbaed0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002901.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00707
+MPRFSRLTPETAVGASRDLLGDLVERHGQVGDMVSTMAHSPAVLGGYLDLSKAMRRAKLD
+RKVSELVSIAVQSKQGCGMCLASHISAARSLGVSDDEIALAQQGTAMTSPVAAMIALGLQ
+VYREPTSITDEQIDELRGYGYSDREISDVVGVVSLNILTGAFNLVAGLTPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002903.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d65fd09c4bf920de4c3c82842d49aa469265c2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002903.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00713
+MTYVIALPCVDVKDRACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+LPDEWSDYSKANVEFFDELGSPGGAAKTGPTGFDHPLIAALPIQHEQTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002908.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d414990fbe00bd61bf204dcb048fc34334bae14d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002908.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00737
+MGQTRRMPDPHELIAAALREQAAAERRLHGAVQAARDAGWSWTQVAEVLGVTRQAAHRRF
+HVAPAVALDDGGARGDGVPADVAAENGPGGASDPWAEARAAAEATVEAWLRGDVAAVHAR
+MTSAARAGLPQSALRGVLLEIEDLSGGLRAVRVTGVHDLDGELLSGEPASGGPSPAGGAG
+RAGRRRAVVVRCVVAGEDADPVVHVLIGPGGRVSGLSVRISDELEQWPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002909.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9d6b20215c987b0b38fbfb1d76cfe802ddb77b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002909.fa
@@ -0,0 +1,6 @@
+>GCF_020097155.1_00739
+MRRPSAPASRPSPAPEGSWLSRLWAAHAAFLVTGGVLLAVVVAFTSLAEEVYDSVTEGDG
+VPAVDHPALQAAISLRGPVLTGLAQFLAYAGDTPGAVAVGLVLLGLLTLARREATPAVVL
+LGGMAGAVLITVVGKSHVGRLRPPVDVALPPIVTSPSFPSGHTLNATVLMALTVYLVAIT
+PRLSLCGTHRRAVTAAAVVAGCYAVLMGLSRVYLAAHWLTDVAAGWTVGLAWAAAVVLAH
+RVWLTVQDVRRSRAGTPAAPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002912.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..285ff9855331bda35dea5d5e4153a75826d650df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002912.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00782
+MTGAERGGAVAAHPVPTHPEAVPGDRATLRWAVPAGLLGMVGPVGDGPAPLEALRADGTL
+RALVAEPAALRLTVGEGRTWRAEGARVRAALQEALALLAAGEATCAPEAPASVVGGPGGG
+GKARAVARAGASADSDAVLRAAVEQVLAGPAGEYLRSHGGTARILGVEDGEVELALGGTC
+HACPARGFTLQMRLEAEIRRLCPDVRAVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002915.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33233d36909ab5d0d5bdb702c225c9319c85f9bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002915.fa
@@ -0,0 +1,13 @@
+>GCF_020097155.1_00824
+MSTHPHPGDGAGIAASAAPQPAPGSPSSPAPTAPSSADRSGGHAAPGHRPATAERARTGM
+LMLAIGALGVVFGDIGTSPLYALQTLFSADHNAVTPSFAHVTGAISLVLWSLILIVTLTY
+VLNVLRADHHGEGGVLSLATLVRRHYDEATTPDSDTDVAQDAAAPGPERRRRGQWAFTAG
+LIGCSFFFGDSVITPAISVMSAVEGVAVAVPSLEHWIIPASLLILIVLYGLQRFGTGGVG
+MLFGPVMAAWFATLAVLGVGPLLDRPDILVALSPLPGLMFALQQPMVALVAMGAVVLAVT
+GAEALYADIGHFGRLPISRDWLFFVLPALALNYLGQGALILDDPGAVANPFFRLAPDWFA
+LPLTILAIAATVIASQAVITGAYSVTRQAMRLGYLPPLAVRHTSGKEAGQVYLPLVNWIL
+LAAVVLVVLMFRSSVALATAYGLAVTVTMIITTTLVLVHMATTWRRPLWQPVLLGTLVLP
+LELSFLAGNLVKVFEGGWLPLTIGGLVLGTMTVWHRGRVAVSHRWSRTEADLETFMAKAA
+HHVETGDLRRVPGHAVYLAPSARLAPAALRINLRANRGVHEKITLVHVVTEEQPYVAEAE
+RCTVREVGPLSGVHQAVIRVGFFDALDIPGTLRAHAAALGLTNRDLVQAVYVLSRSRYLT
+PRGHGPKTWGTRAFVSLSRLADQPVWQYGLPVDHTLEVGSRVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002917.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e45ce58ee571f9799b52fdc2d4ab50755ed74e47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002917.fa
@@ -0,0 +1,17 @@
+>GCF_020097155.1_00869
+MLRLVAGALALAVVLGLFVEAQAARRLRDLVDSSWRGSYDLVVSVPGAASSPASLGAPLD
+TAAWTSAAERLSPADLGRIRAVPGVEVAAPLGDFGVRSVANQDAVMIGYPADGSVQGPRA
+FDVDARVRTDDGLGPRPVLGMDATLIGSFSDGPILDARPLLDDPVVCTPAPPEPGPCTDV
+ELPTVAIGPRGQTPPPAQREIPAGTYWAAPWADPDPQGNRMVVVDAAAEAQLLSLGGHPA
+AADAFRVLAQSSPAGSLPAVVDRLSGATTEEAEALLEAKDRLPAYLQNLADAAGRPVESL
+TAVPLLATNVGSAPLSLEVRATPYREPVTRLDIQQGPVDPRDPTAPRGIVGMPAWALPAG
+GTTGQDEVSTSDISGRFGGLGLGVTVVPLPGLATGQDPVLSYDSPRLSLVEETRTLTRPS
+SADGTLTEAASVETASGTIPGRPDVAVSRALPASTSRESAYYTATDDGRRFGTGDAPLLV
+SVGTLTPEPDTALAGIAPLLTDVELPTTLVADPRGTPQDVRLRPASTGFGLANQMPAAYV
+DAASAEALGLARPFSTVRVRVAGVGEELTPENLATIDAVAQRLEEAGFAATTVAASSLAP
+REMQVVSYRFDSTDGEPRTGPLGTVRQLGPELAASQRVSAAVGTAGTSQAVTVVVLLTVL
+AGLCVAAALRPRRRRAGVLAVQGWTRDATVARHLREDAPTLLVLAVAALAVIGMMSGRLG
+VAVPLVAVGLGTTAGLAAAVVLAAVLAARPAASAVREGGDRAARPARTPAALLTRWTART
+WPRLLTGAAYRAAVAVGSGLLVAVVLQARREAGASLLAGEAVAQDLPFRLALGALSAVVG
+TVLLVQLHRVEGQAVRAEATVLLLAGWTRARLLGRHVPALAVEAITAAVVAGVVPALLTP
+DPDLPLVAGAAGFALLLTLLITLLTRRAQLARAWKGQPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002923.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b32813eb111d3b328acba2536ced3134ee7f2476
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002923.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_00918
+MASQEELTRIIDNINADVNGFIGASIVDMETGMPLASRSTRADFDLEVASAYNSEMVKSK
+LKTIQVLNIRTTLEDMLLTLGDQLHLIKMLDERTFLYVAADRSATNLALLRSAVNRHTVN
+FR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002925.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4084262623f1e12d48703c2560760f87abd86de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002925.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_00934
+MAQDPAGWRRTAVLLSGAWREALRVSAPRVEPEHLFLGVLASGGPAARVSARQGLSLTAA
+RRGAAVRANRQLRAVGEDVARAGRIPRTPLAAVDRGGAATLPLSAASEGMLPARRLAMTE
+AAWALDLLQEPAGAVSALVAAAGVDVDALRHALRAADRDEPRLPGAALDVMPAPCPVPPD
+ALTPPDGIRPSGSRASRAGRLSAIGAEWFVAAPREHVMRLLRDPEPIRAITAQPADAEVD
+DAFGVVTTVRSRGARGGEHRSTSQLFPSETSTPDGAARIRWAEVLDEHRPPHQDSDGTLV
+PDGRDYSGDLAGAYVFTLVDDSGPDPDQPVDYPGHQPLSGAGTRVRLERTRRTVRRRDAL
+ASRATRWPQAWAVAQHLQSLASLAADRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002926.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15ae72783cc4e613442ebc7b3abd2ac8ed8963cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002926.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_00940
+MSVRQPRIYTIPCDRRGDFLDRWQSTAQPLMETLGFRFVRTWEGTPDPVHRPHCRGCWAP
+RSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002930.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86417826b5b6c4bde31d1a313ef50a97a751f965
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002930.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_00973
+MTTAPTWIDAVLALVLLLALASGLRRGLALTLGSALGLLAGVAAAVLFAVPLGGLVPDPA
+WRPLAVVAAGVLLVVLGQGIGLRIGAAVRRALGRGALSRADGLLGGVAGLAVAAVVIALA
+APVARPLLPADAADEAGRSRVVAAAEHLTPEPVRQAAADLGTQARLFVAEAIAPVLPEPG
+LGGREAVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002933.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b643974e4f46be9a17c0e47beab83d1e2560f3c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002933.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_01014
+MSIDQNTADTTTPLATTGVRGRSRRRRTAVGALGAAGALAAVGMASAPAQAATVDASVLQ
+SIQACESGGDYTAVNPASGASGAYQFLDSTWATLAAAQGYASAADAPASVQDAAAQELYA
+QEGTTPWEASQSCWSDAASVAAMSTSTSSTTVSDAAVAQADVATPVETVAQVEPAAGAAD
+EAEADTAAGADAAAEEAAGEETDAGGTAPTAAPDAAASGEQAPAPSEPAPEPAPQGDQTG
+RQPAERPAEQGRGTAEQAEQGRGTADQREQRGQDVEQREGRTGGERQGAAPETGGDAGHQ
+EADAAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002937.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bb698c0c11ab60742b4afca38c2d020aceeb8de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002937.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_01056
+MALFTVLLPVLTVLSVLAIVIGTALSVRPTTTSAALLARVRSHGAATAVTALLLGSISGF
+AGLAAEARPEGPEWTWDAGEWHGVPVFLDAVWLALALALLPAILVAAVTVGAQRSVPAPQ
+GRVRRAVLTPRTAASLVPRGPALPGVGIGLALGATLVLLWAEPSVPRLFPSDGAQEPEGY
+TPLAAGAQLAPWILGALVADLGAAAIGLRAIAHRPPIIGLTAAQDRAARTVAAHRLVRTV
+AWMLWLLTLGAWGSVLLSRTQRDLLHAVFPGHPAALDARPGLGWIGTVDAWTGLATLAVA
+LVLLLWRPPALGELRTGPGIDRARTAETVRTETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002938.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e730dd8b267570e3642eb97bd538a0ac0b45b671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002938.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_01081
+MGAVTEQTPDAPHPSPAPPSATGGPAPAAPPVGPLTVRPITEAEHVEVLRRHPGASFLQN
+PRWARVKTDWSGQSLGFEADGRLVGAALVLGRRLPVPGRTPLLGRSFLAYVAEGPVLDAG
+VDVVEALAALVAELHAQGAFLVRVAPPGVVRRWDADTVRKALPDPAHRMLTDLEPAEEHA
+DALELERRLREAGWRAPEVLPGFSAGQPMFQARIPLEGLDEEGVLARMSGSSRKRTRRSL
+RNDLDVVVGGPERLDEWEALQDETAERDGFTGRRKEYFARLMDELGGSELADVTYYLAEY
+QGDPVAAAFHFRQGHVCWRPYSASSQKERKRDAPRLLEFEQIRQGIADGCHWLDLGGVPG
+SVDSEDRITGLTEFKTTQGADIVQTHGEWDFPLHKTLAHAFGLYMSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002943.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abe8c25dce1a5721334de8069f401b6c5b2499a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002943.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_01213
+MTNPFLGRDDQAIDVSDTPRGELEVVHTFTDGPMPTGVSVSHTGRIFVNFPKWGDEVPAT
+VVELVDGAVKPYPSAEANQAKSKADQDAFVSVQSIVIDPADRLWVLDTGSPLFEETQRGG
+PKLVCIDLTTDEITQTILFEPDVALPTTYLNDVRFDLRQGEAGFAYITDSSDQGPNGIIV
+VDLASGAAWRRLHDHPTTKALPPGEMVPVAEGRVFAERSAGEAPQPVKMGADGIAISHDG
+ERLWYCPLISRRWYSVDTAALRDRALSDEDVAATVVDHGDKGGGADGLESDDQGRLYATN
+WEHNAVLRRLPDGEMQTLVHDERLLWPDTMSVARDGHLYVTANQLHRQAKYQDGQDLRVY
+PYHLFRFAIDAGPVLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002944.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a4a89bfe40695803e8a869dbc6dd1f67c86183e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002944.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_01216
+MLEIADGMVTFTPDSPSAAPGWSVPARQLTLGRAGVRFPGSFVVRGAEAEDIMLEVSTSE
+GARWREAGDARDLPDRSTHREVQQILVGWGARSVRPRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002948.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6349a20eed8e4cc567f850c22d7805a498a02b5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002948.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_01232
+MTENQHPDDPRRPEDTGGGAVPGESARHGVEEGAPEAGAAGWPDKPPSAGWPDHTPVTGT
+GHGSSAYTPGGDGAVPGPYEQPSYGQPAYGQDAGTQQAGAHGQPQGAYGADAYGAGAQHP
+GSYEQQGPYGQPTGAYGQQQPGAYGAYGQPLGGYGAYGQQPGVYVTGAGAPRPASNGLAI
+AALVCGVIALLLSFLPFIGLVSVLIGAAAVITGVLGLRRGQSKGMSIAGIVTGALGLLIS
+IAVTALTAAAVSAAVQEGGPALSSIGASLSSEANAPHEVELRATVDQGDATVNYSIGGSS
+SDQDITAEQISVTDSVTGSETLSISVTEDVTDTGSQNVTCEILVDGRSVAKETGTSSAYC
+NAGYGDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002949.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c55e1a206d1005f159c160f31caee7bdfc77d4d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002949.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_01293
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELLGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDPTSRTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002958.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86441197ac336f588de5bc5653818ebe3b5de46c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002958.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_01593
+MRAGRRSRSLTSETEAKAGSCTTKDGKSYKAFGRFADEGAWWDAERGGFVFDASFDKAFH
+DGQIWFFDVKAGTITIDAYYPLTAPNFSEERRSAPAADRAAPGGPQLTNKLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002959.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7f1f6d0f9f1cd5a46746c547be3ff076a0a4d8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002959.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_01708
+MPRALIVVWALLIVPVLFCLVVVGGSAVAHASSSAGPATLRSALPLGAALLTAVAGTAAA
+RHARAPAARSVLTVAVALLLLAVAAPLVLSLFAAGTEEWCEGQPGGRGGAPITSEADVPL
+LCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002961.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..43efc5dcbd73fefc560efa65268d3b6578b779a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002961.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_01733
+MSETHSTSTAPSRRGVLAGGALAAAGVIAGTAAQAVPAEARGGRHPQGASMPLAFGATRR
+MKIVQFNDTQGGHAADRRTIEFMGKVLDQEKPDFALINGDVIDGSPTTDVQVKQGLNNFV
+SPMESRGVKWAVTFGNHDEDSVEEHGTSMTEDRLLEFVRQYKHNVNPPKMDGVPGHTNAQ
+ILVRGSRGAAPAFAIWLLDSGRYASEADTHGQSTDGLKSYDWIRPAQIRWYEDASAATEA
+RFGRRTPGLMFCHIPTFEHEMMWHASQAAEEASDHAEAVRRHRITGVKHEDVYHGLVNSG
+VYASVKERGEVKGIYCGHDHINTYTGDYYGVELGYAPGTGFDPYGLNDGTWDQHTLRGAR
+VFELDERNASVYAGATRIVWARDLGIDMNPEGQPLATPVPFPPYVKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002965.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7aca08a47f2512ed41be15e453a27dfe9704666c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002965.fa
@@ -0,0 +1,10 @@
+>GCF_020097155.1_01768
+MAVTQWPIEMAELSSLVLDPRNVRVRAGRGDGLAHADDEHAEQAIAKYMVEAEDLFDLMR
+DILRDGYLDNEIPVVVRDADKFIVAEGNRRTTALKIIANPKLLGNPMSLRVERMKARYPD
+HDSPTSIRVMIAPTWEAAQPLLARLHTGQPKKSWIREQQAIFYHAQLSDEVTVDDLRVRY
+PSEASTIPKKIRMGEMREVIRRLKYDDSSLRDFVMNSELKMTTFEYAYTPKKLHSALGLE
+FTKDGLLVSKDISDGQRRGLIYLLGRFKDKSLNTRSPELIAKNATEHEEFSKLLRGIVEG
+TPLEASTEDEGATKDHTNNQDGEPGEASGERNSAAPDDISRDEGRHRGTSETDEASTSGD
+ATASRGPNRGDTKSRLNMEGFEYQGTSPGMRRRFEELRRLDVRDFPNATHDLLRTVLECS
+IKDYFQSKGQPLPPGKTIGACIGELAREFQGNPKMTALINSINRKGRLTAEQYAGTTPSL
+NASNHELDHFAVGPDVHAAWDRIQPILKEIVGTKKQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002970.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6851d11b7ad0dbcda30b007c607801777d0186a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002970.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_01779
+MSPNLYHLARLLAPGSDRSLGRVAGDLASAHVPVFPCVPGQKRPLTARGFHDASTDLAQI
+EHWWARWPEANLGLPTGASGVVVVDVDVREHVDGRESMRCALNAGRVGMPVFTVVSPSGG
+RHGYYPATPDVVQRSWQVARAGVDFRGDGGYILIPPSHTTAGSYRLATVRQGAASGIDSD
+TLRDFLDPRPALKPRAADRGMAQSEPGVVVWRLAAWVAGLGEGERNRGLFWAACRAAEHD
+ITPATAVETLGAAAAEAGLGPREIAATVRSAYRTTHPTTSTARRATEPAAASPVRVPVGA
+GWGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002974.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..125a479e5530dd9921be7ae7057a3d0452e49090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002974.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_01786
+MFWWVHLLGMDTSDRSSRRRLVLIAAGSVTALVCGVGIYGLATGPRTPTSTPGTSPTITT
+SPSPSATSTAKPSASGAPLVPPVASSADPEQFARNVATTLFAWDTTTGLLPLDYTSAILA
+VGDPSGTEQAGLATDVAAYLPSRTAWQDLREYGTSQHLTIARAYIPDQWGEAVAQAPEGQ
+LAPGTVAYTIEGTRHRTGTWNGEPVASAHKVEFTVFVVCAPTYDTCHLLRLSQLDNPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002980.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58e0150c769b50a1aae5d8961c79cb3b9fd14e0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002980.fa
@@ -0,0 +1,11 @@
+>GCF_020097155.1_01800
+MSASQRQSGSMGEELTNAALIGLIALFLLTLVLRAAGSVAAFLTGAPQPTASWAAGAGVL
+FNPGNPAVALGAPGLSPVAYWVTTIVALGGLVALAGWGWVVWRRRSHAQVVDPHRLAGIA
+TRHEVAQVASEKALLKRASTLRPSLKDPALGEVGYRLGTSKGQGVWASVEDSILLIGPPR
+SGKGLHIVIPAILDAPGPVVTTSTRPDNLTATLRARQRRGPVAVFDPQHLAEGLPAGMRW
+SPVRGCEDSLTAMIRATGLASATGLSAGGVESGGFWEGKTRTALQALLHAAALDSRKPAD
+LFRWTLDPAAAAEAVAILANHPDAAAGWADSLGAMIDADPKTRDSIWQGVALALGALADP
+RVLDAVTPRDNETPFDPETFLRESGTLYLLATGAGAGASAALVAAFIEDLIETARRLAAR
+SPGARLDPPLLLALDEIGNLAPLPSLPTLMAEGGGTGITTLPVLQSLAQARDKWSDHQAG
+AIWDAAIVKLILGGASNSRDLQDLTTLIGERDEYTDSVTLGDHGTRSNQRSVRRVPILPP
+DRIRTLPFGTGVALLRSAPPIITDLTAWPTRPDAEALKRDRARLEQLLQNPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002983.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3d30f3fe57444439ca860eabda52e5e09fd6c79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002983.fa
@@ -0,0 +1,10 @@
+>GCF_020097155.1_01804
+MAGQFCFCGDVGRGIDAGVYEDAGGGLLGCVGGVLFVVDGDAGEQGAVEDASFGWVALVV
+ELVEVDEEFGELVQACSGVGVGVGEVVEPSGDLIEAGADAVLFAFEEVEGDRVGVVSLDE
+FEAFGFELVALGGQELAFVLARSFELIEHVVEDLPDVLRLGLGQGIALVGAFDLRFGAFG
+KDRGAGAVGGLAASSGAGEVLVAVPGLVAGAFDHELGSAGAVQRAFEVVVVLLGSFAAGV
+VGVEVGLDAQPGLGVDEGLVGAVVGDAAEGDGALVVGVGQDLVQSGGGDWFGRLRGGGPG
+GQATGCEFLGQARQGPVPGGVGGERETDEVGAFGVDLDLAGLASSGVGGADVEVAQRRFG
+GGATDRGLLGHAFEDFLGQVQRVELGHGGQDAVHQHPRGGLVDVLSDRHQTDVRIPQRGV
+DHGVIEPVAGEAVDLVDDAVPHRMRGRVVEHLLERASLGGLGGLAGLDELLDDDRTELFG
+LALRGFALGRDRQTLFQPVAGGLILGRDPQVADRRHLPLSPGRCGVWAWCGAGEASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002987.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63073f26e0f65698a4cdc3b3c5382f07551f311b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002987.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_01830
+MLFVDAIVVKVRDGQVRNTPFYVVMGVTVHGERDILGIWAGDGAEGARFWLQVFSELKMN
+RPGFVRGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002991.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f32b4ba357764dc7705d527c0eb0b32ed7854964
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002991.fa
@@ -0,0 +1,6 @@
+>GCF_020097155.1_01873
+MTEQTPAPGPGVDSVSTGVHREPFSAVGPWKDDPAAAGQVVFTSVHSGHALRPEVAERMV
+LAEADRFREEDPFTDAIGAGVGSGLVMHRSRFEVDLNRPRATSVYTSPEQSWGLDVWRGG
+RLDEDVAERSRQVHDAWYAELGRRLDVLAGRGPYVVFDVHSYNHRRDGAKAAPAPQEQNP
+DVNVGTGSVDREPWAPVVDGFMDSMARPLVAGLGRRLDVRENVKFWGQNEARWAHRRHPD
+QACVLALEFKKEFMDEWTGQPDAAVVRELSAALADAADAVAQALADVKVPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002995.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbdbc74612a94dec5a4f4f3b61e9a036e28109f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002995.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_01912
+MEHISGRPLTRRGTLLGLGGAGVAGALGLTGCSSAQTTSAPQTSASPSSSPVAATGIEDL
+AVGQDAVVRASLTTAWLKPDVDRGWTDEPVTQADPRPDEWLPRMDDTLQRGLLGRSDTQA
+ALGSRVTVRELSGDWARVSFLDQAAPNDFGHQTSWVPRAHVVRDLGFLSAQQADGAPIMR
+VTAHSTGVYEGEDMEKTLVVVPLGTRLPLLEEGDEASKVLLPDEREGWIAAADTAVGEPA
+LGTAEQVFETARSFEGTPYLWGGMSRFGIDCSGFTYTVLRAHGILLPRDSGPQLYDSGLP
+RVAADDLTPGDLLFYSHVPGGRRIRHVALYLGKGRGINAPFVGRPVTVETLEQLNAKHDY
+AGAVRPRYAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002998.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..815d259a4635badb352deba80ddc9ce13f98e8bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0002998.fa
@@ -0,0 +1,13 @@
+>GCF_020097155.1_01979
+MALTIMSRVPDAQPYRDEDLDGRIGAAGLAGATLEHGLLRFHTHESGSEAARLLAFHFPP
+GFTEGWVPFAVDWRGRQYCRVRQDGVDSAVRADPGLFAASSVVDFEVFMDTVLTDPGAAR
+VLGAEDCAAALAARGISDLPFDQCLGYMLPPFAGGEDHSSNILDVPVNPYWAAMADMKNQ
+WQHRQPGAHAIAVAARDGGLTLVFDTDQDPEHSPGAGTRAERLVVTSPHGPAVYNHGLAR
+ELTDEQAREAAEAVREAFGTPDAAAPFLMDWRARCYAVERVDGRDVVVRSCPVTMTRTPV
+AEADGFRDRLAGNPALLDLFGEAEKSLLCARLRLTEIPAGDVLVPPAPPSVAGPEADDPA
+TFRLQSASVAWWLAGNLARLAREAGPERRLQGYVLTPEGRLGLQTAPADGPTPPPRPSED
+TAGLPPVRFAPRFAALAETGVVQTAQDDDAAPDKDAGDAQMAIAWYGLAGRVYNAGLFRF
+LGAEGVAQAAGHLRESFGGQAAEAVPVIVDWLGRYAVREVVEGQSMLVSYDAASGQREEL
+SRFEDGLEQILVTPVARELFDEAGFRRALDTLGLVRIGQGRCVGVKRPLFLGGDESPENW
+EDDSLDVHWSWHGRVFAQARAMPEGARIQRVEPLEDGRPLIHYTLPDGRTGDGLSGLHDG
+GAPGVSEAAAARQDGSGPKQEKGFFGRMFKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003006.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e89ef6f8f50aa7d217046ae9d7483e831ff83ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003006.fa
@@ -0,0 +1,5 @@
+>GCF_020097155.1_02172
+MDPATISGRALGAVLAVVANAPAMLPRRQPLHPRGRTRRATWRVHAAWPESGIAAFAAAG
+DTPVLARTSRAVGLPEPLPDFTGLALRFADGGALLFASTGTGPFTRRLLAPRVPGAVDPL
+TTLLPLHCRLGAVDVGAQVRGDEVGILTSLDGGPWVDRARVVLGGPADVVVRFDPLRPPV
+GLWWSDFWAAARSPAYALARRLTPGAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003007.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5330105a42bdfdf9a173418cb29bacde8ffff8d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003007.fa
@@ -0,0 +1,2 @@
+>GCF_020097155.1_02173
+MSDQQSPEAKNSDAPGDQDEAMQRQAPAQVDCLAEKAEEEAEQDKGGYDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003008.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3028a797a0cf4f3e06e4e5b088f06a9c58c6a09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003008.fa
@@ -0,0 +1,7 @@
+>GCF_020097155.1_02176
+MYLVPILCALTGALFLALGSERQASGVRALERGDGARPGRGGALRLLTSPVWLVGGVLML
+AGIVLNVIALAWAPLTVVQPLGAVAVVVTTLVHARVAGLRVDPATWRAVAACTLGSAAFV
+VVTVQATLPNPVPDADQETLTAWIAAGVVVVGLVAALALRGRRSALVPIVAAGVLYGFVA
+VCVRMSAVRLVDGRPPAWGVLAVLVAGAVLGVWFVQTAYRHGPPDLVVAGLTVVDPMVGV
+LVGVLVLGEMRPDAPWWVGPCLLAAAAVATVGIVRLSRSHPDVLARREERRVADTPGETT
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003014.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..944422a27152e9da40b541a5e89628e368cd85ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003014.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_02227
+MDTLTGSRHKNLKELHPGSSGRSEIRILFAFDPRRQAILLVAGDKAGAWKKWYATNIPLA
+EERLDAHLHALRSTPPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003016.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a36296c79e057b865f2ab82898614c545716b553
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003016.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_02233
+MTLTLIPPTTPDEATQQLAQLQGTTVALAVLRRVQLVKAAEVGVTQQQLAGALGRAQSSI
+SEYLTRARTSLADRPATHPLWPAEVIDLYAAGLLPRDEVLAYLASYPYIDPAPTDDPAYT
+VTQPGEFGEVAAAHWNDKLSDTDYANLYDLLHADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003022.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2e45ec6dfa0fdb52f7a2c357056b827dc0595da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003022.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_02258
+MTDTFPTPLLRRRASRTLALGGTLALAAAMTGCGPDPDYRQTSEDYAQVCRDETTQERVP
+DEDCDDSAGTSHAHAGHRTGWYFIPLAGGRTVPAVGQRAGGGLTTRPGTGTTTKVPSSGG
+EFAKSGTVSRGGFGSKGGGAGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003024.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f06cc46e802f6c87b36954bccdd8de8853c1532c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003024.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_02274
+MDHRTAAAASPLPSEPAVAAPVGGSDTPLTRFLRAGEAGDAAAARGALHPDVRLVSPMAG
+GAVMRGPDDVALLLGEVYAVLRGLEWVEHYADGRVHTVLGRARALGVALTDAMLVTVAED
+GRVLEIRPHLRPWAGLTAFSAALLPRLLRHPGLLARSTRPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003025.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bb5a3338004762975ca8560ebd2bb233bfb32c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003025.fa
@@ -0,0 +1,15 @@
+>GCF_020097155.1_02279
+MSTAQTPREPEHGGLEPTPDQVPERDLREQHAELVERIRAARTAYYQDDAPEISDAEYDR
+LYRALEDLEALHPELASNDSPTQEVGGEASEAFAPVRHGSRMYSLEDLFSLEELETWFLR
+AAGSLAEVRPGRAPRWLVEVKIDGLAVALRYRRGRLVQAATRGDGVTGEDVTRNVMTIAD
+VPQTLTGEGWPEEFEVRGEVFMPSRAFAELNERRAEEGQAPFANPRNAAAGALRQKDPAV
+TAQRPLSMFVHGIGTVEAFGADGQEEVYGMLAGWGLPVSPYTRVVEGADEAALTRVVDVI
+EEYGRRRHELVHEIDGIVLKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTRLLDIAVN
+VGRTGRVTPFAVMEPAQVAGSTVSMATLHNQDVVKAKGVLIGDMVVLRKAGDVIPEVVGP
+VLPVRERLLAQGEDLREFVMPADCPSCGTPLAPAKEGDVDLRCPNARSCPAQVAGRVEHL
+AGRGAFDVEALGEEAARWLVIGHGPDPAEHEGMVLPEGAGPITAEAQLFDLASGTPEEVT
+GPRGEDGLTDLQRSLGDVRVWREGRTKVDGRMVPSGVFSLKPYFFTAGTAKKPAAPTANT
+LRLFDELEKAKTAPLWRVLVGLSIRHVGPAAARSLATAFGSMTALRAAAEAGERDRLAEI
+DGVGPIIADALIEWFAQDWHREIVDRWAAAGVVMEDEQDADTPRTLEGVTVVVTGSLEGF
+SRDSAKEAILVRGGKASGSVSKKTHFLVAGEAAGSKLEKAEQLGVPVLDEAGFVRLLAEG
+PAAFPSEDADAETVDAAAEGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003026.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81a69ecbf1f3802674be0b9dcf3a0fedc3de4f5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003026.fa
@@ -0,0 +1,2 @@
+>GCF_020097155.1_02306
+MDRPRRPGLTPTPSPDGAAAEEHGVTGLASHVPSQMTPAILGAADLILAATG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003029.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f93d1b74982859db0f59abfefed50d020b768121
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003029.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_02421
+MSDCEPCDLQSVPAMTDTAPALDVDALAADPVEQFHRWIRQVVGSGVPEATTVTFATVDA
+REQPDARTVLRAVRVRGGVRDAPLPEGARMRTVRPERVEFWQGSPEDHRHVRIVYTADDV
+GGFRGEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003030.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ddf36da95039a3803c62afba608f3c951d8d426
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003030.fa
@@ -0,0 +1,4 @@
+>GCF_020097155.1_02423
+MTQPAPGPPAPWPASGGPGLAPAPWPGPDWQRAHDQAIVFGILAVTTGMLGLVFGPLALN
+QANRARAIGPDVGVARVLAWIGIGLAALSLLFLLGYFLFFGVMMAEMLRQLSQLSSGGTF
+AALGAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003031.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d00ac6af9faba070ba429f0c2699d04b5d2cd151
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003031.fa
@@ -0,0 +1,3 @@
+>GCF_020097155.1_02428
+MTAPYRPQPQHQPQTVVVQQSRNTLIAYLLWFFLGNLGVHRMYTKRWVSGVVQLLLAWGG
+AATAWLLIGWIPLAIWAVWWIVDLFLVPGMVRDANAREAVDSWRTVGVRRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003032.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..176b0d137f0604d1dc1799a9c7281684139cc484
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003032.fa
@@ -0,0 +1,8 @@
+>GCF_020097155.1_02483
+MRLRHLSAAMAAAALAASGAAVAHAAPSAHVSASPGARATAVADAHDVRVATYNASLNRG
+TEGELVRDLTTPDDQQAKNIAEVIQTARPEILLVNEFDHDAAGEGARLFQENYLSVGQNG
+HAPIEYRYRYTAPVNTGVPSGLDLDQNGTVGGPNDAWGFGLFPGQYGMVIYSQHPILEDR
+IRTFQDFRWADMPGNVMPEGYYTAKQERQLRLSSKSHWDVPVRIGGTSVHILAAHPTPPS
+FDGPEKRNQRRNHDEIRLWADYITGGKTAEYLYDDAGVHGGLPRGERFVILGDYNADPLD
+GDSWDGAIDQLLQNRRVRDPQPRSAGAAEASVLQGGANRTHRGDPSLDTADFNDVPAPGN
+LRVDMALPSRNLPLRGAGVFWPKQGEPGSELTGTYPFPTSDHRLTWVDVKVPGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003039.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0b37a765280139c6420c792744d94c0fba3b91d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003039.fa
@@ -0,0 +1,5 @@
+>GCF_023573625.1_00162
+MMVFPAKFSELNALELSDEARLILTRIIRVAFPHPDFPDGPYERMAQKIIDASEESRWFR
+MALTQGLVTLDSMSDGHFLELPEDRALAVLKRVADLEFFGFIRRTTVLNLYDDPEVQATL
+GYEGESFSKGGYLHRGFNDLAWLPDPRIEESEEQVTEIGPLPYTVAPATPEGGVKPVPDL
+FKGTGTVDEGSKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003040.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35726080e6c6c60ec9714c0e308575769c1fbb14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003040.fa
@@ -0,0 +1,10 @@
+>GCF_023573625.1_00163
+MSTQEISASIDHEDDSAVVIVGSGAGGGTLAHELVEKGIKVVLLEAGPYLKNEDYEQDEW
+AAFNQMAWLDPRTTSGSFRLARDFPNLPAWIVKAVGGTTTHWSGATPRFKAHEFKARSTY
+GRIDGANLLDWPITLSDLEPYYERAEMKMGSTHRQGRPPLPANNNYKVLANGAERLGYRH
+YATGPYATNAEPYDGRPASIQDGFNFQGDKHGSKWSIMVSEIPKSLRTGLLDLRPESQAV
+QITHSPEGRVDGVLYSDAEGNLHRQKARIVAVAGNAIETPRLLLLSASPLFPDGLANSSG
+QLGRNYMRHTTGSVYAQFDEPVNMYRGETMAGLIADESRHDVDRGFAGGYYMETISLGPA
+FLASFADPGAWGPDFTALLDGYRNTAGLWIVGEDMPQETNRVSLNTTVTDRLGLPVPNVH
+FDDHPNDVAMREHGYQQGSLLYEAVGSVSAHHAPPYPSTHNLGTARMSERPEDGVVNQFG
+QAHDVPNLFISDGSQFTTGAAANPTLTIVALAIRQAEYIADQMAASEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003046.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bd25c090782c743c68f6d52df709586d323401f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003046.fa
@@ -0,0 +1,7 @@
+>GCF_023573625.1_00775
+MSIVIGSLGGIFLWLIYQAIGTRWPEVYATARDSLDLMPRRSSVKYLLIYRGIPTFSVTV
+LALNLAVESGGDPYWTSAFVFWTYSTLAEIRSTFSPKGALRQLSTVNTVYLSASVVVTTI
+YCSVAVLVYPHFSVLVPSVRELVIALWTALFASVLAISFQRFNTRSGPDVQMEIDYSIKD
+IGQKTWSQIDSICMRENIDPCLIKALAAAEAQQRPRWIRQAERVAGRLFGGGTFGVGQWP
+SSRPIDDLTSIEFRAKQLAPVGLTPHECDIAEVYDFLDIDYFIYSWNSDESFADSARGFY
+SAFRRAKMVEHVAESDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003049.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..935b38d163c0cb035f736f932ce55b1fd2d16e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003049.fa
@@ -0,0 +1,2 @@
+>GCF_023573625.1_01060
+MDVLSPVFEITTLVVLGVILLLDLLYVARRPHEPSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003052.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71fa61c3e5f52902477392d39f223b32edbbb5ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003052.fa
@@ -0,0 +1,3 @@
+>GCF_023573625.1_01348
+MCDAHRHPTIIRENASTMKQTYATPAHVGTNARSVTQSRFGAGAVNSRFTRSGCRAAVGS
+GRVVFTRFDLVAPLIPAARMSRPV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003054.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7cef958ee677a3be8cfdb9de2c131a925f0114f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003054.fa
@@ -0,0 +1,6 @@
+>GCF_023573625.1_01548
+MLTLGSFALFRSGERNKFGPLTMLSAQFVSHNLTVQVMQYAHIHDEINEQLFSSRHLGEL
+LLETLGFSYEDFCAVREAIVRVHGEKFFAIRDFIGEMFEQRDEKKNDLAFEKDARSALMS
+MLELPGEGATLTVQEIVEASGVPADRTQAILDRFGLSFNDAEDALAVVTKFLSGDNPFRS
+ASLVKDADGNYILTGKPIGTDCFRQVVEDALKRVPAKFRRYEKRRMLVVVGHEVLDIRTG
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003055.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f885e8f4ca5726d086fb689217e64867eb85c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003055.fa
@@ -0,0 +1,3 @@
+>GCF_023573625.1_01550
+MVTADDEGLAAAFERMGEILGRMNEGENPSEYVRRGPAIIAEHVQAIAESLKDADAFDVI
+ELMRMREMPMILEGYGRVNLSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003058.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..751753b63908841c660bc7c59525078a80b1f440
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003058.fa
@@ -0,0 +1,2 @@
+>GCF_023573625.1_02029
+MAHHWRAVTEHPKGARSIQVLTMPLPELVRTLDAHELDHPQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003066.fa b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1b913729b0db1fface2ff997cc7a03c64f9b05a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/Orthogroup_Sequences/OG0003066.fa
@@ -0,0 +1,4 @@
+>GCF_023573625.1_02210
+MNVPERGEARMRDAIHHAMALPQTALGTHCFVWGEVTTVNHTSAEPPHWFLNVRSGTDRL
+FAFHMSAATAKAVVEAMNHQRGLRWQSLFDAVDAQFMVFGYLKVAKNGVPMVSVKELSHL
+SLRVP