diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5adc3b3f89cde0316de40f2285a04a17a019a2f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000002.fa
@@ -0,0 +1,112 @@
+>0_1024
+MFRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRGLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>0_1339
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>1_304
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>1_316
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>1_751
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>1_1078
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATSITRHTGGW
+IELQESA
+>1_1284
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>1_1610
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>1_2208
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>2_739
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>2_1255
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>2_1278
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>2_1288
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>2_1293
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>2_2281
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>2_2297
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>2_2571
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>3_302
+MSRFQTLSDAQWELIAPMLPARTGRQGRPFADARTMVEAIIYRYRCGIPWRDLPEVYGPW
+QTVWTWHRRMAEEGTWDTVLATLTAAADAEGLIDWSVAVDSTIARAHQHATNTTRLTGGW
+IELQESA
+>3_604
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>3_609
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>3_1758
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>3_1798
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>3_2156
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>3_2179
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>4_108
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>4_974
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>4_1486
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+VELQESA
+>4_1824
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee031c87b5d99186619b85e58931fa73616a7d44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000003.fa
@@ -0,0 +1,104 @@
+>0_1023
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPIGLDADAYKGRNVIERQYAHLKPWRGLATRYDKYAIIYRAAVVLNAVIAWS
+KRLSDMP
+>0_1338
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>0_2219
+MAAEGTWDTVLTKLTAATDAQGLVDWSVSVDSTIARAHQHATNTTGTQGDRSSDTNLREE
+PANHGVGRSRGGLSTKIHQLVDGAGMPLVNLITPGQAGDSPMLLPLLEQLRVARPVGRTR
+TRPEAVLGDKAYSSQPVRAHLRARRIKAVIPEPADPRGHRKRSGPRGGRPVGPDAAAYKG
+RNVIERQYAHLKQWRRLATRYDKYATVYRAAVLLNAVTAWSKLLSDTP
+>1_303
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>1_752
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>1_1077
+MLLPLLAQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>1_1283
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>1_1609
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>1_2209
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>2_740
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>2_1256
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>2_1279
+MLLPLLEQLRVTRPAGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>2_1287
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>2_1292
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>2_2280
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>2_2296
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>2_2556
+MTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPV
+SLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>2_2572
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KALSDTP
+>3_303
+MLLPLLEQLRVTRPAGRPRTRPDAVLGDKAYSSRAIRAHLRSRRIRAVIPEPADQRGHRR
+RRGPRGGRPVGLDATAYKGRNVIERRYAHLKQWRGLATRYDKYSIVYRAAVVLNAVLAWS
+KRLSDMP
+>3_608
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>3_1759
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>3_1797
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>3_2155
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>4_109
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>4_1485
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>4_1825
+MDGTGLPLVSLITPGQAGDSPMLLPLLAQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4101091fad2779fd97a79f5cab76b0f7fda2aef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000004.fa
@@ -0,0 +1,190 @@
+>0_355
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_1345
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_2008
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPLTQTS
+>0_2051
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>0_2216
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_339
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_973
+MGRTQWPLTDVPRDRGGSFTPRLVPKGQRRLGGLDDMIISLYAGGMTIRDIQHHLASTIG
+TDLSHETISNITDAVSEEVLAWQSRPLEEFYPVIYLDAIRIKIRENSQVLNRAAYIAVGV
+DLEGIKHVLGIWVQDTEGSAFWAHVCADLANRGVQDVLIVCCDGLKGLPEAVEATWPDSM
+VQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSAA
+ATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWLA
+ICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_976
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVCKRP
+>1_1086
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1696
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1769
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>1_1964
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_218
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_219
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYA
+>2_625
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_875
+MVQTCVVHLIRAAMRFVAYQDRKKVAAALKPIYTAPNEETARKALAEFEASELGTKYPSA
+AATWANSWERFIPFLQFPPMLRKVIYTTNSIESLNFQLRKVTKNRGHFPSTEAAVKLLWL
+AICNIEDKRAAERARDRGKPAGQRKAQGRLVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_879
+MTDTADAQNPLAGVLSADQVDALVNAAEDLGEGRHGVEELLSRMTQAVLERALETEMSEH
+LGYEAGDPAGAGTGNSRNGKTTKSVQTLQGPGQITVPRDRNGSFEPVIVPKRSRRLGRVE
+DMILSLYARGMTTRDIGSHLEEIYGSKVSAATISRVTDVVADEVAQWQSRPLETVYPIVY
+IDAIWLKIRDGGVVTNKACHVAVGVDLEGRKQVLGLWLGVSEGAKFWANVLTEIRNRGTK
+DILILCCDGLSGLPAAVNSIYPETVVQTCVVHLLRSAMKYASYADRKTMAKDMRPIYTAA
+TVEAAQLALEAFAEIWQTKAPGAVLAWRTAWEDFIPFLAFTPEIRKVIYTTNQIESINYQ
+LRKITKTRGSFPSDEAAIKLVYLGIRNIETRRGGELGTGTQGWHQALNAFAVQFPNRLPL
+>2_1476
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEAPKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>2_2052
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYGKGSEDASKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>3_1790
+MSESTTEMTGPMIDPVTGEIIDQKDLAEQLLAQAKEQGVRLVGPGGLLNQLTKNVLETAL
+EAELTEHLGHDHGQTPIAANMRNGTRSKTVLTEIGPVEIEVPRDRDGSFEPVIVPKRKRR
+LDGTDQIVLSLSARGLTTGEIAVHFEEVYGAKVSKDTISRITEKVAGELAEWSSRPLDPL
+>4_111
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1493
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1495
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1821
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAIEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
+>4_1914
+MTMIDEKNPGEPSGQDLVEQLKASGQLDALFAQIDAGGVELTGDGGFVPALVKAALERGL
+QAELTSHLGYEKGSSEALKHANSRNGTTPKTVESEVGPIELDVPRDRGGSFTPRLVPKGQ
+RRLGGLDDMIISLYAGGMTIRDIQHHLASTIGTDLSHETISNITDAVSEEVLAWQSRPLE
+EFYPVIYLDAIRIKIRENSQVLNRAAYIAVGVDLEGIKHVLGIWVQDTEGSAFWAHVCAD
+LANRGVQDVLIVCCDGLKGLPEAVEATWPDSMVQTCVVHLIRAAMRFVAYQDRKKVAAAL
+KPIYTAPNEETARKALAEFEASELGTKYPSAAATWANSWERFIPFLQFPPMLRKVIYTTN
+SIESLNFQLRKVTKNRGHFPSTEAAVKLLWLAICNIEDKRAAERARDRGKPAGQRKAQGR
+LVEGQAVTNWKQALAQLAAAYPDRINPYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d9dfa0d387170d57881e81d91a055e343d82f95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000005.fa
@@ -0,0 +1,162 @@
+>1_1728
+MDGDQDEMAGPGVLAVPEREWEQARLRAGVIGRLAEHDPVGLAAVDEAAMELGISRRRVY
+VLLERYRRGSGLVTDLVPRRSDGGKGGGRLTEPVEQIIRELVCQRYLTRQKRSIASLHRE
+ITRACAVQGLPAPARNTVAARIARMNPVEVGRRREGAESVRPLQSAGDEVPVVESILDQV
+QIDHTVMDLIVVDDRDRQPIGRPYLTVAIDVCSRCLVGMVVTLEPPSAVSVGLCLAHAAG
+DKRPWLERLGIDAAWPMSGKPKALYVDNAREFKSEALTRGCDQHGISLDYRPLGRPHYGG
+IVERVIGTAMRQIHELPGTTFSNPVERGAYDAEKMAALTIAELERWLVLAVATYHDTVHS
+TLGQTPAGRWVESVAATSTPMTTANPTAFLVDFLPVFRRKLTRTGFVLDHVHYFANALKP
+WIARREALERFLIRRDPRDISRIWVLDPEGTAYIEVPYRALSNPAVSVWEHRQALARLRE
+RGATEVDESGLFRMIEQMRTISETAQKTTKRTRRERQRRTQTGTTTTRPTPPVPEPPVVP
+TDLDVVARFGEIEQW
+>2_1257
+MSHANAALTPRHRLIVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGEPMQDRSSR
+PHHSPNKTNQQTARRCVRLRLRLREGPVQLASRLGIAPSTVHRILTDVHLNRLSHVDRAT
+GEPVRRYEHDHPGSMLHVDVKKLGNIPDGGGWRYVGRRQGDKNRAATPDKPKNKHYDPLM
+GMAYVHTVIDDHSRVAYTEIHDDETARTATAVLIRAVEWFNARGVTVERVLSDNGGAYRS
+HLWRDTCAELGIRHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDDWLH
+YYNHHRPHTACGNLPPFSRLINVSGQYS
+>2_2224
+MSHANAALTPRTRLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTSPAVVKQIVAARWRQRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDAYTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYSSETERRAALP
+GWLHFYNHHRVHSAIGATPATRLNNLPGHHT
+>3_212
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_213
+MVVQLRTVEKWGPARIAGHLSTVGDGSINISPATVWRILNRNGISRLRDLDMPTGESKRE
+PRRYEHAAPGDMIHVDVKKVGRIPEGGGWAVHGRGTEEALASRRVASRRPGYVYIHAAVD
+DHSRLAYAEVHPDERAGTAAAFWLRAVLFYREHGITTFSRCLTDNGPAYRSKVFNDALAG
+TGTAHKYTRPHTPRTNGKVERFNRTMKEEWLYVRAYASDGERTAALAAFLNTYNHDRPHS
+SLGNKPPASRVPITSYRVQPQPKVLDVPQIEGLGHEPTLFDLL
+>3_298
+MSHANAALTPRARLRLAKLIVEEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_301
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>3_431
+MVDRSSRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRL
+ARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGT
+RDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVL
+SDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETER
+RAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
+>3_610
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_614
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>3_624
+MSHADAALTPRHRLKVARLVVDDGWPISEAAARFQVSWPTVKRWVDRYLSGEPMSDRSSR
+PKSSPNRTPRVVAKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARMNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGGRNRAATPDKPRNQYGGPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFADLGVTIERVLSDNGGAYRS
+HLWRDTCEALSITPKRTRPYRPQTNGKVERFHRTMADGWAYARCYTSEAERRGALSGWLH
+QYNQHRPHTACSNQPPFSRLINVPEQYT
+>3_628
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPAQIASELGIPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYARFYGSESERRSALP
+GWLHFYNHHRHHSAIGAPPISRIDNNLPGHHT
+>3_635
+MSHPNAALTPRHGLLVGRLVVDDGWPISEVAARFQVSWPTVKRWADRYRTGQPMQDRSSR
+PHHSPNKTSAKTTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKPRNKYRDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAITATAVLVRAVEWFNARGVTVERVLSDNGGAYKS
+HLWRDTCVELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEDERPGELEGWLH
+YYNHHRPHTACGDQPPFSRLTNVPGQYT
+>3_661
+MDASERWRILRLHVEDAIPLATLARSTGVTERTLQRWLARYRTGGYAALADDARADHGVR
+RTAPELVRLVEGLALTKPRPSIATIHRQVGVHCAERGLPSPSYSAVRSIVNGLDPGMVTL
+ALEGPASYRDKHELLLRRRADRPNAIWQADHTMLDLLIVGPNGKPARPWLTVILDDYSRA
+ICGYMVFLGAPSAANTALALRQAIWHKPEPDWPVCGIPDVLYTDHGSDFTSHRLGDTAAV
+LHLRIIHSQVARPQGRGKIERFFGTINTELLPTLPGHFAAGSSAPTPALDLGGVDSAIST
+FIRSYNARTHRELRTSPLHAWIADGWLPRLPESLEQLDGFLLTVPTTRVVQRDGIHFEGL
+RYTAATLAPFVGSTVSVRYDPRDVTEIRVFHRDVFLCTAISTEHQTETISLKQIQAARNA
+HRRALRGQIHERIAIVNPKLDDTTTPAAVETDRPRLKTYEEDRS
+>3_733
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_1335
+MTHLNAALTPRHRLKVARLVVEDGHPISEVAARFQVSWPTVKRWVDRYLAGESMNDRSSR
+PKSSPKKTNKAVTKRCVSLRMRLREGPIQLAARLGIAPSTVHRILTAARLNRLSYVDRAT
+GEPVRRYEHPHPGSLVHVDVKKIGNIPDGGGWRYVGRRQGQKNRAATPDKPKNKWHSPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFAERGVTIERVLSDNGGAYRS
+YLWRDTCEALSIRPKFTRPYRPQTNGKVERFHRTMGDGWAYARCYTSEQERRDALPDWLH
+HYNQHRPHSACGNQPPFSRLINVPGQYN
+>3_1757
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_1781
+MSHANAALTPRHRLKVAQLVVDDGWPISEVAARFQVSWPTVKRWADRHRAGESMQDRSSR
+PHHSPNKTSPTVTRRCIQLRLRLREGPVQLACRLGIAPSTVHRILTDAHLNRLSHVDRAT
+GEPVRRYEHDHPGAMLHVDVKKLGNIPDGGGWRYVGRRQGEKNRAATPGKLRSKYSDPLM
+GKAYVHTVIDDHSRVAYAEIHDDETAVTASAVLVRAVEWFNRRGVTVERVLSDNGGAYRS
+HLWRDTCHELGIKHKRTRPYRPQTNGKIERFHRTLADGWAYARCYTSEAERRGELDGWLH
+YYNQHRPHTACGNQPPFSRLTNVPDQYI
+>3_1793
+MSHKNAALTPRHRLKVARLVVEDGWPISEIAARFQVSWPTVKRWVDRYLAGESMEDRSSR
+PRVSPNKTPKTVTKRCVSLRMRLREGPVQLAARLGIAPSTVHRILTTARLNRLSYVDRAT
+GEPIRRYEHPHPGSLVHVDVKKLGNIPDGGGWRYVGRLQGERNRAATPGKPKNKWHNPKL
+GYAFVHTVIDDHSRVAYTEVHDDETAITAVAVLHRAVEWFANRGVTIERVLSDNGGAYRS
+HLWRDTCD
+>3_1796
+MSHANAALTPRARLRLAKLIVDEHWAVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTSPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>3_1847
+MSHANAALTPRARLRLAKLIVDEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPATMPTRTPPAVVKQIVAARRRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFARLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWLHFYNHHRVHSAIGAAPASRLNNLPGHHT
+>3_2111
+MSHANAALTPRARLRLAKLIVEEHWPVATAAKMFMVSPPTARKWATRFRAEGPAGMVDRS
+SRPSTMPTRTPPAVVKQIVAARWRRRLGPVQIASELGMPASTVHAVLVRCRINRLARLDR
+VTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFVGRQQGMKHRAATSDREGTRDARY
+QPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVLRRAVAHFAQLGVEVERVLSDNGS
+AYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHRTLADGWAYAKFYGSETERRAALP
+GWVHFYNHHRVHSAIGAAPASRLNNLPGHHI
+>3_2154
+MPASTVHAVLVRCRINRLARLDRVTAEPIRRYEHPHPGSLIHVDVTKFGRIPDGGGHRFV
+GRQQGMKHRAATSDREGTRDARYQPRLGVGFLHTVIDDHSRFAYVEMHSDERSQTAIAVL
+RRAVAHFAQLGVEVERVLSDNGSAYRSHAWRDACTELGIKPKRTRPYRPQTNGKIERFHR
+TLADGWAYAKFYGSETERRAALPGWVHFYNHHRVHSAIGAAPASRLNNLPGHHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8cdd29d6e758d739804ec2bbf299a3488e4de8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000009.fa
@@ -0,0 +1,140 @@
+>0_686
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>0_1352
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>0_1450
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVGPRPRGGRGAPALRPRRPGLPAHRRRPPHRDAH
+RHRGTVPDPGHRRLGRPRYLQHRGGSPVSIHTPNTAAPALPADLEALLRQLKMPHARGIA
+AEVLATARAQRWEPAEVLKALLVEETTGRARSMLAARRKAAGFPTGKTFTTWDPGASSIP
+APTQQSLRTLEWLSRRENLVVWGPPAPARPSSSRPWASRPWRRASGWPGSPWRTSGR
+>0_2167
+MHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDR
+CFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGV
+ENAVKLAKADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETS
+ALHRIPATAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVI
+MHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGA
+RTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAG
+HRTGMHTATEERSLTQGTAGWAGLGTSNTEGAAR
+>1_79
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>1_328
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>1_975
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>1_1349
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>1_2225
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>4_582
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>4_972
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>4_1110
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>4_1301
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>4_2103
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dfa25ce04b5f56b00c115b3a9ee520c40af02b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000010.fa
@@ -0,0 +1,79 @@
+>0_432
+MLHPTFATPDLTTFCRLDELGLVAVGQLIEPDRATIECRVVEDDPWCRKCGVEGVPRDTV
+TRRLAHEPFGHRPTTLLVRVRRYRCGHCRRTWRQDMTRAAAPRAKISRGGLEWALRGIVI
+DHLTVTRVAAGLGVSWSAANAAVLAEGKRRLIDDPARFDGVTTIGVDEHVWRHTRLGDKY
+VTVIIDLTPARNKTGPARLLDMVEGRSKAVFKQWLAARPADWAKRIEVVAMDGFAGFKTA
+AAEELPDAVPVMDPFHVVRLAGDALDVCRRRVQQDTTGHRGLKGDPLYKARRTLHTGASL
+LTDRQRARLDAVFASEEHIEVEATWGIYQRIVAAYREPDKKKAKAMMQEVIATISSGVPA
+ALVEVRKLGRTMKQRAGDILAFFDRPGTSNGPTEAINGRLEHLRGSALGFRNLTHYIARS
+LLEAGGFRPALHPRS
+>0_815
+MRRYRCSGCGYVWRQDTTASAEPRAKLSRRALRWALEGIVVQHLTVARVAEGLGVAWDTA
+NDAVLAEGKRVLIDEEHRFEGVKVVGVDEHVWRHTRRGDRYVTVIIDLTPVRDGTGPARL
+LNMVEGRSKQAFKTWLADRPQDWRDGVEVVAMDGFTGFKTAAVEELPDVVTVLDPFHVTR
+LAGEALDECRRRVQQAICGHRGRKGDPLYAARRTLSTGVDLLNDKQKDRLDTLFADDAHV
+EVEVTWSVYQRMIAAYRHENRRHGRELMARLIDSISTGVPKALVEITKLGRTLKKRAADV
+LAYFDRPSTSNGPTEAINGRLEHLRGSALGFRNLTNYIARSLLETGGFRPRLHPGFG
+>0_1344
+MSLLTDRQEEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
+>1_1085
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQTR
+>2_99
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPRELTGMVDLS
+RDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQRLDDA
+TAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTDKQLAR
+LAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEVARLGR
+TLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>2_490
+MVDLSRDEHGRVRARLLDLVPGRSGKAYAGWLAERGDAFRRGVQVAALDPFAGYKTAIDQ
+RLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLGHRGRKGDPLYGIQTILRAGAEHLTD
+KQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRSGNLADGRAIAERLADSLHTSPIPEV
+ARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGIIELHRRLARGFRNRDNYRLRMLLAAG
+GLTP
+>2_491
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>2_1070
+MLILWRQRVWRCAEPGCARGTFVEQLPSLVAPRGSITTRAISWAIGQLRREHGTIAGLAR
+QLGTSWKTLWRAIRPELEHLADDESRFEGVTSLGVDEHIWHHVDRRRRGPKS
+>2_1071
+MTRSGVACRSRRWTRSCGYKTAIDQRLDDATAVLDAFHVVKLGTQVVDEVRRRVQQATLG
+HRGRKGDPLYGIQTILRAGAEHLTDKQLARLAAAIESDPAHEEVFVAWQCAQDLRAAYRS
+GNLADGRAIAERLADSLHTSPIPEVARLGRTLRRWRAAFLAYFTTNRSSNGGTEAINGII
+ELHRRLARGFRNRDNYRLRMLLAAGGLTP
+>3_613
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>3_621
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>3_820
+MPEPTLYCRARGDYCTCCDLLVGLPGLHVLTAERDDHDRLVVTVESAPEPMGCRSCGVIA
+RGHGRIEVSLVDAPAFGRPVRIIWRKRRWLCPDPACEVGSFIEQDEKVAAPRAVLTTRAC
+RWAIEQIRREHASVNGIRRQLGTGWRTVWDSIQPLLQAADEDPSRFEGVAILGVDEHVWH
+HVSTKPIHHGGRGPKELTGMVDLTRDEGGRTRARLLDLVPGRSGRVYKDWLDQRGDAFRA
+RIEVATLDPFHGYKNAIDDQLEDARSVLDAFHVVKLATTVVDDVRRRVQQQIHGHRGRKS
+DPLYRVRNVLRAGAENLTDRQRDRLETAWAAHEQHIEVEIAWLCAQKVRSAYRQGTHAAG
+RAVAEKILATFTSCPIPEVARLGKTLNRWRREFLGYFDTNGASNGGTEAINGLIELHRRI
+ARGFRNRDNYRLRMLLIGGGLDMTHHTQR
+>4_1294
+MSLLTDRQKEHLSVLFAHEKHAAVEAAWEIYQAMVAAYREFDRAKAKAKMEKVIAALSKK
+VPDTLEELGKLGRTLTKRAADVLAFFERLGTSNGPTEAINGRLEHLRGSALGFRNLTNYI
+ARSLLESGGFRPLLHPQMR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4487c5d836fdee5a78cf29a70167cdcea7e1e87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000015.fa
@@ -0,0 +1,105 @@
+>0_335
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGSARKVVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>0_1602
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>1_60
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>1_1317
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>2_1213
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LDDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQA
+SRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDEHQH
+>2_2549
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>3_1125
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIE
+TAVAAVEKRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSP
+DLGMKLEQADLDVLGSARRVTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDEHQH
+>3_2408
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIE
+KAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENASLDLLGTARKVVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLNAAT
+GEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>4_342
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>4_1532
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEAGHQH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3864a0d34451add24befd19146765200dcb2ee3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000016.fa
@@ -0,0 +1,90 @@
+>0_953
+MTPTPSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAP
+DHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVP
+GVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPT
+EIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEAS
+EKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGLRM
+RRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADG
+APVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWRAQEPSEESVIELLESRG
+VPYTTWAGWHALDEHEKSLGVQATEAGPVARERVKVVDREEMTRISREGVLLGAGG
+>0_1713
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>1_676
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDA
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAGG
+>1_1430
+MTVRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAVLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
+>2_1085
+MTERPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLDVPGVE
+LAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGAGGVRPTDETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDADGVPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDVDGLWTAQDPAEESVIDLLEAREVPY
+TTWEGWQALDAHEKSLGAQATEAGPVERERVKVVDREEMTRISREGAWAPTA
+>2_1859
+MTLTPSSPKPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAWLD
+VPGVELAGSYGGADFASWYDGHPDVPRHWPLDATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDREQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPLDGVEFDAARGVVPNDEGRVLDA
+DGVPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVRYTTWAGWLALDDHEKALGVQATEAGPVERERVKVVDREEMTRISRESVLLGAGG
+>3_1012
+MTERPDRPLRIAVVGAGPAGVYTADILTKEERDFQVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFIGNVDVGTTVSLEDLRRLYDVVVFTTGAVRDAALDVPGVE
+LEGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLVTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRTEQASRRLHLHFLQAPEEFLDADGDGRVDGLRMRRM
+ELDGQGGITPTDETVDYDVQAVYRAVGYFGSPVPGVEFDDVRGVIPNAEGRVLDAAGHPV
+PGLYTSGWIKRGPVGLIGSTKGDSLETIKHLIEDEPGLYTAEDPSEQAVLDLLAERGVDY
+TTWEGWHALDAHEKALGAEATQAGPVERERVKVVDRAEMTRISRAGTGLA
+>3_1805
+MTPTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEQAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEQFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETITHLIEDEPGLWRAQEPSEESVIELLES
+REVPYTTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRKSILLGAGG
+>4_896
+MTLTPSSSRPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGV
+APDHPRIKGIVNALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALD
+VPGVELAGSFGGADFASWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLL
+PTEIPDNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDE
+ASEKAIEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGL
+RMRRMELDGSGGVRPTDETVDYPVQAIYRAVGYFGSPVEGVEFDEVRGVIPNAEGRVLDA
+DGAPVPGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLES
+REVPYTTWAGWHALDEHEKSLGAQATEAGPVARERVKVVDREEMTRISRESVLLGAEG
+>4_1642
+MTARPDRPLRIAIIGAGPAGVYTADILTKEERDFRVSIDLFDRYPAPFGLIRYGVAPDHP
+RIKGIVTALHKVMDRGDIRFLGNVDYGTDLSLADLRRHYDAIVFSTGAVRDAALDVPGVE
+LAGSFGGADFAAWYDGHPDVPRHWPLEATQVAVIGNGNVALDVARILSKHAEDLLPTEIP
+DNVYRDLAASPVTDVHVFGRRGPAQVKFTPLELRELAHSRDVDIVLYEEDFDFDEASEKA
+IEENNQVRTMVGTLTNWLMEQEDRQQSASRRLHLHFLQAPEEFLDEDGDGRVDGLRMRRM
+ELDGSGGVRPTGETVDYPVQAVYRAVGYFGSPVEGVEFDEVRGVIPNAQGRVLDADGAPV
+PGLYASGWIKRGPVGLIGHTKGDSLETIKHLIEDEPGLWTAQEPSEESVIELLESREVPY
+TTWAGWHALDDHEKSLGAQATEAGPVARERVKVVDREEMTRISRDGASVPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea3ff9d6915c076d9631f00a69ad8ea28d00b6ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000022.fa
@@ -0,0 +1,109 @@
+>0_608
+MSTPHHHDHPTDQTAEHPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>0_1241
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>1_969
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>2_389
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVLREGSVIGAVALE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>3_693
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQHTGHQGHAMDHGQHSGHT
+GLDEHGGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGY
+EVPGWAGWVAAALGTVMYVWGGRPFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATL
+GLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAALLPDEAERVEGENVVKV
+APADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATD
+SGLRVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWT
+LIGMPDEAVVRTITVLVIACPHALGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDA
+VLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEHPLAKAIVTAAKDKGFAL
+QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEAWRSEGAIILHVLRGGQ
+VVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPED
+KSAKVSQLQEEGKRVAMVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSV
+LSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGILAPVGLVLPMSIGAILMSASTVVVA
+LNAQLLRRIDLTPEASTRSVLERQK
+>3_2144
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>4_573
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>4_1198
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9a909a0f9cc0e55e959422f8b8cd12a81254bc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000023.fa
@@ -0,0 +1,52 @@
+>0_2177
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>1_1890
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNILAQFRLV
+KAALPHLKPGSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>2_495
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVAQAVEAMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNILAQFRLV
+RAALPHLKPGASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSYVVGATIAVT
+GGMPTP
+>3_423
+MTDVSTSTDTAVGDSDTRPAAARTDAPAATVLLAGRAALVTGGTLGIGSGIAASLRDAGA
+RVAVTGLTEQECAAAREAGFPAYVLDVRDRAACAEVVGAVVEEFGGLDVLASNAGIYPQA
+RIADMTDEDIDLIFDVNVKGTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYG
+ATKAAQLGFVRSAAIELARQGVTVNAVLPGNIITPGLEEMGQEYLDSMARSVPAGHLGEP
+ADIGATVAFLASDGARYITGQGIVVDGGQILPETPEALEGL
+>3_437
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVERAVQELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINILAQFRLV
+RAALPHLKPGSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>3_633
+MGIHYARDSTAAEAVVERVNEAGASGVLIRADLAEGAAGAAHLATRWRDEVRRHDARGTD
+VLVSNAGINGAQSLSELDEGTVARVVNVNLVAPLMLVHHLSDHINDHGRVIGISSGFARI
+AAPTHVAYTASKAGLEAAFRAIAAELAERDITVNTVRPGVIDTDINADWINEPGARDAVA
+AAAALRRVGQPDDVADIVAFLASHSSRWMTGQSLDATGGTQL
+>3_1824
+MSTHDLPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLKGRRALVTGGD
+SGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVDLRDEAATRAL
+VRDAVKFLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVFALIWIVQEALPHLPAG
+AAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTPRGIRVNAVVPGAIWTPIQV
+SLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASYVSGEVLGATGGTLY
+>4_2110
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94dc33d3de8bb0ce0918bb34b5d6343737288b62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000024.fa
@@ -0,0 +1,101 @@
+>0_2236
+MSSDQRTASAPRHALPPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTG
+GAGPIGQLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAEAAQQAARE
+SRAAEQSKRAEASASASPGSAAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGTDVTLIGDSVSLSAAPTLMEELPGMLLEAEVGYQIWDAADELEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMAAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>1_1940
+MSSDQRTAPVPRHALSPQDGVPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTF
+LRGGFVGVDMFFVLSGFLITTGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTAL
+AWLAVDEFPAGLGRQWFGALTYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILW
+PLLLWGLLLLTWPPRSTVNSGRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGT
+DTHAFGLLFGACVAIGLAHVPRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHAS
+TYRGVLAGLSAVVAFIVWHVVQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMR
+VMVPVDAPGWVEPVAAGAILLLTALIADLSTRLIEEPILHEGFTGAFGRWGAAARRAFTG
+GAGPIGRLAAAATALGLVAVPAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARE
+SRAAEQTKRAEASASGAPGSAAPGDAEGSAGATPSPGSSAEPSGLGLGDPAVTRPTYSKE
+QLTAALPPSELGPDVTLIGDSVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKAD
+GQLSDVVVVALGANGTTHRGDWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKA
+HPDRIVLADWDAAAKQHVTDFSADGVHPRADGQAMYAQLVRLTIEDRLGARR
+>2_421
+MVRRDVWPTIAGVPSLTPSSPVRSAEERTDRGGGSRTRPLVHADRPGIRVSPGPGRIPAL
+DGLRGVAVLAVLVFHAWPALLPGGFVGVDMFFVLSGFLITTGLVRGVDGGRGLRLGPFWM
+RRVRRLVPSMVVALVCCTALAWLAVAEFPAGLGRQWLGALTYTSNWVMILSGSDYFAAAT
+PPLFEHLWSLAIEEQFYVLWPLVVAGLLTLFWPREPTLRGAFRADRARVLTVLALAAASA
+VWMAVGLRGGAPHTRLYFGTDTHAFGLLLGAAVALMLAHTRRPEHGGAVMRNPPVRSAIA
+WGLFAALLAAFVLVDGREDVTYLGVLAGLSLVVTLLLFHVVQGNRQDSFSRAMSGDVLRW
+WGRRSYAAYLWHWPLLVILRTALPVDAPAWVDPVAAGGVLVLTAGIADLSTRWMEEPIVQ
+RGFRGAFAHWRAGLRTATRGIGGKAAAGAAGLALVAVPVAAVAAVVHSPAETALQRQIAE
+AEAALEQARQAQAAARAEASARAEAERAGAAEEAVAKDSQEDAPGAGAGGDAGSAAPTAS
+STPSDTAAPSAGEDPAVEVAADPTASAEPEPTAEPEPEPPLTGDPSVTRPAFTGAELTEP
+MPPSSVGPDVTLLGDSVALSAAPELLAALPGIAVEAEVGFQVRDAAARLAELDAAGMLTD
+VVVVSLGANGNAELGDWDRILAAAGPERLLVLVVPHGPMDWIGPAQQEMAEQAALHPDRV
+VLADWDAASAHVDEWSADGVHPKGNGQGIYARLVRLTVEARLGLR
+>2_1803
+MAVLSVLVFHAGVTALPGGFVGVDVFFVISGFLITGLLLKEVDRTGRVGLAEFYARRARR
+ILPAALAVIVLTVAAGLLVYPVSEWTRLGSVAVASALSVVNWLFARESTDYFAQEEAASP
+FQHYWSLAVEEQFYLVWPLLLILVTVGVAALRRRGAGDAAPDADAGARRRPSAPVAARRV
+LLASAVIGLASFVHSVSYSASDPGAAYFVTTTRVWELALGAGLAAALVVLPVIRPAVRTV
+LGWAGLGMIAVSLVLITGAMAYPGSVALLPVVGSALVILAGAHEDGSTPGHPARLLATRP
+MQWVGDLSYSLYLVHWPVLTLAAWRFPDGRLPLWLGLILAVVSVGLAWALRRWVEVPAMH
+GSLLAGRRRALTRGGLGMAAVAAAGALVLAAGAALAPARPGEESPVAGARAVMDGQDPMA
+ALAAGMRIVPDPAVAKEDRSPRSAAGASSRTPRPRAWSPRRACWRTASPTRSATSGTAPC
+PTSWTGSTRTSCWSRAPGGRPWRRTPRRRWPRRGGS
+>3_375
+MTVSTSDHHAARPAPRHAQAALADGPAPRTGLRVSRGPGRITALDGLRGIAVLAVLVFHA
+WPEALPGGFVGVDMFFVLSGFLITTGLVRGVDAGKGLRLPSFWMRRIRRLVPAMVVALVA
+CTALAWLAVAEFPTGLGRQWLGALTYTSNWLMIFDGGDYFDRASPPLFEHLWSLAIEEQF
+YVLWPLIIGGLCLVVRPKRDTYASGRVADRRRILVVLVVALASAAGMVLGSLGGADQTRL
+YFGTDTHAFGLLLGACVSMGLAHVPRPEHGGPELRTGPARTAAAWLAVVVLFTGFALVDG
+TQDATYRGVLVGLAAVVAFIVWHVAQGDRRDSLSRALGNPFLRWWGRRSYAAYLWHWPLL
+VIMRIVVPVDAPSWAEPVAAGAVLLLTAGIADLSSRYFEEPILQKGFRGAFGGWGDAARR
+AFGGAFGPGGRLAAGATALALVAVPVAAVAAVAHSPAQTQLQEDIQAAEQSLQDAQAQQQ
+AQLEARRSAQAEKSKDAEAGGAEATGSAGASASPSGSTLGDPQVTRPEFTQEELTASLPP
+SDVGSRTTLIGDSVALSAAPALLEEMPGIVVDAKVGFQIWDAADKIRAMDREGTLGDVVV
+LSLGANGTAGRGDWDKIRQAVGPDRLLVVVVPHGPMSWIEDAQRKAVEQAEAHPDQVVLA
+DWEAASTYVPGWSADGVHPGHEGQGIYAQLIRLTVEERLGLR
+>3_2381
+MPRPVDTKASYFPGLDGLRALAVGLVVAYHLGVPGTDGGLLGVGVFFTLSGYLITSLLLR
+RHERHGDLDLKNFWIRRFRRLLPAVVLVLIAVLAATALVSPDLLGARLGQSVAALLYVAN
+WHTILSGRSYFDQAEGAGPLDHLWSLAVEEQFYLVWPLVLLGLLALTRRLGPDARRRVLA
+AATLVLGAVSFVLLAVFADPAGDSTRAYEGTDTRAGGLLWGAVLAFLWRPDRVARLTGRA
+SRVVVDLVGVLGLAGVLALSATTGQEDAALYTWGLAALTVATCAALLPLVHPGSWVARVL
+GIPPLQWIGARSYGIYLWHMPVVAFLPDRVLFGQPVLRGLLIVALTLVLAALSWRLVEDP
+IRRHGLVAALARARGVLGVGAVAVLASGALVLTAALPQTSAQEIAAQEPAAPAGDAVAHP
+ALDGRTSCTSVLHVGDSTSLASGNTDRTRIADPAQRITGRYEAVGVETVVEDIAGGRSTR
+EHIDGSADLNAPEAVAAGVSRLDAGGCVVVNVGLNDAATMTKDDAWDQAAARIDAVVDAA
+DGRPVLWVGPAIMPWSSRPYYEPAGAERFTRALVDATARHPDLRVHDWARESRSHPDWYL
+SDDANHNTEAGAVAKARSMAAALTAAFPAGRPASAEKVVLGE
+>4_562
+MTNPPVYPRGYRPRHAADGPDSTPAAARRRADWRPEIQGLRAVAVLLVVVFHIFTDRVSG
+GVDIFLFISAFFLTGSFTRKMESGRPLAVGRYWLHVFTRLMPMAVLTILTTLVAVATVYP
+LADRASWRTEALASALYVENWALAFNAVDYYAADNTSLSPFQHFWSLSVQGQVFILWPLL
+FLVSALVARRTGARPRAVLTTAFASVFVVSLLWSVTQTSQNQAFTYFDTRARLWEFALGS
+LLALALPFLHLGRRTRVFLGWAGLASMIAVGVVVDVQGAFPGWIALWPLMSATAVIVAGT
+SGSHFGVDRILASRPLTRLGDSAYALYLVHWPLLITYSVLTGSQKPGAAAGVALVLVSLG
+TAILLSARVERPLRAWGWPQTAAWRSAVVLGACAALVVAPVTLWRGAEAAESARVLEAAD
+RNNPGAAVLRPDYEPAGDPGAPVLPVVEGRYPFPEYPEECDPALEAQLTEVGAESCHVLV
+PQADPAGVVLMAGNSHVMQWSPALRRLGEERRLEVVSYTRGSCLVAPMEEQVDDSPKCPD
+FLADLNLVVEHVRPDVVFMQGTRSTYEDEEMLTPGMTGRMEEIAGTGAHVLALRDNPRFA
+AGSPTTCGTMHGVDAVTCRWTHAVLDPNTSPLAGLADAHPRIAQVQLNDMICPDRQCQPT
+VGNVHVYWDDNHLTPTYVETLAPVFIERVLAALEHDGMRLGR
+>4_2178
+MPAVKVGTRVSRGPGRVTALDGLRGIAVLAVLVFHAWPTFLRGGFVGVDMFFVLSGFLIT
+TGLVRGVDAGRGVALGTFWMKRVRRLIPAMLMALVGTTALAWLAVDEFPAGLGRQWFGAL
+TYTSNWVMILEGGDYFNRASPPLFEHLWSLAIEEQFYILWPLLLWGLLLLTWPPRSTVNS
+GRVADRRRILAVAVAAVASAAWMAWGSWHGFEQARLYFGTDTHAFGLLFGACVAIGLAHV
+PRPEHGGPEPRTSATRVAVAWGAVAVLAAGFALVDGGHASTYRGVLAGLSAVVAFIVWHV
+VQGDRRDSLSRALGNGFLRWWGRRSYAAYLWHWPLLVIMRVMVPVDAPGWVEPVAAGAIL
+LLTALIADLSTRLIEEPILHEGFRGAFGRWGAAARRAFTGGAGPIGRLAAAATALGLVAV
+PAAAVAAVVHSPAQTQLEQDIAQAEESLKAAQAAQQAARESRAAEQSKRAEASASASPGS
+AAPGDAEGSAGATSSPGSSAEPSGLGLGDPAVTRPTYSKEQLTAALPPSELGPDVTLIGD
+SVSLSAAPTLLEQLPGMLLEAEVGYQIWDAADEIEKLKADGQLSDVVVVALGANGTTHRG
+DWEKILAAVGEDRLLVLVVPHGPMDWIADVQVQMEAQAKAHPDRIVLADWDAAAKQHVTD
+FSADGVHPRADGQAMYAQLVRLTIEDRLGTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbce9a8dc72c74757bdb4d33e3b99b5193c932d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000025.fa
@@ -0,0 +1,21 @@
+>0_95
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>1_2059
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>2_277
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK
+>3_600
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+>3_653
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
+>4_90
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>4_1954
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..642f185a946e286aac0590875eb8a4c7f04c8a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000034.fa
@@ -0,0 +1,35 @@
+>0_592
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>0_2014
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>1_324
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>1_1730
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>2_700
+MNLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLRAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHILF
+PIVLIGLGIVILVSGGAFGL
+>3_2162
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>4_1943
+MTLSSALQAIGLFLVTNIDDLIVLSLFFGRGAGQRGTTVRILVGQYLGFAGILGAAVLVS
+LGAGVFLPPEVIPYFGLIPLGLGLWAAWQTWRGDDDDDDDEAKIEGKNVAAWTVAGVTFA
+NGGDNIGVYVPVFLSVGPGAVVAYCVVFLVLVAGLVGLAKFVATRRPIAEVLERWEHILF
+PIVLIGLGVFILISGGAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb6221651d57b550f51e5639834d8dfa9c029937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000040.fa
@@ -0,0 +1,63 @@
+>0_974
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+SAVVRDPNERTHS
+>1_697
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTVV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>2_804
+MSSVLDAAGTPATPHPSPAAPSARVPSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAG
+GITSNFAVTGLLGVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAGVG
+AALVALVSYACMQVGIAGMFGFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFS
+AKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQLFTSGVGAALVFSVAAFMGFE
+SGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSAWAMVMTEGPGGVVAAAQAVGPDVVF
+AFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGA
+PVGGSLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLMALTSVSVI
+GYLRRHRDEFGVFTRVVAPALAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTP
+GALGTAWALWLRARRPATYAGIARGGELS
+>2_1837
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTALDSTDPDYG
+SGSSVFGVGTVFVLGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>3_2203
+MLSTHQSVSVSTSSVAPVYSAVVTVPLVVGLVGSGAPLAYLLALLPILGVWAGMSANDER
+EPDKGSVYSWAVTGHPVLGWTAGWCLALTGIVATSGLAYVALDAWLPGLGAGVKVLIGAG
+IIAAATALASANVRITAAVQTAGVLVQVAATAYLAWVLARVGLTPLPPAGTVQDWVHAVL
+LAVFAFWGFDAVYALSEESHRGVPRRSAAVSLGLLAAIFLVFSALGASEDPAAVAALTHP
+VVMAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLAPLRAAEVVSALLAIAWLVVSL
+AVPGVFEDSIEMLSVFVGGYFTISSATAAAHASGGARMLHAATAVVMGLITAASLAWMFE
+PDYGATVVGGVGGVGLLAVGFAVLGLILAVGAGHRGRAVHPTSGV
+>4_917
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALG
+>4_918
+MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIA
+DLAGNLWVNIPLTLVYLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG
+AGFDPTPVQLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAA
+VTVFVIIAVYILSALAVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAIL
+VSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTR
+LLSENALWDTITALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLV
+MFCVTAMDSTDPDYGSGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQT
+DSTRPIPIIRPDDDGTAVVRDPNERTHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf00258e789b27597593ab0b93af4e4c4822fca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000042.fa
@@ -0,0 +1,35 @@
+>0_1240
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>0_1573
+MTMRFWTRTVAVTAASLLALTGCATGGEEAATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLMADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+SAG
+>1_968
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>2_602
+MKTRRLTLAAVGILASAGLITGCSTADDAGPSASPSSGQSAATSSSQPASESGSASESAS
+GGGHMDHKMDGGPAPEGIAEAASPAHPVGSEITLTADHMPGMDGATARITGAFDTTAYSV
+DYTPTTGGEPVEDHKWVVHEELQDAGDAPLQVGDTAVMEAEHMAGMKGAEATVASVTDET
+VYMVDYTADGMTMTNHKWVVESEIQPKG
+>3_694
+MQRRLRTGLAAGALGVALVLAGCASGADDNQQTDPSATEEHQGHGGNNAESGDEEMEHPM
+DGGPAPEGIAEASEPTYPVGTEVQLTADHMEGMEGATATISGAFDTYTYSVNYTPAGGGD
+PVTDHKWVVQEEIEDAGDARLADGTEVTLLAEHMEGMEGVKAIIASSTDETVYMVDYETD
+GMKMTNHKWVVESEIQPAS
+>4_1197
+MRKHLMTTVAAGVLGGALVFTGCSTGGGQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANATIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>4_1502
+MTMRFWTRTVAVTAAGLLALTGCATGGEEVATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLVADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+PAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a5ce0dcab97661e72df6320f32f8488eb641244
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000045.fa
@@ -0,0 +1,66 @@
+>0_1536
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRELGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>1_1258
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>3_626
+MLFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRIGDDYGR
+RRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAK
+AFGAYGAVQGLASVAGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDSRA
+AARSRLDGVGALLAAVGVLLVLLPLVQGRDWGWPTWGWALLAAGVLVLAGFLRYENALAR
+RGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTGRSAWDTGLVILPY
+AIGSMLTSGAGVALAARAGRALLLTGSLTLAASQALLWWLVRDGSTTPDYWPLAGAMFLG
+GLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGPA
+TAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD
+>3_696
+MAGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTL
+LAALLYLGPLSDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPA
+LSAMMIDFESPSHRNIAALWNTIGPMIGLGAGALGAALLLDLTSEPTTAVFGSLVLAFLI
+VATVVWSTPELVPKTQIRRGDLRPRFTVPPHLRRMFTVGVPVIIAGWATNGLFLALGADL
+VGSELGGSTHTQAGIVLFALAISGVTASSVLQRRSARTISLYATSALAFGTAVSIGALAL
+GSYPAYVASVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAG
+LLVPVLTLSGTMTILGAIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPD
+REEQP
+>3_1216
+MNPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSIS
+GYTLAFGMVLVPAGRAGDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGA
+GLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVAAGPLLAGGLIAVLGGDLGWRATFL
+VNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFLDRGLGPWRFA
+LLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVA
+MFMQNGLGYGALQAALVGLPSAVCSSVMATVAGRLVLRAGRRLVVVGVSLVLAAVVGSIG
+VVAAHQAFGLSPWWLLATLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVG
+TSVGSAVIVGVYLGVAGTGGPDRGFMAALGLIAVSIAAALAVAVADQRRRARQGGR
+>3_1789
+MPRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIV
+WGACSDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILS
+HLFEGKARAQAFALFGTINGLGLAAGPALSGLLLSAWGWQGIFAAHTIVLIVAFIGAARL
+PQLGRGGTSLREILDFSALKAPKFLAMTLVPIAGAIGFVTFLTYLPSALGAIHGLTAGVT
+GALMLVMTIPVLIAPVAVHRLMERSHLTPTAIVAVSFACLIVGGIGVLLLLRPDLPVALG
+VTPMILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAV
+ITTTLPGTTGELIASGSPGEPWIYHSGLMAAAGTMIGLVAIAGVTFLALTRAANRSAVTA
+RQVEVAR
+>4_1463
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASSADWDGAFMAAFALVAGCMALALLVALADLRGPRTAAPR
+G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e1eca95d82f72edf382522775d339bf1e8ffd2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000051.fa
@@ -0,0 +1,27 @@
+>0_2033
+MNMLQAIRRYYAGYVQFSGRASRADFWLAALYVWLLQAAVRFVSTALDVFVLGAPDPSLR
+DAAILLVGITHALPSLALLARRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGATAARR
+>1_1752
+MTMLQAIRRYYAGYAQFSGRASRADFWLAALYVWLLQAVVHFVSTVLDVFLLGSPDLSLR
+DAAVLLVGITHALPSLALLARRLHDAGFSRAWLFLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGATAARR
+>2_666
+MNMLQAIRRYYAGYAQFSGLASRADFWLAALYVWLLQTAVHFVSTALDVFILGSPDLSLR
+DAAVLLVGVTHALPSLALLARRLHDAGFSRAWLLLGLVPFVGPLTLLVFALQPSAPRLGH
+PADASDPVPAGVTASATAARR
+>3_582
+MSTALDVFILGSPDLSLRDVAVLLVGITHALPSLALLARRLHDAGFSHAWLFVGLVPLVG
+PLTLLVFALQPTAPRFGHPTDASDPVPAGPRPRGADPRRHVRPDQ
+>3_583
+MTMRQAIRRYYAGYAQFSGRASRADFWLAALCV
+>3_2050
+MTQPHDPSQNPYGQQPAAGQPPYGQAPSGQSQYGQADYGQTQYGQTQYGAPSPGYGYGYQ
+PGVPFPEDPRVAPAPGVGPVEAVKRFYTRYALFYGRASRSEFWWVQLYLVLVSLVLTALM
+FAVLVPAGAFSNTTTELSEAGAVGVLAITGLFLVFVLAHLVPSIALQVRRLHDAGFSGFW
+FFIGLVPYVGELVLLVLSVLPSKPEGARFDR
+>4_1971
+MTFLRAVGRFYGRYAQFGGRGGRAEFWWVVLYLSLASLGITLLFGALGADTTTAAPSAVV
+FPGFAVSGLSVPAVDSMTEAYQAFSGVWGLLHLVPAWALTARRLHDAGLSRAWLLLALLP
+VLGAIALLVMVLQPSDPRVAAEHVVEVSVGHAPERESIGGLRDHPTILPTALNRLLVFDM
+CVKPPPPRSPRCRRRGLPRSPHEDAEGVAGRVREHVQGLVLVVGAVQDEAPAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21702870502553bceec13d23d0db6448bd322ff5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000063.fa
@@ -0,0 +1,52 @@
+>0_101
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR
+>1_2065
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR
+>2_31
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF
+>2_270
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA
+>3_217
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS
+>4_96
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65ec1d507738a11e7bcb8e2535ac2613cc50964e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000069.fa
@@ -0,0 +1,108 @@
+>0_213
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKAH
+GAKAEISFQRAVNAFVAELTAEEAQSIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPDTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAADKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATVVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGREVNVPSLAIPDVVG
+SATVTRTVTALENGRWQFSASVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSAAVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLVSSALAVSTVTVEEGTKSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>1_2177
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKTH
+GAKAEISFQRAVNAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPNTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAAGKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGRDVNVPSLAIPDVVG
+SATVTRTVTALENGRWRFSANVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLESSALAVSTVTVEEGTQSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIADPAPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>2_77
+MTPPLSRRHRALGMTSALALVLTGASAAGATSGTGAPAAAEADAVTAVTGAAGTADQGPR
+TAPEVFEDGGYIVLMAEAPVASYDGGTPGYAPTKPGKGLGRDKGFNPKSANAKKYAAHLE
+RGQDRALERAGAEAAPHTRYTTSLNGFAGELTAQEAAALASDPAVLAVVPDEIRQPDTVS
+SPDFLGLTGKKGLWAQVVGKKAPATDAGRGVVVGVVDSGIRPEAASFQDRGHPAAPADWA
+GGCETGDEEAFPADSCNDKLIGAKYFVQGFGAGRLAPVETLSPLDAGGHGTHTASTAAGN
+AGVPAVVDGTPRGEISGMAPGAHVAAYKACWEGVPSGGCATSDTVAAINAAVEDGVDVLN
+YSISGTTSNVVDPVEVAFMHAAAAGVFVAASSGNSGPTVSTTAHPSPWITTVAASTQAVY
+EQTLVTGDGQRFIGSSITAPLEAETPMVHAADLAADGVDAARAALCLPGTLDATAAADML
+VVCDRGENARAEKSQVVADAGGAGMVLVNVADSGLNADLHALPAVHLPHTERDRLLAYVD
+TEEPTGRILPTTEGTTTRVPEVAGFSSRGPSLAAASDLLKPDVSAPGVDVLAAYSPDEAG
+EDFAYASGTSMSSPHVAGLAALVKQGRPDLGPMEIKSSLMTTAGDHASATSPFAEGAGFV
+DPMKILDPGLVFDTDQGDWYDYLAGQGIVFSGSGEPVSETPIDASDLNVPSIAVGELYGS
+QTVTRTLKNVGGNNGVWTARVEGMEGMDVSVSPQVIKPRRGQEQDVEITLTAAGAPAGQW
+ATGHVVWSGPAGKEVRIPVVARPGVADAPASVTVDRDADGLELPVLSGVDGTFTTRVNGL
+TAGTEHIGTTVRRMFFDSTDPALTGHDFAYPRGYPTVRIEAETSAEDVDLDVYVTGSWTS
+YPVARSVTRGTGMEVFQGPIYSSAPQHRIFVVAKTGADGVEHDEPIDYTLRVFFPQAGGG
+DNGVLSFDPASAAVKPGQTHVFHGTLNTDGTSVYTGTVDILHEGKVVDTTQIRVQ
+>2_149
+MRKAEAMPHIPTPARRRRALAAAVVGASLVAAPALAASAIAVELPDGSVVTSPQGEAKVE
+QQFEDGRYFVVLKDAPSVTAQEAGAPAPGAAPKAKFDPDHPRVKNYEAKLQRQQEKVARD
+NGVEPKTTFQRAVNAFVAELTAEEAMRLSKDSAVLGVAPDEQVAPDYSSTEFLGLPGKKG
+TWNTTYGKPENAGKGVVVGVIDTGIHPDNPFIDAEPVKPLKGKAKVGEPYRTADGDIAVL
+KADGTTATAECETGPGFPADSCDTKLIGAYAFSDDFERFVPVENRHPAEQLSPLGVFSHG
+THVATTILGNTGVEQTIDGTSFGEGAGVAPAASLISYKICWEDNDPNTGGCYTSASVAAI
+EQAIENNVDVLNYSISGSNTTIVDPVAMAFKSAAEAGIFVAASGGNSGPTPNTVNHSSPW
+LTTVAAETFSNELTGTVEFSDGTKYRGASSAGSDAGPAEVIHASEVAAGDAEAARLCLPG
+SLTAEAADKIVLCERGQNARVEKSAVVAEAGGVGMILANTPTGSLDADIHSVPTVHINDT
+DGVIEKVKSSDLTATIVRGDTTGLPQDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNV
+IAGVSPLDPDYNGNEFGLMSGTSMASPNLAGMAALLIGKEAAWSPMAVKSALMTTAGDVF
+NADGSVNEDNFATGAGSADPKAAARPGLVYEADSTQWDALLLGEIAGREVNVPSVAIPDV
+VGSASVTRTLTATENGRWQFSGSVPGFEVTASPSMLDLKKGQSAEVELTFTRTDAEVNTW
+AHGSMSWSTAKGKAVPTVTSPVTLKALSATATSAVEGSGAEGSATVEIEPGMTGELTPQI
+LGLGKVEAAEVSAVANTSASGAALAGRVVNVEEGTKALVASINAGAEGVDWDLYVITPQG
+RQLNMATAAGDETLTIQNPVPGEYTVIGHLYSAPAGTDTASLETLKLREDVGNLTVDPNP
+VPVTTGEATTAELAWSGLTEGTWKGLVTWDAGVTTDVTVTVP
+>3_107
+MNRHPQRLRLLGAAVTAVGLMAAPLAAPAFAAPQAEHAVGVQAATPLKAGRYFVILKDAP
+SAVAESQATAPGAAPSAKFDANHPRVKNYEAKLKRQQEKVAAQQGVTPKVTFQRALNGFV
+AELSAEQAQAYAEDPAVLAVTADEQVAPDYTSTDFLGLNGKKGAWNTTFGKAENAGRGVV
+VGVIDSGIYPDSPFLDGTPVGPRTNNGKLKAGDTFRTADGRIAVQKADGTLATAECQSGP
+DFPASTCDSKLIGAYAFSDDFVRGTPVEKRDPAERISPLGVKSHGTHVATTIVGAKDVEQ
+TIDGASFGLGSGVAPAAKLISYKVCWEDTDPDTGGCYSSASVAAVEKAIENNVDVLNYSI
+SGNNTSVVDPVALAFRSAAEAGIFVAASGGNSGPTPSTVNHSSPWVTTVAAETFSNELTG
+TLELSDGTKVRGASSARTGVGPAPVIHAADAAAAGVSADDARLCKPGALDPAKAAGKIVL
+CERGVNARVEKSAVVKDAGGVGMILVNVTPGSLDADIHAVPTVHTNDASLIAKAKAGGLQ
+ATIVPGDTTGQAPDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNVIAGVSEYDSDYHG
+NVFGLMSGTSMASPNLAGMATLLIGKHPEWSPMAVKSALMTTAGDVYNADGTVNQDNFAT
+GAGSADVAAANRPGLVYESDATQWNALILGDLAGREVNVPSVALPDVLGTASVKRTVTAL
+ENGRWTFSGSVPGYTVTASPSVLDLKAGQKAEVTLTFTRTDAALSQWTHGSFSWTTAKGK
+AVPSVTSPVTLKSVPATADASVTGTGASGSAAVAVQPGFTGQLTPSVLGLNKVESQAVTL
+QPGGSKVTPVTVAPGTKSVTFAVDSGVDTADWDMLVQTPSKKQFTSATESSDESVTIQDP
+EPGTYLVLTQLYANPAGADTAALETVQLRSDAGNMTVTPNPIPVTTGQETSATVNWTGLT
+SGTWRGQVTWAEGTATQVEVTVP
+>4_214
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0777c24d36767421cb106a092cae2aeacc96c16e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000070.fa
@@ -0,0 +1,41 @@
+>0_215
+MTAPAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADD
+LARPYRIAGPDPTARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
+>1_2179
+MTAPAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADD
+LARPYRIAGPDPTARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
+>2_147
+MAHGLARSFGDVHAVRDVSLTVPSGSVTALVGPNGSGKTTLMLLLATLLRPDAGAVTIGG
+VDAVREPQEARRRLGWMPDTLGVWESLTCRDILTSLGRLYGMGAAEAAARAGEQLERVAL
+TEFADRPARVLSRGQQQRLSLARATVHRPGVLLLDEPANGLDPAARIRLRDDVRAMAAEG
+TAILVSSHVLAELEEMSDRAVFVREGATLSTQEFREDAAQTRPYRIAGPASARPDVLVRA
+LEARGLAVEPAAAHGQPRAGVVVGLRGETAAAELLADLVREGVPVSHFAPEGSRLENAYL
+GLHLDRDTAEGDRP
+>2_570
+MITVNEVSKSFGSTPVLQDLTFSIRPGLMTGFVGGNGAGKTTTMRILLGVLDADSGRIEV
+DGAPITRDYRAGIGYMPEERGLYPKMSVLDQLVYLGRLHHMRGADAKARALELLERLNLG
+DRAGSRLEELSLGNQQRAQIAAALVHDPVALVLDEPFSGLDPNAVETTLQVLRETADTGV
+PVLFSSHQLDLVERLCDELVILAGGRVRASGTRDELLAAHADPEWELHADADTGWVRGLP
+GIEVLHFDGGRARFRADTPQAAQRVLADAAARGPVHRFGPVTRSLHEIFTEVTR
+>3_105
+MTSSVLPQPPSGIVAHGLARSFGSVHAVRDVSLTAPAGSVTALVGPNGSGKTTLMLLLAT
+LLRPDRGSVSVAGVDAMADPGQARRLLGWMPDTLGVWDSLTCADILTSLGRLYGMGQAEA
+ATRAREQLAWVQLEPFADRPARVLSRGQQQRLSLARATVHRPAVLMLDEPANGLDPTSRI
+RLRDDVRAMAAAGVAVLVSSHVLAELEEMADRAVFVSEGATVAVRDLSGADDAGRERPYR
+IAGPDPSRRDELVRALQARGVPLAAPLEGHRPGVVVRLRGEDAAAALLADLVAAGVPVSR
+LAPEGSRLENAYLDLALGGPAPHAAGPVTAAGPAPTVEGGRA
+>4_216
+MTAPAPPPASPVLGAAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADG
+LARPYRIAGPDPTARDTLVRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a0cbe735cc0ef5845eb164a3ad3465747f6ef10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000074.fa
@@ -0,0 +1,47 @@
+>0_270
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>1_190
+MPSLFDPLDVGALRLDNRIVMAPLTRQRAGEDGVPTELPAEHYAQRATAGLLVTEGAFPS
+FRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGRMCHPDLLRGAEPEAPS
+AIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFADAARRAVEAGLDGVEVHGANGYLL
+HEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAIGAERTALRISPEHNVQGTIEEDR
+ADVLATYDALLAGLADLDLAYLSVIHQDVAGDLAAHLRESFSGPLVLNSGFGAVTGLEEA
+RRIVEDGLADAVAVGRELIANPDLARRWREGLPLNEPDPTTFYTGGAHGYTDYPFVDGSP
+SS
+>1_2236
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>2_65
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>3_2291
+MPDLFDPLPLGGLTLPNRVTMAPLTRQRAGEDGVPGDLHVEYYRQRASAGLIVSEGVFPT
+VDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGRMCHPDLLRGAEPVAPS
+AIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFASAARRAVDAGADGVEVHGANGYLL
+HEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEIGAERTALRLSPEHDVQGVLEQDR
+ADVLATYGAILDGVADLDLAYLSLLHRDVAGDLVAALRARFGGPVLLNSGFSEVTGAAEA
+RRIVEGGLADAAVVGRALIANPDLVRRWREDRETNAPDPSTFYVGGAHGYTDYPSLEG
+>4_269
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7941b38837a2b4c360394312ba5b0a88ac957704
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000076.fa
@@ -0,0 +1,165 @@
+>0_278
+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
+>0_1898
+MTTSVEGFSALDPVIQHHIVNTLRWPDLRPLQKASVASLLAGHDALLLAPTAGGKTEAAF
+FPVLTRAEREQWTGTSVLYVAPLKALLNNVESRAMEYTSWLGRSASVRHGDTTQAERRRQ
+GTERPDVLMTTPESLESMLISPTVNVTDFFSELRTIIVDEVHAFAGDDRGWHLLSVLERL
+SAVVRRPIQRIGLSATVGNPEELLTWLQGGNAAAGLPASVIAPPVDRTGAAAPELRLDFV
+GSEDNAATVISRLHGGEKRLVFAESRRTVELLGNALHERDVTTFLSHSSLSLSERRRSEQ
+AFAEAQDCVIISTSTLELGIDVGDLDRVLQLGAPSTVASFLQRLGRTGRRPGAQRNMLFL
+ELKPADLLRAAGLLLLHGEGYVEPIQPPPAPHHIVAQQILALTLQKGQLQRGAALAGLQA
+LGMSDSTTYRTIEDGLLEHGHLDSDGGLLFVGPETQRRYGGLYFRDLMAVFTVEAEFPVF
+HGRTEIGSVAPNWIATDPDDQPLLILAGRSWKVSFIDWKRHLVHVERSDRGLAPRWASPP
+RALSWALSDAMRRVLLGADPAGVVLTGRAQDALADHREAEGYTAAADHTVLASTADDLRW
+WTWGGAGANALLVAALEQVAPELLGEKLRFDNFSLRLRGDVDAASLGRALRQATSNFGGD
+LAGVDPLVDDAAVRGLKFHEMLPLDLARATLAARLADHTGVARVLERPVQMLRTAEDGRM
+WG
+>1_2251
+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
+>2_58
+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
+>3_37
+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
+>4_284
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee17c286722e4274c21f4820af5c0eea6eeca50a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000077.fa
@@ -0,0 +1,50 @@
+>0_286
+MLSEKSRPVIEATAAAVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPE
+VADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTFRFEPADDTP
+QSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDAS
+WEAVALREQVTESLAALAHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>1_3
+MLSEKSRPVIEATAAAVAEHMPEITPKFYAHMFEAHPELLDGLFSRANQRNGEQAQALAG
+SIVRFAVHLLENPGTLPEAVLARIAHKHTALGITEDQYQIVYENLFWAIADVLGDAVTPE
+VAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTFRFEPADDTP
+QTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>2_50
+MLSEKSRPVIEATAAVVAEHMPEITPKFYAHMFEAHPELLDGVFSRANQRSGEQAQALAG
+SIVTFAVHLLEHPDTLPEAVLARIAHKHTALGIVPEQYQIVYENLFWAIADVLGEAVTPE
+VAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTFRFAPADETP
+QTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEV
+GDVIELSNPYGDITLRDDAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASW
+DSVALREQVAESLQALENGTGRLWLGVPPQEAPAAFTTTEGLMEFDDVELPADASYLLCG
+PLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA
+>3_28
+MLSEKSRPVIEATAAVVSANMPQITPAFYGHMFEAHPELLDGTFSRANQLNGEQAQALAG
+SIVHFAAHLLEHPDSLPEAVLARIAHKHTALGITEDQYQVVYENLFWAIAQVLGDAVTPE
+VAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTFRLEPADDTP
+QTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEV
+GDVVELSNPYGDITLQDSDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWD
+SVALRDQVLEDVASLPHAQADLWFGVAPETAPEGVSVHEGKVDTAAAALPEGADYILCGP
+LAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>3_1198
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPP
+PLTPAPGPAGIRDRPAGRIPAWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTS
+LGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHRRVGFTSFTLMFAHLALITAG
+YAWDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESWHLIHLYG
+YLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSARAGLRVQS
+VTAAGPHAVTVTVAGRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTA
+AVVGDGTGRLWDMRPGTRVLVEGPYGRMHDGVRTGRKALLMGAGIGITPMKALLESLPAD
+AGEITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRPGADSWLPASAGDVDDVTA
+LRRICPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF
+>4_293
+MLSEKSRPVIEATAAVVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPA
+VADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTFRFEPADDTP
+QSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b5b9f0c9e98c43ccf422cbcf77fc692130aff63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000080.fa
@@ -0,0 +1,30 @@
+>0_339
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>1_64
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>2_1227
+MIPVLLIEDEERIAAFVTKGMAAEGIAVTTAGTGAEGVGLAMTGAFELVILDLGLPDADG
+FDVLARIRRQDAHLPVIILTARSSAQDTVEGLTSGADDYMPKPFRFAELLARVRLRLRPG
+APAPEPTDTVMRHGDLELDPASHTARVDGRTVALSAREFALAEEFLRSPGQVLSREQLLD
+GAWGEDFESGSNVVDVYVRYLRAKIGAERILTVRGLGYRLAGEDELSG
+>2_2545
+MQSQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVGDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRAADKR
+>3_2404
+MQSQTPEARLLVVDDEPNIRELLSTSLRFAGFEVRAAGNGREALEAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRLFPVVFLTARDGTEDKVTGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTAPLDDDSAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGRDKMIHTKRGVGYMFRTADKR
+>4_346
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLS
+KAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d6450fe458bc87a50ea219c8bde416203e0333c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000081.fa
@@ -0,0 +1,72 @@
+>0_346
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAADGRYAELYTTQFADAE
+>1_71
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
+>2_183
+MAPARLDPADRTQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVI
+DDALPNQDVPLLIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQP
+LAFFTRTRGGEVQSRLTHDIAGMQSVVTSTATGVASNLTAVVATAAAMVALSPRLSLISL
+VVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLGTTGHDAERF
+TGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTAL
+QGQVFRPVMGLLNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEG
+VDFAYDDGAPALSGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDV
+ARLDPADLAAIVGVVSQETYLIHASVRDNLRLADPEATDERLWAALETASLARTVAALPE
+GLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQAALDELAE
+HRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAP
+AEPALAR
+>2_2538
+MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASP
+VLAGDVVNAITGGDDGGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVF
+DHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVATSW
+QVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFGRP
+AAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGD
+VVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPLS
+VRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGSTVALVGSSGAGKS
+TIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLLARPD
+ATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVL
+DEATAALDSTNERAIQEALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAE
+LLAAGGRYAELYTTQFADAE
+>3_2397
+MSMESVARVSMMRLQRGGTAPQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVAS
+PVLAGDVVNAITGGTDRALVVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRV
+FDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANAVSLALTLAVMLATS
+WQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFGE
+PGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAG
+DVVTMALLLTRLYAPLTSLANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL
+AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVLHGVDVDVPAGRTVALVGSSGAGK
+STIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLLARP
+AATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVV
+LDEATAALDSTNERAIQEALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHA
+ALLAAGGRYAELYTTQFAEGA
+>4_353
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef3097adbf17d5432dec3531e839256132aac14f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000082.fa
@@ -0,0 +1,65 @@
+>0_365
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>1_98
+MSDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPMLVVASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAITVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESARWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWEHLLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>2_2513
+MTDEQTTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVE
+NNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVPLVVVASQIPLSGLGAR
+RKGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLL
+GEVLVPPVQDALAVPYDHPPRAELVDESVRWLRDAQRVAIVAGGGVRRSGRAAMESLREV
+AELLQAPVVCSPGGNTAFPWQHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYF
+TLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAEDAPVWHGRTP
+AEVVAETMGRVAARLDAQDLGVERRLLADIRAAVPSAMQTYWDMTIAAYWAWNCWDAREG
+EFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSIAELAAARQHD
+AAVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGAL
+ERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>3_1719
+MSARHDAAVPQEAADMAAAAGGAGGGTARRNGGDLAVETLHALGARTVFGIPGQHALGLF
+DALSRSSLRFVSSRVENNAAFAADGYARATGEVGVLFLSTGPGALTSLAGLQEAYATGVP
+MLVIASQIPLSGLGARRKGMLHQLDDQKASAKNVTKAQFTVHHASGIPSAIQDAWAEAVT
+VPQGPVWVEIPQDVLLGEVMVPPVQDALAVPYDHPPRAELVAESVRWLRGAERVAIVAGG
+GVRRSGRAAMASLREVAELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRHVTELLEDAEV
+LLVVGSSLGEVTSNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALAALADALRA
+DETARPAERPWHGRTPADVVAEVNAKVTARLDAQDLGRERRLLADIRAAVPSTMQTFWDM
+TIAAYWGWNCWDAQDGEFHSAQGAGGLGYGFPAAFGASVGLASAGRDARVLAVAGDGSAM
+YSIAELAAARQHDADVTWLIIDDGGYGILREYMEGAFGKATATELARPDFAALATSFGVP
+AETVGVEDVRGALERAFQEDGPNVVVVQTRLAMWAPSHLEAPVPADEAGPGLAETTRPEG
+RAA
+>3_2388
+MRALEDRRPRNSRSETLSGRGVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQ
+DVLLGEVMVPPVQDARAVPYDHPPRAELVAEVVRWLRGAGRVAIVAGGGVRRSGRAAMES
+LREVAELLQAPVVCSPGGNTAFPWEHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVT
+SNYFTLEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALQALAAALRESGSVARDAAVWH
+GRTPAEVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWD
+AQDGEFHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIDGRVLAVAGDGSAMYSLAELAAA
+RQHDVDVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDV
+RGALERAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
+>4_371
+MTDEQTTTAAPRRNGGDLAVETLHALGARTVFGIPGQHALGLFDALSRSPLEFVSNRVEN
+NAAFAADGYARATGEVGVLFLSTGPGALTALAGLQEAYATGVPMLVIASQIPLSGLGARR
+KGMLHQLDDQKASARNVTKAQFTVHHASGIPSAIQDAWAEAVTVPQGPVWVEIPQDVLLG
+EVMVPPVEDALAVPYDHPPRAELVAESVRWLRGAGRVAIVAGGGVRRSGRAAMESLREVA
+ELLQAPVVCSPGGNTAFPWGHPLSLGGWVEDRLVTDLLEDAEVLLVVGSSLGEVTSNYFT
+LEPRGRLIQVDAEPRVLETNHPTLGVRADAGQALEALAAALRESGSVAQDAAVWHGRTPA
+EVVADVNARITARLDAQDLGVERRLLADIRAAVPSTMQTYWDMTIAAYWAWNCWDAQDGE
+FHSAQGAGGLGYGFPAAFGGAVGLAHQGRTGIEGRVLAVAGDGSAMYSLAELAAARQHGA
+AVTWLIIDDGGYGILREYMEGAFGKATATELDRPDFQALAASFGVPAETVGVEDVRGALE
+RAFQADGPNVVVVQTRLAMWAPSHLGEAPEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..963f6b7661ad4e747bfefce8c955a93795972296
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000083.fa
@@ -0,0 +1,42 @@
+>0_391
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>1_120
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFTYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>2_2491
+MSHVDTAPAASTPRTAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVMYPILQALY
+DSLFKYRLTAPDDREFVGLGNYGVILSDPVFWKDLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+SNTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>2_2587
+MFTEVLPQQQVAPRPEAATAEPGIAESGIAESRTATDAPRPAKQKSRRTGRSFSIVPYLY
+VLPAVALLLLWTYLPLAQTFELSFYDWNLLPTKAKEPVGLENYATVLTLPEMQQALGNTV
+LYIGAFFLLSVALPVIFALLSKRVSGRAKTIYQALIFVPYLVTPVATSAIWRWLFAEEGG
+TIPAVAHFFGIDMGNVFREPGASMIAVMVIVGWQLLGFGVLVVSAGLSGISPDYEHAAGV
+DGARRWQITSRITLPLLSPSLVFLSLMTILLSAQWTFPMIDIITQGGPSGSSTNIYYLLY
+EFGFKNFDAGISAAAGVLFFIGFGLIALVFVELSEKLSFHDN
+>3_2359
+MSHVDTAPAASTPRAAEGRRPRRVKSARAKSEARLGWLLAGPAFFIMLFVVLYPTVQAFY
+DSLFKYRLTAPQDREFVGLGNYGVILSDPVFWKDLGVTVLITLVTVLVELVLGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGFVNNWFDWVPGITSDLNWFAQ
+SGTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAISVILFLC
+VALMAFTAVKVFKVDLADRGGSK
+>4_394
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d795e0b5894d8aeb80cf1637fb3f9fbc74f6f5bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000089.fa
@@ -0,0 +1,48 @@
+>0_486
+MIPEAARTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGAGPLEGELRAQAEALGVAEAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVVRAAADGPGEVRVGDVETMARATA
+EATLEVLGRRVGKVGTR
+>1_215
+MIPEDATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRV
+TLAGSGPLEGQLRAQAEDLGVADAVHLPGFVEPWGTMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPEAIADAVVRAAAEGPGEVRVGDVETMARATA
+EATLEVLGRRVGKGGHR
+>2_1193
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIGR
+FLRDNITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAHGIDLFEERQSTDYLP
+GRAINLGALDELHSVSRAGAEYLRARHPEFVEKIKVSYLGTEDHGVRPPRSSSQVLRLVS
+CSEVAPVKRLELLVEALREVSDSIQVEWSHYGEGPDMDRVRAMASTLPGHVSATFHGWTR
+NDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSCGLPTIATDVGGTGEIVSDGVNGRLI
+SANPMPREIAAAVEEFARMAPEAFARRSAAARETWSTHFDSDRNYRQFVAKMLS
+>2_2388
+MTPEAATTTPAPLTLWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAP
+ALVSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPI
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGVGPLEGQLRAQAEALGVADAVDLPGFVEPWGAMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVMRATVEGPGEVRVGDVETMARATA
+EATLEVLGRRAGKTSG
+>3_2271
+MIPEAATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRL
+TLAGSGPLEGQLRAQAEDLGVADAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVTRAAAEGPGEVRVDDVEGMAEATA
+RAERDVVETQDARRRKTR
+>4_485
+MIPEAARTALAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGSGPLEGQLRAQAEALGVAEAVDLPGFVEPWETMAEHDVLAQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPAAIADAVVRAAADGPGEVLVGDVETMARATA
+EATLEVLGRRVGKAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000093.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19f430642f247016274b7d039c5ffd5a090e65fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000093.fa
@@ -0,0 +1,33 @@
+>0_579
+MPKMSGIETAFCRSALWGRFARDIIVPWSLGGQDLGGDVLELGAGSGQMAAALLQRSPGM
+RLTLTDIDERMVATARRRFPTSPRLTVQQADSTALPFAESSFDVVLSFLMLHHVVNWKAA
+VAEAARVLKPGGMLIGYDLTAWSSPS
+>0_2113
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>1_1838
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>2_560
+MFDAVAERYDLMNTVMTWGQEPRLVRHTVARANVPAHGRVLDLATGTGDLAFEVLRQHPD
+ATVVGADISAEMMEVGRRREGGDRVEWVVADAQDLPFEDASFDSVTHGYLLRNVADIPAA
+LAEQFRVLRPGGWMAALETSPPPANIIRPFSTFYMHQVMPRLARVITDKPEAYEYLSSST
+KAFHAPEEIADMLAHAGFVNIGHETHMFGTLATHWAMKPVA
+>3_488
+MSETSPSPLPRPASLAHDADHGARVSGMFDAIAGRYDLMNTVMTWGQEPRLVRRTVERAN
+VPAAARVLDLATGTGDLALEILKQHPDAHVVAADFAPEMMEVGRTRPNGDRIEWVEADAL
+ALPFADGEFDSLTHGYLLRNVANIPAALAEQFRVLRPGGWVAALETSPAPDNLIKPFSSF
+YMHRIMPRLARLITDRAEAYEYLSSSTRAFHTPEEIAGMLADAGFVNIGHELHMFGTLAT
+HWAMKPLD
+>4_2059
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78ef00051c55dad181c2960c0a84952f57597e63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000094.fa
@@ -0,0 +1,36 @@
+>0_585
+MSLGGFFAEMVQSGALLVAMPLAAIAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFILGFAAVFTFYGAAFGVIGGWLLQWQDALIRALGVFVVLMGLVLIGWLPFL
+QNTRRMSFQPKTGIVGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGILLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>1_1720
+MSLGGFFAEMVQSGALLVAMPLAVVAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFIMGFAAVFTLYGAAFGVIGGWLLQWQDALIRALGVFVILMGLVLIGWLPFL
+QNTRRMSFQPRTGIAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGVLLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>2_383
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMFTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTVWIYQLQNLA
+GTFTTPV
+>2_2583
+MDVQQLVADGQLLVASVIALAAGLLSFLSPCVLPLVPGYLAYVSASAGAAPGEKPARGRL
+VLGSLLFVAGFTAVLVALLAAAGTVGVWLLEWEQLITRVMGAVVILMGLVFIGAFGFMQR
+TTKLRIKPRTGLLGAPLLGVVFAIGWTPCLGPTLAAIMTLSVQQGSVARSVVLALAYCIG
+LGLPFVLAAFGFGWMTQTMTFFKRHIRTVNLIGGVLLILIGLLMVTGLWSQMMYALQAVI
+GGYVTPL
+>3_2150
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMLTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTAWIYQLQNLA
+GTFTTPV
+>4_1944
+MSIGNYFAETVNSGALLIAAPLAMIAGIVSFLSPCILPLVPGYLGYVSGLSNPTHPDNRR
+RVLTGVGLFILGFAAVFTLYGAAFGTIGHWLVRWQDPMIRVLGVLVIVMGLVMVGKFSLF
+QRTLKPTLAPRTGLAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFLLAAAGINWVTTALSYIRRNIRVFNIIGGCLLVLVGVLMVSGLWMLWMYQLQN
+LAGTFTTPV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000097.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a7e52e3cf7f6cbcec8889776a64b42734f65e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000097.fa
@@ -0,0 +1,30 @@
+>0_595
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFQDKISGSSRAKRTGLAELMQYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMIEMGIPKAEVARTFGVSRQTL
+YTSLRRFESG
+>1_345
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRAGLAELIGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGADVEQARVMIDMGIPKAEVARTFGVSRQTL
+YTSLSRGAGAEG
+>2_1285
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFRDKISGSSRAKRAGLAELLGYVREGDLV
+KIASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQAKAMVDMGIPKSEVARTLGVSRQTL
+YTSLGRIASS
+>3_672
+MVGQTVGYVRVSSVEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAGFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKMSDLDVEQARVMISIGIPKAEVARTFGVSRQTL
+YASLRRVAP
+>3_2159
+MVGQAVGYVRVSSAEQNLDRQLEAVGECDRVFEGKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMINMGIPKAEVARTFGVSRQTL
+YTSLARMGL
+>3_2163
+MHVGYARVSTLEQDLSAQREALERLGVENKDIYFDHGLTGTTRARPGLREALAATRDGDT
+LVVTKLDRLARSLPDARDIADELTTKGVALSLGGSVYDPNDAVGRLLFNVLGMVAEFEAD
+LIRLRTREGMAIARSKGKLKGKKPKLSPSQRKHLLTLHAAGEHTQAELAELFNVSRTTIY
+RELRRTTTDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9648734973d498d78c57a3bed92b8d0d0888257
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000099.fa
@@ -0,0 +1,34 @@
+>0_605
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>2_386
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDTDPARYIDTVRGVGYRMAE
+Q
+>3_435
+MTGPDLLLIEDDDRLGPLLRDLLSLDWEVTWSPTLAAARAELDRRLFAVLVVDRGLPDGD
+GVDLVRELRARGVAVPALLLTAYGELEDRVHGLDAGANDYLVKPFEVAELQARLRALTRD
+YSGRGAGVEIGSWMFYPDNRTVESPYTGRILLTEKESALLAVLASAPDTAFTRAHLLSAV
+FEHGEQEGTVDTYVHYLRRKTDRSLVETVRGVGYRLGTPT
+>3_1037
+MARLLMLTRAASAVEVLPALDLLTHDVERADPRAALAAGREDVDGVLLDATSGLAEARTL
+ARDLASLAPEVPVVAVMAEGALTAVGPEWSLADIVLTGAGPAEVDARVRLLRPADAPVAG
+GAAERLAVGGVEIDPVGYRARLDGRALNLTFREFELLKHLAQSPGRAFSREQLLREVWGD
+DYFGGTRTVDVHVRRLRAKLGPDREQMIGTVRNVGYRFTPRPDGDA
+>3_2147
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVMVLDLGLPGLDGIEVCWRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLAAHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
+>4_576
+MNSGTGTGTDTGTGPAAGRVLVVDDEKPLARMVATYLERAGYEVALTHTGPAAVQAARVH
+EPDVIVLDLGLPGLDGIEVCRRVRAFSECYVLMLTARGDEHHRLEGLAVGADDYITKPFS
+VRELVARVGAVMRRPRTTVSAPEPERVCGDLVIDLATHEARVSGQVVQLTRTEFDLLAAL
+SGRPHQAFSRRQLIDIVWDPAWVGDERLVDVHIKNLRRKLDADPARYIDTVRGVGYRMAE
+Q
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c61ec982ee6be0b391a8d7e5caf868d25c71206
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000101.fa
@@ -0,0 +1,47 @@
+>0_624
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLIEAVARRTDAPGPEGADVEVEVAMLI
+SDERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILT
+LHDLIYYEHRTPPRNLPEPIRWLWRAYHLTKTPQRLLLDRADAVATVSRTTAELIDRHRL
+TRRPVHVIANAAQTVPEPRDPDETPDRTLLYMGSFMDYKDVESLVAAAPLLPGYALHLLS
+RISPERRGQLEARLAARRAAAGAAGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGL
+PVAEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAEFAAA
+SRASVAQAARFSWDESARRLLDLTAALGAARRAARARTDRSSR
+>0_811
+MRGQRMMSTSHEPLATTFIIPTGLPGPSGGSRYNKALIRALEAAGCSVSVCGVPGPWPRP
+EARDLERLRAALAGREQVVVDGLIASSAPDEIQAAAASGTRVHVLFHLSLLVDGAVPPDG
+SGRAAALERRALQSAHTVICTSNWAARDVVNRYGPLPTRVVSPGTDQAPLAVGSAPPQLL
+LLASVTPRKNQLAILRALAALTELDWQALLVGPDAADPDYAQRVRLFAEAAFPPGRVQVL
+GSRTGPGLERIWSASDLLLLVSRAETFGMVVTEAVARGIPAIVGAGTGAEEALALGPHAP
+PGIAVAPDDTAALEEVLRGWLSDPAQRAAWRRSAEGARGMLPTWDDSADLMLRILTP
+>1_370
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLLEAVARRAAAPGPAGVDVEVAMLISD
+ERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILTLH
+DLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLLLDRADAVATVSRTTAELIARHRLTR
+RPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMDYKDVESLVAAAPLLPGYTLHLLSRI
+SPERRGQLEDRLAERRAVAGADGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPV
+AEAMAHGTPVVCSDLPIFREIAGAGTASFRGVPLEGDRVAALAARVRELEDPAEFAAASR
+ASVAQAARFSWDESARRLLDLTAALGVARRAARARTGRSSR
+>2_2263
+MSPSRPLRLLMDARYTRTDFHDGISRYGASLTEAVAHRAAAERGEGADVEVVMLISDERQ
+LALLPKGVPWHRVSGPTSPREPFVARQMARLRPDVVFSPMQTMGSWGRRHALILTLHDLI
+YYEHRTPPQNLPEPIRWLWRAYHLTMTPQRLLLDRADAVATVSRTTADLIAAHRLTRRPV
+RVIANAAQPVPRPRDPEEAPERTLLYMGSFMDYKDVESLVDAAPLLPGYALHLLSRIDPA
+RRAQLQERLEARRAAVGEDGAEVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPVAEA
+MAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAVFAAASRAGV
+AQAARYSWDESARRLLELTRELGQARRAEAPRAARGRRDRSSR
+>3_2119
+MTGSQLLLMDARYTRVDFHDGISRYGASLTEAVHRLADPAGLRVEMLISDERQLALLPDG
+VPWHRITGPTSAGEPFVARQVRALRPDVVFSPMQTMGSLGRDYALILTLHDLIYYEYPTP
+PRNLPEPIRWLWRLYHLGYAPQRFLLDRADAVATVSQTTADLIAAHRLTRRPVHVVPNAP
+QPAGVPRDPEAAPTRELLYMGSFMDYKDVESILDAVPLLSGYTVRLLSRLTAERRRELAE
+HLRRARAAAGARGAEVVFHDGTDEAEYTALLRRATASVTLSRAEGFGLPVAEAQAQGTPV
+ICSDLPIFREVAGHGTAAWNGVPLEGDRGAALAARVRGLEDPAAFAAASRASAEHAAGYT
+WDRSARRLLDLVEGLLADRGR
+>4_594
+MVRVSPSRPLRLLMDARYTRTDFHDGISRYGASLLEAVARRAAAPGPAGADVEVAMLISD
+ERQLALLPDGVPWHLVSGPTSPREPFVARQVARLRPDVVFSPMQTMGSWGRDYALILTLH
+DLIYYEHRTPPRNLSEPIRWLWRAYHLTKIPQRLLLDRADAVATVSRTTAELIARHRLTR
+RPVHVVANAAQAVPEPRDPDETPERTLLYMGSFMDYKDVESLVAAAPLLPGYTLHLLSRI
+SPERRGQLEDRLAERRAVAGADGADVVFHDGTDEAEYVRLLRRATAAVTLSRAEGFGLPV
+AEAMAHGTPVVCSDLPIFREIAGAGTPSFRGVPLEGDRAAALAARVRELEDPAEFAVASR
+ASVAQAARFSWDESARRLLDLTAALGVARRAARARTGRSTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a406250fac4f1299943c42bb9bdfe482e0990cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000103.fa
@@ -0,0 +1,48 @@
+>0_666
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARAIALLGMITVHVLDPVTAD
+GAPHPAFLWFAGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRRR
+VAAGILGGGATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAV
+GGR
+>1_412
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARAIALLGMITVHIVDPVTAD
+GAPHPAFLWFAGRASVLFVLLAGVGLALSTGGATPATGVRRAALRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARALGLIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRRR
+VAAGILGGGATAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLTALVVLSLAAGLAAELSGRRGPLEAVMARLSRTGGERAV
+GGR
+>2_2212
+MHGACERSPPCTPPRPPAATTPTPSVRRPRLRGVDAARGVALLGMVAVHVVDPTTAAGDP
+HPVFLGFAGRASVLFVLLAGVGLALSTGGTRPAEGARRAALRRRITRRAGLLFVVGLACG
+ALGTPVAVILGHYALLFLLAVPLLGLRAPALGAIAGAWLVLGPVAVFAASTAGQALLGRD
+EFLLDARLWLSPMPEDLLTPGVLLADLVVTGYYPVLSWGAFLVLGLALGRLPLDRARVAA
+ALLAAGALAWGAAAAAGAAVLRAPGVLERIAAGTGADPAQLTATLRTGEHRLAYLPPDPL
+WLALPTPHGGSPVAALLAAGWACAVLGLCLLVGAALDRALAGRTPADRGGGGRRGRASCG
+RRRDPSRGRGGSR
+>2_2213
+MRAASRPLTGAGRIPLTLYVGHLLVLAAASRLEIDASDAQLLTVLVALCLAAGLAADLTG
+RRGPLESAVARLSRAGEADAPSHLRR
+>3_2387
+MTPKHRQDPLAEPPEGDFTEARPAPGRRPSRTPWTDISRRRADAAPDTAAPPPPPPPPGK
+VGHRDAPPVSWRTQALRSARRLHGLDLARFLALAGMMAVHVWADAIDDRGLGGFIGTVVA
+GNAAAVFAFLAGITLIFLSGGSRGARGRDLQRARVAIAVRAVMLLVIGLGLNLIDFPAYD
+ILPYYAMLFLLAIPLLGLGPAALALCAAAALLTGPVLRMVLVSTGTPVPGFDPTLISLFA
+RPGPTLIQLFVTGTYPAITWMAYVCAGMAAARLNLFDRQRQAFVAVGGLAATGVAAGLSW
+AALHVWDGRERIAEVTGIRPDLVELRASRGLSAEMLSTTPWWLAARGPHLDTPLSTLHAV
+GVAAAVVGFVLMLTSGLMRPDGSLPAWTEPLRAAGSMSLTVYVSHLLLLTVPGWEERRGW
+FFVGQLVLLVSFATLWRRVSAQGPLETVVSRVPKAVARALVPGRPAGAGPDYEPLEAADP
+R
+>4_636
+MAPPRRAATREEPALRPAPPPAAVRPDRPARRRLPGVDAARGIALLGMITVHVLDPATAD
+GAPHPAFLSFAGRASVLFVLLAGVGLALSTGGATPATGARRATLRRRIARRAGLLFVLGL
+ACGTLGVPVAVILCHYALLFLLALPLLGLRARTLGVIAGAWLVLGPVLVFAVVAAAQAAV
+GRQEFFVGGRLWLSPGPADLLRPGLLLADLTVTGYYPVLSWGAFLVLGLALGRLPLDRPR
+VAAGILGGGAAAWAAAGVVGAAVLRAPGTVGRVAAAIGTDPVETALTLRTGEPRLALLIP
+DPLWLALPTPHSGSVVAAVLAAGWACAVLGACLLARPLVGHAALRPLVGAGRIPLTLYVG
+HLVVLALVDATGLDPADGALLAALVVLSLAAGLAAELSGRRGPLEAVMARLSRAGGERAV
+AGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18f39807ab0c6d24c75e229599899208c9ceb64c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000107.fa
@@ -0,0 +1,51 @@
+>0_742
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKPG
+DPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVITD
+VDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG
+>1_481
+MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGSDPYIVLSAPDARAAARDALATRMGNW
+GQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPGDPTSRDADVYGPLSSESAADGLTEQI
+AAAKEAGATVHVGGERVSGPEGEGFYVSPAVITDVDQENPAYTQELFGMAAVVYKVSSAE
+EAVALANDSQYGLGGAVFSTDLDEAKRVADQLEVGMANVNLASAAGANLPFGGVKRSGFG
+RELGPMAVDEFANKRLYAVQGPLEG
+>2_788
+MARYITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLARAADLYE
+ERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGGGTAYVRR
+DPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLLDAGLPEG
+AFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGGSDPFIVA
+GDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPHGDPTDES
+TVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGPGAYYPPTVLTDVDESARAFRE
+EIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLETGMVWVNSTSK
+SSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA
+>2_2112
+MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVKR
+ISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSGQ
+EAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFRE
+AGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKAA
+DPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVITD
+VDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLEV
+GMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG
+>3_2007
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATVVGGERLSGPSGEGFYVSPAVITD
+VDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLEV
+GMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG
+>4_706
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPG
+DPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVITD
+VDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af853e46afb86c3dec8094c417f82de4a76d2794
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000110.fa
@@ -0,0 +1,31 @@
+>0_929
+MTEHSAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVLQ
+PAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPGR
+EHVTWTALTPPRGGWTPVAEVADEELTEVATRGADAVWDALPENPGEALVRKIRAQMWGP
+LLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>1_651
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKVRAQMWG
+PLLGGEALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>2_1882
+MTEPSAAPVLRFADERAVRDLEQFATRARRVSDTGMRLHVVPAAGPSRTPMLAQWVSVLQ
+PAGLGDEVPVVLGLRTVPLATAEMAADLDAVVALGAVTERTARMRSRQPVDLDFSVPPGR
+EQVTWTALTPPRSGWTPAAEVADEELADVAERGVAAVRETLPENPGEAMVRKVRAQMWGP
+LLGGDALGFPAGMAFGAHALGFLQPGGRARLSTAGPWTRLDTPGGFVLGRPAMAV
+>3_691
+MPARLILADAPPARDALTFAQRAAQAGAHGVRLQAAAALTPRGPLDRTPTILVLRTLRSD
+PELQCDVTVDTLTATADPLTLALPETALAPAWTSVEPPQHGWRLIADVTSLTLMRSARAG
+IEAVAQALPDKPGDDVVRKIRGTVWGTPDTALASLPQGVAFAAYVFGFLSRGNGATISTA
+GRWTRLTLPTGHVLLRGPVASGLTPIRRTRPRVSKSVTSIE
+>3_1830
+MPDQPSSRRDARDAARAAVPVLRLTDERAVRDLDQFATRARRVADTGMRLHVVPEAGPRR
+TPMLAQWVSVLQPHGLGDGVPVVLGLRTVGLTSADAVEDLDAVVPLGAVTERTARMLGGT
+PVALDLPVPPGRERVTWTALTPPRAGWTVRAEVPDDELAEVAVKGAEAIRDALPQDPGEA
+MVRQVRAQMWGPRLGGEIGFPAGMAFGAHALGFLRPGGRARLSTAGPWVRLDTPGGFVLG
+RSAVGV
+>4_875
+MTEHSAAAPVLRFVDDRAVRDLEQLATRARRVADTGMRLHVVPEAGRSRTPMLAQWVSVL
+QPAGLGDGVPVVLGLRTVPLATADGVADLDAVVALGSVTERTARMRGQDPVDLAFAVPPG
+REHVTWTALTPPRGGWTPVAEVADEELAEVATRGADAVRDALPENPGEALVRKIRAQMWG
+PLLGGDALQFPAGMAFGAHALGFLRPGGRARLSTAGPWTRLDAPGGFVLGRPAMAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9967c0e641eb20c9b5d11f2286782f4b18d3e381
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000111.fa
@@ -0,0 +1,31 @@
+>0_954
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETTRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESATGGSL
+PAPRSFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>1_677
+MTTFAAAERARLADLLLEKGPDAPTLCGGWSTRDLAAHLWLRERRPDAFAALFIPPLSRH
+LDRLTAETKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSAGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>2_1785
+MAAMADFPVTADRQGPDYAAASRAALVEALTAAGPGMPTLCAGWRTEHLAAHLALRDSSP
+TAPGLFLPPLAAVLERRTRALGDAHAGDRGYAELVARIGRGPLPAPADDGVRGRLRGLAA
+RARGSRPGRAVAGRVQLLEFFVHTEDVRRAQDRWAPRILADDYADALFTRLHARAALLYR
+GEETGVVLVRRARAGSRTDNAPLTARRPGPDGVGVRVTGPAGELAMHAFGRRGAALVTQD
+RFDADPAEDGPGAA
+>2_1858
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSCH
+LDRLTAETTRRDYVEVVREWALGPSALNPMRAADKHVNAAEHFIHLEDVRRGESAAGGSL
+PAPRSFSPDEEDALYRSLRRMAPLVLRTSTAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVELDGDASAAVRTAL
+>3_1804
+MTTFAAAERARLADLLLEKGPHAPTLCEGWSTRDLAAHLWLRENRPDAMASMFVKPLAGH
+LDRLTAHTKRREYVDVVGEWSQGPASLNPMRVADRHVNAAEHFIHLEDVRRGEAVAGGVT
+PAPRDFTPSEEDALYRSLRRMAPLLLRKSAAPVVLQAPGRAPITVAREAVAVKAPVTVSG
+PVGELLFWASGRDAVHVDLDGDHAAVVRGGI
+>4_897
+MTTFAAAERARLADLLLEKGPHAPTLCGGWSTRDLAAHLWLRESRPDAFAALFIPPLSRH
+LDRLTADTKRRDYAEVVREWAAGPSALNPMRAADRHVNAAEHFIHLEDVRRGESSTGGSL
+PAPRPFSPDEEDALYRSLRRMAPLFLRKSAAPVVLQGPGRAPVTVTRGAVALRAPVTVTG
+EVGELLLWASGRDAVHVEIDGDASAAVRTAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7d4a093f471369d34fff35d19f045feffd595b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000113.fa
@@ -0,0 +1,41 @@
+>0_987
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>1_711
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
+>2_175
+MTSRSPLSSRSPLSPRPSRRALLAGLAGVGSAALLTGCGLRTGTAAGGGGASRTITLCAT
+EDAPYQEPVRIAERLLAERGWELKTTFVTDIIQPNIAVDRGEFDANFFQHIAYLKQFNAD
+NGTSVVPAFNVYTSPAGLFSTRYSSLEELPDGARISVPVDPSNNGRALRLLAQAGRITVR
+EGVSVIRLSQHDITANPHGYEFVEVDQQSLALTIEDADAGFLFARQSAKIGLPISESLLF
+ETAEDAVPFRVVVATREGFRDTEAGRALREAFQSEEVRRWYADYLDGALGTEAWGDDPQE
+AIAALEI
+>2_1816
+MALSPLSRRTALGAGTAALALVLSACGAGGSDTAASSAPTPDPANPVVVKVGANPVPHAQ
+ILEYVDENLAKEAGIDLEIQEFDDYQMPNTALDEGKIDANYYMHEPFFNKQVEERGLKME
+HGKGVHIEPYAAFSKKFDSVDQVPEGATVAITNDPGNQPRALKMLEQAGLLKDVKDDSAA
+LTLTPEQNPKGLTFEENQPEILVQILDDPAVDLAIINGNYFIQAGMTLEDAVVVEEISGE
+NPYANFVAWREGEKTPGVEKLDELLHSPKVKQYIEQTWPGGDVTPAF
+>3_1707
+MPTRAGDVAPSSKENPMTTPSNISRRSFAGLSLAAVGALALTACNSQAEKKGDDGAQTVR
+IGVVSENETHRALVKLAKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYN
+QASGKDLTLIGTTEIIPLPLYSKKYKDVSEFQKGDTVAIPNDTVNQARAINVLVAAGLLK
+LSNETIRPEPKDIDEAASTVKVQTVAAQQTVNALESVQGSVINNTFSADAGIDTNTALFK
+DDPKADSAKPFVNGFAVRRADRENETYKKIAALYHEQAVLDESAKLSSGTSVPVQLDAAQ
+IDETLKQYQDAIAKQGA
+>4_931
+MTTPSNISRRSFAGLSLAAVGAFALTACNSQAEEKSDDGAQTVRIGVVSENESHRALVKL
+AKEKHGIDVEIRNFTEYTQPNPALDNGDIDMNWFQHIAYLADYNQASGKDLTMIGTTEII
+PLPLYSKKYTDVSEFKKGDTVAIPNDTVNQARAINVLVAAGLLKLSNETIRPEVRDIDEA
+ASTVTVQPVAAQQTVNALESVQGAVINNTFSADAGIDTNTALFKDDPEDDSAKPYVNGFA
+VRREDRDNETYKKIAALYHEQPVLDESAKLSSGTSVPVQLDTAQIDETLKQYQDAIAKQG
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a9a8954b6ce9bf9b3dcb3d5733dfbb71ce99fb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000114.fa
@@ -0,0 +1,46 @@
+>0_988
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>1_712
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>2_177
+MISIQNVSTAFGEHRAVDDVSLEIPTGSIQGIIGFSGAGKSTLLRNVNLLLRPSAGRVVV
+DGTDLTALSPSGLREARRGIGMVFQHFNLVHNLTAAQNVALALKFAGVDRRARQARAHEA
+LEIVGLADHAGRYPAELSGGQAQRVAIARALSTRPSVLLCDEPTSAVDPRTTATVLQHLV
+DINRDLGITTVIVTHEMNVIRAVADDVAVMEDGRAVERFALADLERADFAPRTGIGRYLL
+EDEIALERPPLRGAAGAPDGDRAGSGTTPGTSPGTTSIPGDVREAVVAGV
+>2_1818
+MSSSPTVSTSAHPVGTPMIEVRGLEKTFRQGAKEIRALRGVDLAVAPGRIHGIIGQSGAG
+KSTLVRCLTLLEPPTSGTVSVAGKDLTRESRSGLLDSRRRIGMVFQHANLFSSRTARDNV
+AYPLEVAGGSDAAARRARADELLALVGLKGFEGSYPAQLSGGQKQRVGIARALASDPDVL
+LCDEPTSALDPASTEGVLTLIQDLSQRLGLTVLVITHEMHVVKRLCHEVSLLQDGRIVQS
+GDLGDVAADLDSPLSSALLPLPAPHAAPDQRLIEVLGRGAAASLPITQLVRDAGAGEVEV
+LAGTVEDLAGERFSHQLLGLAGTWAAGDAAVARLQEAGLTARTLSARQASQDQHTADEIG
+GAR
+>3_1706
+MAGSHSSDRDAVTPGRHSEGAPGEPVIVFDHVSRVYAAKKGRGVTAVDDVSLSVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSTRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DTGRVVETGKVYDLFSRPAHSADAASFVATALKDRPNADEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
+>4_932
+MAGSHTSDRDAVTPGRPSAGAPGEPVIVFDHVSRVYAAKKGAGVKAVDDVSLAVNRGEVF
+GVIGFSGAGKSTLIRMINGLEKPTSGTVTVLGQQVSHLSEAKLRPLRTRIGMVFQQFNLL
+TSRTVAGNIEFALDTAGWPRSKRRARVAELLEFVGLADKAKHYPEQLSGGQKQRVGIARA
+LAAEPEILLADEATSALDPSTTHEVLSVLRRVNEELGVTIVAITHEMEVIRSIADRVAVM
+DSGRVVESGKVYDLFSRPAHSADAASFVATALKDRPNAEEVARIRARTEGRLIMVSLKDS
+AAVSAVLGTASTRGVGFEIVHGGMSATKDSAYGLLTVALTGEAAAVDAFVADLAGAGDVQ
+EVHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffa139eb536069f7b324ed8a041d425d6c46fe2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000118.fa
@@ -0,0 +1,90 @@
+>0_1060
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>1_788
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>2_1756
+MTSPLTRLHDALGLRTTPAIFFGSAAVVVLFTLAMGLFPGPVQAGFGVVSSWLRYDAGWI
+YTLSLTVLVAFLLLLAVTRYGRVKLGDDDAVPEYSGLAWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPLAGTEPFSDQAASQAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDIVSVVSTVFGLGVSVGLGALQINAGMNYVFGTPVAGWVQA
+LILAVITAVGTASVLAGMDKGVKRLSYANILMAIALLVYVLMWAVSSMDVIRGTVQAVGE
+YLTMLPMLSTFNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFAKISRGRTIRSFIAAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAAAPGTGGDLTETIVTEGNVQAALFQHLQGTPLYT
+VAAVLALVVITLFFITSIDSGALVMDAMANGHEDPAPRRQSVIWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAGLLLQALREDAGTARPLRTRQWKPVLPAEEYHRR
+AHEEGVDVSDYVIRPEFEVGTEPEHDTHTPNTWHQQRTVAAKALVTVGLTGGIAAGRTVV
+GEELERLGAVVVEFDDLMGEILVPGSPVLEELREVFGDDVVRADGTLDARTLNRLTAEST
+TARTRMYEIVSPAVRDEANRRARAIGEDSVLVVDLALLAETGSAGDFDQVLAVSAPAEQR
+VARLMDSHDLPREQAWAFIDEEALDAERAEIADTVIENDGTLEDLHEAVRAYWEAKIQPQ
+IEAARGVSP
+>2_1757
+MNSLLTRLHDRLGLRTSPAVFFSAAAVIILFTVAMGVLPGPVQAVFGAAAHWLRYDVGWF
+YTLAATLLLAVCLILAVSRYGRVKLGDDDASPEYSGLAWFGMMFASGIGAVLMFWGIAEP
+MTHYALPPLEGTEPYSDQAAVQALNIANLHFGLHMWAILVVPGLCFGYFTYKRNLPPRVS
+SAFQLLLGDRIHGPIGKTIDVIAIVSTVFGMGVSTGMGALQINAGVNYVVGVPVAGWVQA
+LILAVALMLWVLMWAASSMDVVRGVIESFGRTLGALPLLTTFNDTLGGGTWSGDWTLFYW
+AWTVSWAPSVGMFVARISRGRTIREFVFASLGLPTAFVIVWMGVYGYSAIFADRAAAPEA
+GTGGPLAQTIAVEGNVQVALFQSLQEMPLYLPIAVLALIVIVIFFVTSIDSGALVMDAMA
+NGHEDLAPRRQRVFWGVSVGAVCTAIIVTAGDDGLNALREVIIVIGFPVMVLTVLQALLL
+LQALREDAGAARPLRTRQWKRVLPPEEYHRRAREDATVREEYAIRPEFEVGTEPEYETHT
+PNTWHAQQPAARRATVSVGLTGGVASGKSAVAAEFERLGAVVVDYDDLMREILVPGHPAV
+DELRDVFTAEVVADDGTVDWLALDALTAESPSARTRLHEVVAPVVRAETDRRATDAGESS
+VLVVDLALLVDAADVRDFDQVLEVLAPAEVRVARLMDERGLDREQAWAEVDADEQRRPAL
+GGTHTVLANEGDRAELERSVRDWWDEVVEPARERGRRPGPRLRRLTRTVPPPPPAAGGGG
+RGWRPGAGSPYRRDRVPDGTRPSARPLDRPPRSVGDPVPGDS
+>3_1647
+MNSLHTRVHDALGLRTSPAIFFTSAAVIVLFTAAMGLFPGPVQEVFGVVAGWLRYDIGWF
+YTLSATLLALFAVLLACSRYGRIKLGDDDATPEYTGVAWFGMMFAAGVGAVIMFWGIAEP
+MNHYANPPMPGTEPFSDQAALQAMDIANFHFTIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDVISVVSTVFGLAVSTGLGALQINAGMNYVLGTPVAGWVQA
+LILAVITAAGVCSVLAGMDSGVKRLSYINIVVAVALMLFVLMFSISTNDVLRGTVQSVGS
+FVGHLPVLSTFNDVFGSGRWSGDWTVFYWAWTVTWAPFVGMFVAKISRGRTIREFVTAGL
+GLPSIFTMIWMGIYGYSAFQADRATAAGPGQGGDLTRTIVEEGNVQAALFQHLQGMPLYL
+PVAIVALVVITLFFVTSIDSGALVMDAMANGHEDPAPRRQGAFWAISIGAVCAAIILTAG
+ENGLDALQEVIIVIGFPVMLLTLVQAAMLLQALREDAGAARPIRTRQWKQVLPAEEYHRR
+AQEDGVDIQEYVIRPEFEPGTEPEFDTHTPNTWHQQRTVAQRALLTLGLTGGMASGRTAV
+GEELERLGAVVVEFDDLLDELLVPGAPVLDEVREVFGDDVVRADGTLDARAMNALIDASE
+AARSRFYEIVSPLVRAEADARAKAIGDDAVLVVDLALLAETGSARDFDQVLAVSAPAEVR
+VQRLVDERHVTRERAWALLDEGAQDDERAAIADTVIENGGTREELRAAVEAYWAEKVAPA
+VEAARIAGGVG
+>4_1009
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d05ec71cd5f1fa7e905003931d7bbfd7bdc0bd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000122.fa
@@ -0,0 +1,36 @@
+>0_1106
+MGEVGTREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSARIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>1_834
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>2_1709
+MAEPAATAEPDGREVRLARAEDLADPRLVPYTTLTDAALRRRVDAEHGVFLAESSQVVRR
+ALAAGHTPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRP
+APRPLADVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVS
+MGTVFRLPWARLEGPVAEAVPALREAGFAVAALEVTERAVGLDSPELEPLRSADRLALVL
+GQEGPGVRTETLEHTDADVVIPMPDGVDSLNVAAAAAVALWELRAR
+>3_528
+MSSESPAQPASADQPAEAPAGVIVDPKDARLRKVRELLKGKNKASRAIIVDDEENLLAAL
+AAGVELFTVFHGEDAELPAALAAVLPADQDVQVVSTHAAKELFGVERRSRVFALARRPKP
+LTVAEVLEHPGDVLVLDGVKLMGNIGAITRSARALGAAGLVLVDADLASVTDRRLIRASR
+GMVFSLPVALASADDVAAQLAEAGVPLVSLDLGSEKALDSVAEIPGRVALLLGSEKHGPS
+ARLAETAEHTVSITIHPEVESLNVSVSAALALYERRASNPLPQA
+>3_1602
+MPDDGAPAPFPGEVRLQSAADLADPRLAPYTTLTDAALRRDVDAAHGVFLAESSPVVRRA
+LDAGHAPRSFLLGDRYRETFADVIAAHPGVPVFTGPDEVLTALTGFHLHRGALAAMDRPA
+PRSVAEALDGAHRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPRAADPLYRRAIRVSM
+GTVFRLPWARADGPLEEALPALRAAGFATAALEVTDRAVGLDSPELEPVRTAERLALVLG
+QEGPGVRPETLAAVDAHVVIPMPAGVDSLNVAAAAAVALWELRPRDTPAA
+>4_1056
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4159ba5c616a03e6900198e3fa7e4c71a8818101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000131.fa
@@ -0,0 +1,30 @@
+>0_1495
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>1_1215
+MSALQPQPTVKHASWAWSESRATEDDVVLRARERAAELEVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
+>2_1351
+MSALQPQPTVKHASWAWTESRGVEDEVVLRARERSAELDVRPVSEGTAALLTVLAATRAP
+SAVVEVGTGAGVSGLAMMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTGRTRMITGR
+SRLVLPRLTSGAYEMVVVDGDPASRQFDVEQAARMLAPGGVLVLVDALDADRVPRPAVRG
+ESTVSARAVDRLIREDEGWVSAVVPSGTGVLIAVRR
+>3_1243
+MSALHPQPTDKHASWAWAEARTAESEVLLRARERSAELGVRAVGEGTSALLTVLAATRAP
+SAVVEIGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEAHLPTSRTRMISGR
+SRLVLPRLTTGAYEMVVVDGEPASRAFDVEQAARMLAPGGLLVVVDALDSDRVPRAAVRE
+DSTVSARDVDRLVREDEAWVSAVVPTGTGVLLAVRR
+>3_1272
+MDPRRRALLDRLWQEGRDFDAAQPDRLDRRRNLEPESAELLNILVRTLAPAEVLELGTST
+GFSALWIADALEPHGGRLTTVDPDAPRLAEARTNLEAAGVADVVTVRQADAADVLADAED
+GCLPLVFLDAERPAYPDYWPDLARILAPGGLLVVDNCLSHADDVRPFRALVDASPGFRST
+LVPVGAGLLLVSKDRPGHGSGVG
+>4_1422
+MSALQPQPTDKHASWAWSESRATEDDVVLRARERAAELDVPPVSEGTAALLTVLAATRAP
+AAVVEVGTGAGVSGLALMRGLPERTVLTTVDPDAEAQRAAREAFSEARLPTSRTRMITGR
+SRLVLPRLTSGAYEMVLVDGDPAARQFDVEQAARMLAPGGVLVVVDALDGDRVPRPAVRD
+ESTVSARAVDRLIREDEHWLSAVVPSGTGVLIAVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..017a68f1583e8ed60b626f2924bd571fb7264761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000132.fa
@@ -0,0 +1,25 @@
+>0_1509
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRADRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGVSWTAGLWAAAPGAVVASVAWNVGQPALGLVL
+LAVGRRLDRRPAGAADGATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
+>1_1229
+MPERPRRRARPADVVGGALLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQR
+WWMVRRAGRGGRALPAGAAVVAGAFTVVLALQRLPVDDALGLSWTAGLWAAAPGAVVASV
+AWNVGQPALGMVLLAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRA
+QREVDGQP
+>2_1338
+MVGGALLGVVAGALGTAVHLTLSPLPGGWTLPWGAVLALVLAGSVQRWWMRRTAERGGAP
+LPAGAAVVAGAFTAVLALHRLPVHDALGVSWTAGLWAAAPGAVVASVAWNVGQPVLGLVL
+LAAGRRLDRRPAEAADGATRPRRTSVTARETRPGERVPWTAAPQPRAQREVDGQP
+>2_2218
+MSRRVLLLLTAAVLVYALQFLPPLIFHDLVIAPSLGEHFGWALPYLAPVMVVPPLAWAAV
+AAAPVLRGGSTRRASGLSMTLLFFAPFAYAFATPVTWVAVRGVDAIGGLEDDPLLLGMVL
+PFLSGMILSPVLVGVVLQWWLRRTARRAAAGGAQAEAAPERPAPEAPTHDASGLPLP
+>3_1230
+MLPGLALGVGTGALGTATHLSLLPVGSWLLPWGLVLALVLVGSTQRWWMRRAAAAGGRPV
+RAGAAVVLAAFTMASALRWLPATDRLDLPWTAGVAQAMPVAFAASVGWTLGLPVLGVVLL
+WLGARAGEGRAAGESTLERTPNPVPARKVDGQP
+>4_1436
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRAGRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGLSWTAGLWAAAPGAVVASVAWNVGQPVLGMVL
+LAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54363ba9fa0f44e74054f67254b63c404191cec3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000133.fa
@@ -0,0 +1,60 @@
+>0_1515
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
+>1_1235
+MTDTAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAMPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRAHGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPTRPFVMLCQQQ
+AADPSRATGPARGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIGAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASPRPHRAGRTGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
+>2_1330
+MGGGETGIGSGARPRPHRTHQHRRVHDRLAHPVAGPAAGPRFALPRGVEPGRAVVVGAGP
+NGLTAAALLAREGWEVDVYERAPVPGGASASAPVLGEGTVVDLGAAGHPFGAASPVFRDL
+DLAAHGLQWLHPAVPMGHPLPDGPAAILHRDLDATAEGLGPDGRAWRAVHGALVEHIEEL
+VADVLGPLVRPWPHPVAMARFGLRAPWPAAHFGRAVFRTEQARALYTGSAVHAIMPPGRP
+LTSAFGALFGALGMSSGWPVARGGSGVITDALVSVLRAHGGRLHLDQEVTDLRALPDVDA
+VVLDMTPRQVARLRGTDLSPSYAAALQRWCPGPAVSKVDFLLDGPVPWRDGRLAGAGTVH
+LGGTAADIQRAEADVAAGRMPARPFVMLCQQQSADPSRAAGPAAGRTVLWSYAHVPHGHP
+GDVRPLIEAEVERHAPGFRDRILGAVDMRPADLEAWNPNLVGGDIAGGSMAGLRLLLRPT
+ASPRPHRAGRPGLYLASASTPPGAGVHGMAGAWAVRTLLADRARATSR
+>2_2521
+MNAAPTQDTAEDHARFPLPRDAEPGRAVVVGAGPNGLTAAALLARAGWEVDVHERHPSPG
+GACASAPLLGEGTVVDLGAAGHPFGVASPVFADLDLIGHGLRWAHPEVVMAHPLPDGEPG
+LLYRDLERTAAGLDADAARWWAVHAPLVEGAEQLVDNVLGPIVRPWPHPLTMTRFGLRAP
+WPASWLTGGLFRTEQARALFVGSAVHAVMAPSRPFTAAFGALFAALGMSSGWPVAEGGSQ
+AIVDALVRVLRTHGGRLHLGSPVEDLRAFADVDAVLLDLTPTQVARLRGTDLPKHSLSRM
+RRWRHGSAAFKVDMLLDGPIPWADPRVGQAGTVHLGGTAAQVQRAEADVAAGRMPDEPFV
+MLCQQQSADPSRAVGPAAGRHVVWSYAHVPHRHSGDATHAVLARIERFAPGLRDRIVRIV
+ATSPAELEAWNPNLVGGDIAGGAMDGLQLLARPRISAAPHRLRAAAPSAWRTSSGRTAPG
+LYLASASTSPGAGVHGMAGAWAVRTLLSDRRCAR
+>3_1224
+MPRDAAPIDAPAARDRGFALPQGAEPGRAVVVGAGPNGLTAAALLAREGWEVDVYERHHA
+PGGASASAPLLGRGTVVDLGAAGHPFGVVSPVFRELDLTGHGLRWVHPEFPMGHPLPDGP
+AAVLHRDLDATAEGLGVDGRAWRALHAPLVRDADRLAADVLGPLLRPWPHPVSMARLGLR
+APWPAGWVNRAVFRTEQARALYTGAAAHAILPPGRPLTSAFGALFGALGMSSGWPVAAGG
+SQSIVDALLAVLRAHGGRLHLDHEVTDLRELPAADAVVLDLTPRQVAALAGTDLPPAYAR
+SLRRWRHGSAVSKVDFLLDGPVPWTDVRLAGAGTVHLGGNAAQLQHAEAEAVAGRMPEHP
+FVMLCQQQAADPSRAVGPSAGRTVVWSYAHVPFGWDGDVRPLVEEQVERFAPGFRDRIVH
+AVATRPADLEAWNPNLVGGDIAGGSMGGLQLLLRPTASPRPHRAGRPGLYLASAATPPGG
+GVHGMAGAWAVRTLLRDRARAAF
+>4_1442
+MTEIAAGPGFALPRGVEPGRAVVVGAGPNGLTAAALLAREGWEVDVFERAPVPGGACASA
+PVLGEGTVVDLGAAGHPFGVASPVFRELGLTDHGLAWLHPAVPMGHPLPDGPAALLHRDL
+EATAAGLGVDARAWRAVHGALVAHVDEILAGALGPVLRPPPHPVAMARFGLRAPWPADLL
+GRAMFRTEAARALFTGSAAHAILPSSRPLTAAFGALFGALGMSSGWPVARGGSGAIVDAL
+VAVLRALGGRLHLGHEVTDLRALPAADAVVLDLTPRQVLRVAGTGLPPRYAAALRRWRPG
+PSVSKVDFLLDGPIPWRDARLAGAGTVHLGGTAAEIRRAEDDVAAGRMPARPFVMLCQQQ
+AADPSRATGPAQGHTVVWSYAHVPHGHPGDVRPLIEAEVERHAPGFRDRIEAAVAMRPAD
+LEAWNPNLVGGDIAGGSLAGARALLRPTASIRPHRAGRAGLYLASASTPPGAGVHGMGGA
+WAVRTLLADRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ff6a4c6f9f2f426242ada14b486fe263ff0f38d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000136.fa
@@ -0,0 +1,34 @@
+>0_1530
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>0_2188
+MISSLFSWFADPAHWAGPNGVPARVLEHLGYSVLALVIAAAIAFPVGVWIGHTGRGRRVV
+VALSSALRALPTLGLLTFLAIVLDIRLRQALIPTVMVLVILAIPPLLAGTYAGLQAVPRE
+VVHAARANGHSTGQLIGQVELPIALPMAVGGLRSATLQVIATTSVASYLGLGGLGRYLFD
+ALAVQDYVTMLAGAVLIAVLALLCDGLLLLVQRILTPAGLRARG
+>1_1251
+MIARLRAASAEDRLLLIGLPLLVATLLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>2_1313
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>3_441
+MIADLFAWFADPAHWTGPGGVPARVAEHLGYSLLALAIAAVIALPAGVAIGHTGKGRRVV
+VAVSSALRALPTLGLLTFLAIVLQVGLRQALIPAVIVLVVLAVPPLLAGAYAGVHAVPRD
+VVVAARANGHSTRQLVSQVEVPLALPMIVGGLRSASLQVLATTSVAAYLGLGGLGRYLFD
+ALAVQDYTTMLAGAVLIALLALVSDAVLLLFQRLVTPA
+>4_1457
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3125195156ef866b95f0513575f7c7d5fe621f6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000137.fa
@@ -0,0 +1,40 @@
+>0_1531
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGEPVLDAATPISEALAALVMA
+PTEEIAVVRDGTVIGLLDYPTLRAHARASDEQARP
+>0_2190
+MIRFEHVEKTFPDGTRAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTGGRVL
+IEGRDVASLDPVKLRRGIGYVMQNAGLLPHRTVLDNVLTVPRLTGRISRQDRDHAHELLE
+LVGLPAAVASRYPSQLSGGQRQRVGAARALAPDPDVLLMDEPFSAVDPVVRADLQAEMLR
+IQRELSKTVLFVTHDVDEAVLLGDEVLVLREGARVAQHGTGEDILLRPADDFVRSFVGGA
+RRELHVEDRTGTPIVVDASGRVAGTLVQP
+>1_1252
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDTL
+TRQRLQKEMLDIQARVGKTIVMVIHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAALVMA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>2_1312
+MSTDRDAGAEIRLESLTKRYPGQDRPAVDALDLLIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAVYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQQEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAHHPTGTLPDGPVLDAATPISEALAALVTA
+PTEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>3_439
+MIRFEHVGKVFDDGTAAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTSGRVW
+IDDADVASVDPVRLRRRIGYVMQQAGLLPHRTVLDNVLTVPRLTGRVSAADRSRAHELLE
+LVGLPADAARRRPDQLSGGQRQRVGVARALASDPDILLMDEPFSAVDPVVRAELQAELLR
+IQRELAKTVLFVTHDVDEAVLLGDEVLVLRTGAQVAQRGRGEEILLHPADGFVDRFVGGD
+RRRLHVEERAGTATVVDAAGRVAGLLETP
+>4_1458
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELFGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAVLVTA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b25635c5388baddd347d5aa026292ecfb122e2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000138.fa
@@ -0,0 +1,36 @@
+>0_1547
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTRSAPVTVPTTYVWGTRDAALGPRAAELTAGQVAGEY
+RFVKLDADHWLPEREADAVARAILDRVR
+>1_1269
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
+>3_257
+MLHRREYGDPDGVPVLHFHGTPGSGREAAALDAAARAAGVRLIAPDRPGMGRTPHLPGRR
+LAHWPAEVTRLLDELGIDRAAILAWSGGGPYAVACLARIPERLTAVALLAPAGLLRGIPW
+ANRLFPRLYLPAAGAIARARDWAPAAALGVFRWRRMRSRLADGPPAASPEREPLAPSSAA
+VLAASWREAFRQGHAGPVQDEQVINEDWSPLLTSARRAPVPVRIWHGRRDRVVPHRHSRR
+LAAALGAFLVDAHDGDHPGALLTAGPEALGWLAASAE
+>3_1177
+MTGGDALWGRVDAFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDSTSWRHVEPLLHAAGLR
+TLAPDQRGYSPGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATA
+HPERVASLTVLSTPHPAALARALRGSDQLRRSWYIAAFQAPALPERILSRRLGSLLQRGQ
+VPGAEHYARRFSTPQSLRGPVNWYRANPDLVTTTRSAPVSVPTTYVWGTRDAALGPRAAE
+LTAGQVAGEYRFVALDADHWLPEREADAVARAILDRVR
+>3_1785
+MTIPGFALEHIPLPSGVTLRVATGGEGPAVVLLHGHPRTHATWHRVAPALADAGLRVVCP
+DLRGYGQSSAPEPSDDLHTHSDRTMAGDIALLMTHLGHDHFSVVGHDRGSYVAYRTALDF
+PERVDRMAVLDCVPILEALERADARFAEKWWHWFFFASPHAERVICADPLAWYQPDAQKM
+GQENYQDMVAAISDPQTVRSMIADYRASLHVDRDADARDRARGHQIQCPTLVAWSKHDDM
+EDLYGNPAEVWESWCAHRPESAVIDSGHHMAEDNPEQLTAVLTEFFLPS
+>4_1474
+MDTFRHQGLTFDVRDGGPAEGEVVLLLHGFPQDATSWRHVEPLLHAAGLRTLAPDQRGYS
+PGAAPRATAAYRLPALVGDAVALADAAGARRVHVVGHDWGGAVAWALATAHPERVASLTV
+LSTPHPAALARALRGPDQLRRSWYIAAFQAPALPERILARRLGSLLQRGQVPGAEHYARR
+FSTPQSLRGPVNWYRANPDLVTTTSSAPVSVPTTYVWGTRDAALGPRAAELTAGQAAGEY
+RFVALDADHWLPEREADAVARAILDRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e768ce5d6dc99b4b5b42e363946458112d8e98bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000139.fa
@@ -0,0 +1,59 @@
+>0_1550
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>1_1272
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>2_1250
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN
+>2_1265
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>3_1174
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER
+>4_1477
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17d9c61d460dbd0aeb47a53d8720b525c7cce06c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000141.fa
@@ -0,0 +1,30 @@
+>0_1582
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSSKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADTLRIDKDVQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
+>1_1297
+MTENANQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFDVNTTVKDAKAEDFDGLVMPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRRLTSYPSLKTDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>2_1234
+MTENAAQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFDGIVLPGGTLNADAMRVNKDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVEGRKMTSYSSLKTDLKNAGAQWVDEEVVVDAGLTTSRSPEDLDAFNAKL
+VEELAEGKHEDQTA
+>3_1144
+MTENAVQNAPLTGKTVAFLATNGVEQVELTSPWEAVIAAGATPVLVSPESGTITAMQSDW
+DHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADAMRVNKDAQAFVRAFFDQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDNGLTTSRSPEDLDAFNAKL
+VEELGEGKHEDQTA
+>3_1186
+MAVDLQGKRVTILAADGVERVELDQPREALDRAGARTEVLSVDEGEIKARENDLDPAGTF
+GVDGLVAEASGADYDALVLPGGTVNPDKLRIDEDAVAFVRDFAENGKPVVAICHGPWTLI
+EADVATGRTLTSFPSIRTDLRNDGANVVDQEVVVDKNLITSRSPEDLPAFSEAIVAQLAG
+TTTKEEETS
+>4_1511
+MTENAVQNAPLSGKTVAFLATDGVEQVELTSPWEAVIAAGATPVLVSPKSGTITAMKSDW
+EHGESFEVNTTVKDAKAEDFHGLVMPGGTLNADALRIDTDAQAFVRAFFEQHKPVAAICH
+APWTLIEAGVVDGRRLTSYASLESDLKNAGAQWVDEEVVVDSGLTTSRTPDDLDAFNAKL
+VEELGEGKHEDQTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6e353272e66387bb3a8a61aca5b37419eaad3fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000146.fa
@@ -0,0 +1,66 @@
+>0_1736
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>0_1989
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSRWQTTTYAAVWERV
+RRIAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPDGVRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETGGLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>1_1706
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALRAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRDDVLSYEALLDGHEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSGVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
+>2_1060
+MSTAPRRRVTGYPSTSGDDVQLNTTTLIRHAARTHGDQEIVYRTPDGGWDRYTYAEAYER
+IRRAANAMTGLGVSPGDRVGVIDWNSRRHYELYWAIPGIGATMVQVNLRLAPEDLVHVLT
+DSGCTTVFVDESLLRHAEVIAPRLPEVTTWVVMTDRPLSEIETTLPGVRHYEDLLASASP
+DVDWPEVEETSAYGACYTTGTTGRPKGVFYSHRAIVLHSYALAASIGMTLRDATMIITPM
+FHGQAWGLPQAATLMANKIVLPGRYMAEDTAPLTDALIAEEVTITSGAPAIFQPMLAYIE
+TLDEKPDLSRLRMISGATEPSLSLMRGFRDLTGAEVVHAYGATETTPLVTVNRYKPGVLA
+RLDEPALMDLKRKQGLPLTNVDLRIVGPGDENLPFDGVSQGEICVRGPWVTTGYHGMSEA
+DAEGRFLDGYWRSGDVGTVDSDGYLKVTDRLKDVIKSGGEWISSIDMENLLTSHPAITEA
+AVVGLPHPKWQERPYVQVMLRPGATITLAEVHEHLSGAFASWQLPERVDVVTELPRTSVG
+KIDKKTIRGRHTDLYADASEAARPGGGAGDVEEGGRA
+>3_712
+MNSATAPVLGTPSTMGDDEQLTTSRLFRDAARTYPDQSITHRTIDGEWKVTDYAATWERM
+QRVAAGLASLGVGPRDRVGLLLWNDLRHFECYFAVPLTGATMVQLNLRLAPQDLAYVIGH
+SGARTIVVDATLLPLAEALGPHLPEDTRWIVATDGALPDSWAGRADTMSYEDLIERSAPI
+EDAPDMDERSASGACYTTGTTGRPKGVFYSHRATWLHAFAIAANTGMTMDDTVMLLTPMF
+HAQCWGLPYASVAVGARVVLPGRFTMQDTALLTESLVEHGVTVAPAAPAILLPMLHYLEG
+MEETPHLPGLRFLCGATEPPVALMQGFDRLMGAEIIHAYGATETSPVVSVNRLRPALAER
+LSEDEQWDLKRYQGLVVTGVDVKVVDPMGQPLPPGERNVGEVMIRGPWITRSYFENPEAT
+EKGFDDEGYWRSGDVGHLSEEGYLKIADRMKDVVKSGGEWISSIDLENHLLTVPGVSEAA
+VVGVPHPTWQERPIALVVRTAGADLSEEQVKAALGARFASWQVPDRVLFVDELDRTSVGK
+LDKKRLRQVYADALAQGDGPGAPSA
+>4_1924
+MQTTDTVLGTPSTMGDDEQLTTTRLLRDAARTFGDQQIIHTRGGGSPWQTTTYAAVWERV
+RRMAAALHAEGVGPGDRVGLLLWNDVRHLESYFSVPLLGATMVQLNLRLAPTDLAYVITH
+AQVGTIVVDETLLELAAALEPHLPGGIRWIVAGDGELPADWAGRGDVLSYEALLDGQEPL
+ETADLPNVSERSASGACYTTGTTGRPKGVFYSHRATWLHAHAVVSTLGMTMADTALLLTP
+MFHAQCWGLPFAAVAVGARLVLPGRFNLTDTPWLTSTLVDHGVTVAPAAPAILMPMLHHL
+RTLETPPRMDGVRLLCGATEPPVAMMRGFDELTGAEVIHAYGATETSPIVSLNRMKPSLM
+DTLSEDERWNLKRFQGLVVVGVDVKITDPLGELLPPGEENVGEIRLRGPWVTTSYADNAE
+ATEAGFDDEGYWRSGDLGYLSPEGYLKVTDRLKDVVKSGGEWISSIDLENHIMTVPGVRD
+AAVIGVPHPQWEERPLALVVRDEDSDVDQDAVLAALAERFATWQLPDEVRFVTEIDRTGV
+GKVNKRKLRADYADALTSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21701925d059323409a3c1d54e02d78a70cb8d11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000147.fa
@@ -0,0 +1,30 @@
+>0_1750
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>1_1458
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>2_1044
+MQTPATVHLVRHGEVHNPDRVLYGRLPEFGLSELGRQMADGVAAWFLERAEQTGRRPDVV
+AASPLTRAQQTAEPIAAALGRPLATEPDLIEAENDFEGMSQVAASLKRNPRLWPKLRNPL
+RPSWGEPYRQQAARMLAVVDRVRDEAEAAGGPGAEAVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVFEEGRALPRVEYHEPNQALLKDASSLPGA
+>2_2585
+MSDKLLHLVRHGEVHNPDRVLYGRLPGFRLSEPGHRMAEAAALELAGSDRVVARLLASPL
+ERTRQSARPIASALGLEVSIEERIVEPANVFEGMVNSGSDSAFRQPRYWYRFVNPFRPSW
+GEPYRQIAARVREAMDEAWETTRDGDIVMVSHQAPIWIAHLDVAGKPLFHNPATRRCELS
+SITSFEKRGERWFEVDYRTPAAGLVDDAVDVGAV
+>3_980
+MQTLATVHIVRHGEVHNPDRVLYGRLDGFGLSELGQRMAVGVAEWFLDRATELQRRPAIV
+AASPLLRAQQTAAPIAGAFATQLRTEQDLIEAENTFEGMSDVAATLRRSPRLWPLLRNPL
+RPSWGEPYRQQAARMLAVVDRVKDEAVDALGPGAEAILVSHQLPIWVTRLAVEGRPLAHD
+PRRRECSLTSVTSLVFEDGRALPRVEYHEPNAALLKDASSLPGA
+>4_1672
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFEERAAQTGRAPAVV
+AASPLTRAQQTAAPIAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAAEGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRWRECSLTSVTSLVYEEGRRVPRVEYHEPNQALLKDASSLPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..468d2d60bbcff1c23f5cff90e8e79b3046883cea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000148.fa
@@ -0,0 +1,47 @@
+>0_1771
+MTAPLTSPPAATASPDPVDVAVIGAGQAGLAAGYFLARAARDVDRGRRAGPAPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVTAVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPDGVRWDHDAGASH
+GWPAASRAAARVRGTEHPVDDVVWCTGFRADLRHLRSLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILAGLTAG
+>1_1479
+MTAPLTSPPAATASPDPVDVAVIGAGQAGLAAGYFLARAARDVDRGRRPGPAPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVTAVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPDGVRWDLGAGASH
+GWPPDSRAAARVRGAEHPVDDVVWCTGFRADLRHLRGLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILTGLTAG
+>2_726
+MAGAVDVLVVGGGQAGLAAGFYLHRLGRDAGRDRGGPAPSFAVLDANDQPGGAWQYYWDT
+LELFSPADYSSLPGYRMPAWTGPGNPSAAHVVDYLRSYEDRYGLPVHRPVTVHAIEDHPD
+GGYLTRTDRGTWTSRAVINATGSWRRPFVPRMPGAEDFTGSQLHTTGYRGREPFAGQRVV
+VVGGGNSGAQIAADLLPAAAEVTWVTRRPPRYLPDDVDGRALFALATGHVQATRRGEPSP
+GGVGSLGDIVAVPPVRAARDAGRLQAQPTFSGFTPTGIRWDDGRKLEVDTVLWCTGFRPD
+LAHLRPLRPAMEGTVPATAGDPPTRSRDRDGLFFLGYGDWCGPASATLIGVGAPARATAT
+AAARHVLSGG
+>2_1017
+MTTRTAPASPPSAVDVAVIGAGQSGLAAGYFLARAAREAERGRRPGPPSSFVLLDASPGP
+GGAWPHHWDSLRLFSPAEHSSLPGRRMPPSPGPDTPGADHVVAYLADYEQRYALPVRHGV
+RVTRMEHDADAPHPFTLHREDGPPVAARAVISATGSFTRPFLPAVAFGDGFRGEQLHSSA
+YRRPGPFAGRRVLVVGGGNSGAQIAADLLLAGVETTWATRRPPRFMPDDVDGRHLFQTAS
+ARVLGRSEARVGDLGDIVMLPPVRRARDEAGLHAVPMVSAFIPDGARWDPDAGAVHGWAA
+SSRLAAEVRGAERALDAVVWCTGFRADLRHLRGLDLTHRSSGVPATRREVPTASADVPGL
+HLLGYDDWCGAATATLVGVGVHARGAVDDVLAGLAAG
+>2_2284
+MGHYLNRAGLHPLLVDRAPALGHSWRSRWNSLRLFTPARHNRLADLLFPGDPEAYPGKDA
+VADYLQDFARHQSLTPATGTAITDLHGRLGAFTATTATGRQLRARSVVVATGAFGTPFLP
+DWAARDGRGPRQLHAKNYRTPASVPGQEVLAVGGGNTGVQIALELAATGKRVHLSTGRPR
+RHLPQRLGGKDMFWWLTRTGAMSAPAGSVPGKWLRAHDPIIGTDRAALTGVNIRTRPRAT
+GLQGGIVGFADGTRYTPEVIVWATGYRHADRWIRIPAALDPTGVLHAPEGVSPVAGLYTI
+GRSWQRNRGSALLGFVSTDAAPLAQTILTALAKAP
+>4_1693
+MTAPLTSPPADAASPDPVDVAVIGAGQAGLAVGYFLARAARDVDRGRRPGPPPSFVLLDA
+SAQPGGAWPHHWDSLRLFSPAEHSSLPGRPMPPSPGPGTPDAGHVVAYLADYEDRYGLPV
+RRGVRVAEVTHDAAASPPFTLRLEDGTALSARAVVSATGSFTRPFVPALPGADRFGGTQR
+HSAAYRSPDAFAGRRVLVVGGGNSGAQIAADLLLAGVATTWATRRPPRFMPDDVDGRVLF
+DRASARVLGRSEARVGDLGDIVMVPSVIRARDEAGLHAVPAPTALTPEGVRWGHDAGASH
+GWPAASRAAARVRGAEHPVDDVVWCTGFRADLRHLRGLELTRRPSGAPATERALPTASVD
+VPGLHLLGYDDWCGAASATLAGVGVHARRAVDAILAGLTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c1731d656ffec372e70ab665f627e4586d94dd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000149.fa
@@ -0,0 +1,71 @@
+>0_1785
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>1_1493
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>2_1003
+MSPRRRTGSTAAPETSTLSVVDPAAARDLRVLGVRAEETLEYTPEERRHVRRRSWALLRQ
+LAGPAKGMLWLTVVLVVVSNAARAAVPLVIAWAIDWGLPQVVEAVRTGADAWGVVVLVGG
+AYALTGVTGGVLLGLYQWLTARASQRMLLALRVRVFRHTQRLSLGFHEKYTSGRVISRQT
+SDLEALRELLDQGVSSLVSGVLFMAFTAVSIVLLDPPSALVLLVAFIPVAVAVRWYQKRS
+EEAYRRSRVSSARAIVHFVETMTGIRAVQAFRRQRANEAKYTRLATDYRDDMVHTLTLFG
+VLQPVLVVTGNLTVAALLVFGGLRVLSGDLEVGVLVALVLAGRRVFQPMEMVAMFYSSFQ
+SAGAALEKVSGLLEEEPAVVEAPEPTPLPGAAAAGEGVASGRIEFRDAVFGYGPEKVVLP
+EFDLTVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKELASADLRRNVV
+MVTQEAFLFSGTVAENIALGRPGASEAEIQAAARAVGAHEFILDLPEGYDTDVSKRGGRL
+SAGQRQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLST
+VEIADRVLVVHDGRVVEDGSPAELVAAGGRFAALHRAWEDSLVPDDA
+>2_1306
+MPALFVGRRRLLLLGLAGLGLLQAALSVAVAVLTPRLLTAGAGAWGLAAALLVAALLVGG
+ARILERVAAEDLGQDYVRETRRLLVTSALVPEKSLNLGSTIARTTNDLTAVKNWIALGIS
+PIVVGVPLIVGIVIGLFVLLPTLGLVVVVTLGVFFTGLWALSRVFFRRAVAVRRVRGKMA
+GYVADTVTAAGSIRTAGGVQREVGRVDRISGQLQDAAHRRAVVSGTMRGSAASITTVLGV
+LVAITGSAAGSTGAAITTAVFIAGMLGAPVTELGRVGEYRQNYNAACRVLRPIIENARGH
+ARRERRQKRARTRMRHHGNPRGLSRDAVHLADLRDAEGTIPALVAAPGSRVLLTGGSRER
+LERVTREITGDMPASDAWITVAGRHLYAMTAKDRRELIGVAARDVPLQRGTISRIVRYRH
+RGAGETVAQVLDRVGMAERVARLPEGDATRLKRGGEPLSINERALLKIAGAVAGNPPLLV
+LDHVDDQLDARDRPILRRILADYPGCVILRSASPHELLERYEVYNVDELAPTLVVAPSVL
+HSRIQGERPTTYVIGADRDPFGPPVRHSAVELAGTRAASAPRLGESADDLEGVDE
+>3_945
+MSRRADTAPVTSTLTVVDPAEAAGLRVLGVGAEESLDYTPAERRHVRRRSWALLRQLARP
+VRGMLWLTAALVVLSNAARAAMPLVIAWSIDDALPRALEAVRAGTDPTGVVVQTGALYAV
+TGLVGGVLLGLYQWLTAKASQRMLLALRVRVFRHTQRLSLGFHETYTSGRVISRQTSDLE
+ALRELLDQGVSSLVSGVLFTAFTAVSILLLDPPSFLVILVAFVPVAIAVRWYQVRSEEAY
+RRSRVSSARSIVHFVETMTGIRAVQAFRRQRAGERAYARLATDYRDDMMHTLNLFGVLQP
+VLVAVGNLTVAALLLFGGLRVLSGDLAVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATA
+ALEKVSGLLEEEPAVVEPAHPVALPGAERPGEGVASGRIEFRDAVFGYGSDAVVLPGFDL
+TVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKDLAGADLRRNVVMVTQ
+EAFLFSGTVGENIALGRPDASEAEIQAAARAVGAHEFILDLPEGYATDVSKRGGRLSAGQ
+RQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLSTVEIA
+DRVLVVHDGRIVEDGSPTELVAAGGRFAALHRAWEDSLVGEG
+>4_1707
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLLTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGLSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIIEDGSPA
+ELVAADGRFAALHRAWEDSLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc49ebd800a77d19988a90194f94df111985ec0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000158.fa
@@ -0,0 +1,97 @@
+>0_1968
+MVTFAPDRASFMLSPSDITVAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRSRLEALLQDHVAAGEPARWGDDRLSVCGACEVCEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+GGVPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAVKPLVVV
+>0_1970
+MAASTSETTCPTTGRYTTMRDSTERAALEEFVAFVEARRAAHPGMRIYHYAAYEVTALKR
+LTVRHGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVT
+TAADSVTEYHRYVAAMEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHG
+ATAPRPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGF
+YQREDKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTL
+EPGSSLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKI
+PTQDVEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDI
+LARRPPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKT
+HVGSHAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWA
+TVSDAKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLL
+GDPQQLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSY
+AGELGAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGP
+DDPGRPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAAS
+SPQEVPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>1_1688
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLTRPERYTPEGVQAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPTRWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAVSVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVTGLPAPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALEQFVAFVEARRATHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVTTAAD
+SVTEYHRYVAAMEAGDTEVAKAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHGATAP
+RPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGFYQRE
+DKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTLEPGS
+SLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKIPTQD
+VEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDILARR
+PPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKTHVGS
+HAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWATVSD
+AKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLLGDPQ
+QLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>2_771
+MFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTLTVTGRLEPGTEVRPRRN
+SQERFKLNALYEQPPRGAELAPNAVRWQSRSPVDVTEVEEIAPGRFRVSLLQRLSAKYEP
+EPHAEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPEGAVFDILARRAPRTTGRTLA
+AIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVGSRAVKELLDRGWTVGVT
+AQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGLHRWTSLGSSEVHAFLAPGRVLGGTAW
+TFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQQLPQVSRGEHPQPIGDA
+ALTWIAEGAPVLRADRGFFLDTSWRMHSALTRAVSELSYAGRLGAREEVTDARRLDGVEP
+GLHPWPVSHTGNAVSSPEEAAAVVEIIQSLLGRTWSTGPDDPGRPLEPSDVIVVAPYNAQ
+VATVREALDAAGLEGTAVGTVDKFQGREAAVAILTMAASSPQEVPRGLDFLLNRNRLNVS
+ISRGQWAAYLVHSPALADALPTGPEDLPMIGAFLRLVHR
+>3_732
+MASFSPVDPASFLLSPSDITAAATCEYGWLRGAVDPKLGRADGAPEDDAFLARVSALGDA
+HEARTLDALVAEHGAGGVVVLERPSPYTPEGIAAAAERTRQALASGAAVVFQAMLHDGSF
+GGLADFLVREPTAEHPEGAYQVVDTKLARHARVTALLQIAAYADLLDGMGVPRTRHGSLW
+LGDGARHTVDLAEVIPVYRHQRARLERVLRTHVTEGTPVAWGDERHAVCGQCRWCEEAIA
+EHRDVLLTAGATRVQRTRLRAAGVRTVEELAASTAPPEGMSRRTWEALRDQAAAQLEPAG
+ADGVPPHRIVDPAPVRALPAPDAGDLFFDFEGDPLWVSPRGDMEGLEYLWGWVEAAPGRT
+TEGTGFDQFRFTGLWADTRAEEKAALEEFVRFVEARRAVHPGMRIYHYAAYEVTALKRLT
+VRHGVGEAELDDWLRAGLFVDLYATVRASLRAGVPSYSIKKLEPLYMGADHRAEDGVTTA
+ADSVTEYHAYAEQAERAGEGDADAAAEAARLRAGIEDYNRYDCVSTARLRDWLLGQVGGA
+STGVAVDAGEPAEAGEDAPAATDEDAALEQALLDLVPADPADGDDETLGLAMLAAGLGFF
+RREAKPMWWAFFDRGISPVDEWQDPRANVVADRVDVAEDWHRPSSRARTRQRVLRVTGRL
+EAGTQLTPGAEAKTVYEDVPAGRVEGLQPNAVRWVGAAAVVEDVEDHPDGTSTLRLREKV
+ALDAEPHPELPMAAFAHTVIPSATLQERIREDGLRARALGALPRPEEGAAPTAAFDILAR
+RVPETAGRPLAQITADARAGRLEGADALVEALVSARGSYVAVQGPPGTGKTHVGSHAVKE
+LASRGWRIGVTGQSHAVVENFLAKLVAVGVPAGHVGKEKPRGGEDRERPWTVLDDRGDAF
+EHLSQPGHVLGGTAWTFAHPKAPDLDLLVIDEAGQFSLAMTLAAAATARTVLLLGDPQQL
+PQVSQGTHPQPIGDAALGWLMEPGEEVLPPERGFFLDTTWRMHSALTAPVSRLSYDGQLR
+SRSEATDARHLEGIVPGLHPVPVEHTGNAVSSTEEARRVVEIIEDLVGRAWTPGSGEEPR
+PLTPEDVIVVAPYNAQVATVRAALDDAGLQGTTVGTVDRFQGREAAVAILTMAASSAQDV
+PRGLDFLLNRNRLNVSLSRGQWAAYLVHSPALADALPTTPADLPLIGAFLRLLQP
+>4_1906
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPARWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGIMTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALERFVAFVEARRAAHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGVEHRAEDGVTTAAD
+SVTEYHRYVAALEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLAQVEPEEAAVADRP
+VDDAATGNEPLVEAAPSLQEQDAALAASLQALADVERDEAGGTGAPEAELDGGRRGIALL
+AAGLGYFARENKPLWWAMFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTL
+TVTGRLEPGTEVRPRRNSQERFKLNALYERPPRWAELAPNAVRWQSRSPVDVTEVEEIAP
+GRFRVSLLQRLSTKHEPEPHGEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPDGAV
+FDILARRAPRTTGRTLAAIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVG
+SRAVKELLDRGWTVGVTAQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGPHRWTSLGSS
+EVHAFLAPGRVLGGTAWTFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQ
+QLPQVSRGEHPQPIGDAALTWIAEGAPVLRPDRGFFLDTSWRMHSALCAPVSELSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c2e6e40050d1f13c6ea4ba7aef2476e7e5c59f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000160.fa
@@ -0,0 +1,25 @@
+>0_2011
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST
+>2_718
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT
+>2_722
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN
+>2_723
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS
+>3_471
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA
+>4_1940
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba5e0549da3b2fb7ddab9383511d9a23059b33a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000165.fa
@@ -0,0 +1,24 @@
+>0_2101
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVRTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGW
+LLDTYLRGLRP
+>1_1825
+MILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGWLLDTYLR
+GLRP
+>1_1826
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPRP
+SSPRPSV
+>2_577
+MRADARANRQDLLAAAGRLLEEQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARVSGILHAFLDGGGSADRRWRRLAEELAAVNLTSLVTAGDDLEAADRPQEALIVEAE
+QVIISLTDRAVTEARRAGLVALGVTGTRYLTGLLAVTRPPAGELLARHADQRDWLLGVYL
+RGLRP
+>3_501
+MQEEDTPPAEAMGRAEDAVMGLADRAVDLAREAGLVGDDVTGRAYMNGLIAVTRPPLPAL
+ESCRDDLEDWLLTVFLRGLRPAA
+>4_2047
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLMGPDVTGADYLLWVMRFLARGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c24751c67e8df739a4a98dc6f6d5b2f05d95d19b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000169.fa
@@ -0,0 +1,50 @@
+>0_2204
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPVVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGVRGHL
+>1_1910
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRRVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPEVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGGGGPSMTANGLLRSPHAARDREGVDSRGSPGVRTEVLEDLQVEKP
+LVRAGGLGEHRLVGADVDDLPHTEAGGLLRLKDRQVSVAGDAVDLGEPPRGPHLVCRPHH
+GPHTTQRDRPGGAAVVVMGDDPACRGQGPSLTHSPGGQQDQLVDFPHGDRVTAAFLLPVR
+ERGAADGADGDVHGRSVGAGPHPGARGASSPVMLGIGLEARRVKARTTHPHRVHRIDAMT
+RTGAFTIAGLAAFAISTGILVLLLITGSETPRETMAFFALIIGCYALSALCFAAAKRVLL
+ALLSGALAVVSFPLALFIGYVVEMLQSQQ
+>2_451
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPLVTRPEAEEAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDE
+ATAREKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVARMDARNTASARLAETLGMRREAHHRQDWWSKGE
+WTDTLVYAMLASDRG
+>2_623
+MAERFRGRGLGAQILAALTRHVFETMPAVDRFEGQTREDNIPMLRAFRRAGWVKEAHYRR
+GWPVEGGEPLASVAYAVLRQDWETGTTTPVPADVDVPSRRKRDVGAESNGHIPDWPMRTE
+RLTLRPHREDDLGWLQEMYAQPEVVRHLLDEPWDEPTARQKLVRRIEWNDLAGPSGVASL
+VIEHAGVPVGDVILWLTNRERGVAEIGWALDPRHAGQGFAREAAAAMLALGFEVHGLHRV
+VAQMDARNTASARLAEAIGLRREAHHRQDWWSKGKWTDTLVYATLSSDRD
+>3_402
+MDVTFTPLDPAGADRDALVALLTENVWPFHMRPRITRSEAEEAVDGGAWEDEDHRTLWIE
+HPEHGRVGVVRLDELTDPTPLFDLRVTERFRGRGLGAPILTALTRLVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVEGGEPLASVAYAVLRQDWETGTTTPVPAEVD
+VPPQVEHGEGAAAVGPAPDWPLRTERLTLRPHREDDLGWLRDMYARPEVVRHLLDEPWDE
+ATARQKLAKRIAWDGLAGPSGAVSLVVEHRGVPVGDVILWLTDRERGVAQIGWALHPEHA
+GQGFAREAAAALLTLAFETYDLHRVVAQMDARNTASAQLAEAVGLRREAHHRQDWWSKGE
+WTDTLVYATLASDRG
+>4_2138
+MVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTAITRHVFETMPAVDRFEGQTREDNVPM
+LRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVDAPPPAGRK
+EGAAEGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDEATARAKLA
+KRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHAGQGFAREA
+AAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGEWTDTLVYA
+MLASDRGVRGHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..559156165324c7e8e79f31406c0105dcf7b316bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000178.fa
@@ -0,0 +1,65 @@
+>0_4
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>1_1960
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
+>2_401
+MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH
+HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI
+LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ
+GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV
+DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI
+AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA
+REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL
+GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR
+CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN
+IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK
+WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT
+LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV
+>3_354
+MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH
+LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL
+HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG
+EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE
+DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA
+FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK
+EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW
+LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV
+YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE
+EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN
+APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ
+VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI
+>4_4
+MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG
+MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT
+EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF
+ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL
+TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN
+SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG
+FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE
+ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP
+GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN
+AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG
+HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ
+ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c302799fc7555daa3e99e32dd525cb68656357a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000180.fa
@@ -0,0 +1,20 @@
+>0_6
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGIGVTLTDD
+>1_1962
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD
+>2_399
+MSTSASSRPGKAAGAGRTAERSGRPVRKASGSSQENLVRAVPKAKVRRARLMLNRVDPWS
+VLKLAFLLSVALGILTVVAAVALYSLSDALGLFQRINDALGTVLGAESGRYTVQSLAPLS
+TVVSLATVLAVLNVILLTALATVAALLYNVCAALVGGVGVTLTDD
+>3_352
+MSTSASSRPAGAKGASASRPARRSSSRDSQEDLVRAVPKAKVRRARLQLTKVDPWSVLKL
+AFLLSVALGIILVVATVGFYTLAELTGVFGKINDVLGTVLGTESGTYTVENLAPLSTVVS
+LATVVAVLNVILLTALGVVGALLYNVCASLVGGVGVTLADD
+>4_6
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e667b9f6fdb65acdd0e84eb652a478f1fb907a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000183.fa
@@ -0,0 +1,40 @@
+>0_11
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
+>1_1980
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR
+>2_367
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR
+>3_349
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG
+>4_11
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c03df3150415a46f90f2a080c8f00a7ea058434
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000187.fa
@@ -0,0 +1,25 @@
+>0_15
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>1_1984
+MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD
+>2_363
+MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL
+ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV
+RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ
+FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD
+>3_345
+MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA
+VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS
+VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG
+VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD
+>4_15
+MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG
+PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE
+HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE
+SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54d7f094b9652636f41a17b82e51d4eb59154099
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000194.fa
@@ -0,0 +1,35 @@
+>0_28
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>1_1996
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
+>2_351
+MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV
+HSTRYPDQDNAITAPSDTYHY
+>3_290
+MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA
+PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV
+MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG
+LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP
+EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL
+AHIPDQENRAAAPSDTYHY
+>4_27
+MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA
+VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA
+GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD
+TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL
+APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV
+HSTRYPDQDNAITAPSDTYHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e052563523a3af2f4210235558535134f70d1c66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000195.fa
@@ -0,0 +1,44 @@
+>0_29
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVA
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV
+VPAAVQSVLTEDNAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
+>1_1997
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV
+VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
+>2_350
+MTRIPAPDEAAAAPSSPLDNALAQLAAAVRTLGYDEGLHQTLAAPRRELSVSIPLRRDDG
+AVEVLRGYRVQHNISRGPAKGGVRFSPDVDLDEVRALAMWMSWKCALVGVPYGGAKGGVS
+IDPRRYSKAELERVTRRYTSEIQPIIGPEVDIPAPDMGTDEQTMAWMMDTYSVNVGHTTL
+GAVTGKPVSLGGSLGRASATSEGVVHVALAALRDRGIDPQGATAAVQGFGKVGAGTVELL
+AAAGVRVVAVSDQYGAVRCEDGVDFATLSAHVAETGKVVDCPGTEAMDADELLLSDVDLV
+VPAAVQGVLTAQNADRVRARVVVEGANGPTTGEADRILNENGVLVAPDILANAGGVIVSY
+FEWVQANQAYWWTREEVAERLERRMVLAWEAVQAAAREHDLTLREAATVLAVKRVAEAHR
+TRGLYP
+>3_446
+MTSASSPLANALAQLERAVETLGYDEGTHQLLANPRRELSVSIPLRRDSGEVEVFHGYRV
+QHNFSRGPAKGGVRFSPSVDLDEVRALAMWMTWKCALVDVPYGGAKGGVAIDPRTYSQAE
+LERVTRRYTTEILPIIGPEKDIPAPDVGTDEKTMAWMMDTFSVAMGYTVQGVVTGKPVSL
+GGSLGRAEATSRGVVHIALAALKHKGIEPAQATASVQGFGKVGAGTVEFLADAGVTVLAV
+SDQYGAVRREEGIDYAALAAHVAETGSVVDCPGTEPMDPAELLTMEVDVLVPAAVEGVLT
+KDNAGDVKAKIVVEGANGPTTGEADAILNENGVLVAPDILANAGGVIVSYFEWAQANQAY
+RWTLQEVNDRLAARMRTAWDGVLAASQKHGVSLREAATVTAVKRVKEAHEIRGLYP
+>4_28
+MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG
+STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT
+IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL
+GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL
+EAAGVKVVAVSDQYGAVRDDEGLHYDALQKQLWDTGSVKDTPGTAPMDADELLEMDVDLV
+VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY
+FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR
+TRGLYP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dc8506f9985cc531377b60dfeb4807d82145e29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000196.fa
@@ -0,0 +1,24 @@
+>0_30
+MHAITPGTWNLDPAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>1_1998
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD
+AQA
+>2_347
+MAQVTTGTWNLDPAHSDVDFVVRHAGISKVRGTFAAVEGVLVVAEDFNASSVEVTVDVAS
+INTKNEGRDQHLRSGDFFDVEQFPTMTFRSTEVRGAAEEFTLVGELTLHGVTRTVELEAE
+LGGQDVDPFGTTRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLPEAD
+AQA
+>3_289
+MAQITPGTWNLDAAHSDVDFVIRHAGISKVRGTFHTVDGQLVVAEDFNQSSVQVTVDMAS
+INTKNEGRDQHLRSADFFDVEQFPQMTFRSTEVRGEAEDFTVVGELTIHGVTKTVELEAE
+FGGQDKDAFGATRVGFEAKGEISRKDFGLTWNAATEAGGVMVSDKVKIEIGAAFVLPEA
+>4_29
+MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS
+ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE
+FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGLLVSDKVKLEIGAAFVLPEAD
+AQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000197.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd94c8016c5148841747884e14fa415de9c2d1b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000197.fa
@@ -0,0 +1,88 @@
+>0_31
+MRRIPRTGPLDEGPGLLTLFSAFMDTPSDAARVAAEERARALIDEQFRRAGWSVQDGAQK
+NLMASAGVAVREVTMRAGHGRVDYLLYVDRRPVGVIEAKPVGTTLAGVEWQSGMYADGLP
+DDALKRAVVVDGRLPFVFESTGSESYLTNGYDPNPRARRVFSIPRPEYFSQLMRDAEADP
+DAPTWRGKVRAMPPLQTEGLRPAQIDAVRGLERSLAEQRHDRSLIQMATGAGKTFTAITA
+AYRLLAHGGFRRILFLVDRNNLADQTLAEFENYRLPGDGRRFTEVYPVDKLRRAGMRDSA
+NVVISTIQRVYAGLQGKEVPDSDDPMLDEFVPDRPVTVDYSADLPPESFDLVIVDEAHRS
+IYGVWRGVLEYFDAHVVGLTATPGKQTLGFFRQNLVSEYTYPQSVADGVNVDFDLYRIRT
+QISEEGSTIEAGTVVPVQDKSTRIERFETLDEDLDYTRTQLDRAVVSTNQIRLVLEVFRD
+RLFTEIFPGRTEVPKTLIFAKDDNHAESIVRTVREVFGRGNEFAAKITYSARDPKGQLQA
+FRNSPALRVAVTVDMIATGTDVKPLECVLFMRDVRSAQYFEQMKGRGARTIPDADFQAVT
+PDAATKTRFVIVDAVGVTEHDFVDPPLNRQKAVPLKKLLEKAASLTITEDEAATLASRLA
+KLELELSDSERQELDDVAGGSVRQMVKDLVAAVDADEQASVRAEAAARGEDEDRALEEHI
+ERAVTPLAANPDLRMRILELRRAHDRVIDEVSADVLLDAYGVVDADKARSVVESWSAYLE
+EHRDEITAVQVMFEAGEGRLQYAQVAELAERIKRPPYSWTPEILWKAYESLDAGRVRRSD
+HHTLTDLVSLLRFATGTDDELVPFADRVRENYAGWLLAQEQAGAEFSDTQRWWLDRMVEV
+IGASAELTVDDLEGAPFTDRGGIDGAVRDLGPRAGLLIEELNEELTA
+>0_182
+MATGTGKTCTAVALVDQMARAGWVKRVLFLADRQALVKQAADAFVEHGFVGTTVNLLKNR
+HGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAHRSVYAKYGEIFRHFDALL
+VGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLVPPRGVSVGTTFLRRGTRY
+DQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDRVLSTLREHGHKVAGSERL
+GKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYPDALLDDFKTPGKAPHIAI
+SVDMLDTGVDVPDVVNLVFFKLIRSKTKFWQMIGRGTRLRPDLYGPGRDKEDFLVFDWCQ
+NLEFFNQDLPESDGFTQRSLTQRLFEDRLALVVALDALDDDAGAPAAVGPEERAVRELRR
+TAAEELQAAIARLTLENVLARPLRREVEEFQRPEAWTSLSAQAAERARALAGVVTGLPGE
+DVDAKRFDLLIVRRQLADLTGEAGTAERIRATVQSLGENLLSKDAIPAVKEQIILLEAVA
+GEEWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQLEEVDVVRPTPGVDI
+ERFWAKVSEPLRHNESSLALQKLRHGKQLTEPDLESLEQLLRSIGAEDAHLAAAKSEGEG
+QLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQARIRFLGHMVEELTANGVLDAGRLFESP
+YTDDAPEGPFGLFEEAQVYSLRERLDFVRTSAMVPGPEANAGGDEARGVVA
+>1_1968
+MAVDITYDEALIEEIAARFDLRDPNKNALTEIVQRIADGGIGYQEMVADLATGVGKTFLM
+SSLIEYLAQQGVRHVLVVTPGSTIQRKTLANFDAASAKYVAGADIAPFVVTPDNFQAANV
+GSVLRNPQRLKVFVFNVQQLIRPTDKVSRKVRSEDENLGDALYSHLENADDLFVIADEHH
+VYREKAKAFSAAIRDLNPVALVGLTATPDKDDYGKVVFQYTLGEAIADGYVKVPVIVYRK
+DGTKDERTQLRDACQLLGHKEKSYAVYRETNRDAPTVKPVLFVVCQTIEHATEVGQLLAQ
+SGMIGDGSQVLEITSQSSDVALEALAKVEEPDSPIRAIVSVNMLREGWDVKNIAVIVALR
+RLASQTLTEQILGRGLRLPFGARTGIADVDQVDLVAHDSYQQLLAQKDVLRQRIQLPSTA
+VEVDDQGFATTTEVDPNQPVPVEPLAGSSQHDQIGGSGGSSSLAPAPGQWTLFDWEEDDS
+AQGEDYQPNPGLIFEETEQRVESQVPEPQYRVKDAPQIIFPRREPRLVHSPFSLSDIPDG
+DAQKAGAAFVKEVPTFIFRDALEAKRKGDQVEIISTPQGTSEAQQTLAGLDVVQAELTEA
+IMQQPEVPAERPSKNAAKRLVKAFMKGAGVTNDEETAQWGTKRRQQAVEGMRTMIRDKIT
+SRPRQEKFEFVKIELPLEPVTVAADAVKAHNVVKFKKGLQYVGWEKNVMPVATFDAGTTE
+WELARLMDRDPNIKWWVRVYVGGQAFIPTPEGRYFPDFIALDVDGVHWLIEGKADDHAKD
+DSVLRKKKAAENWARAVRDDGDFGTWRYMFATESNIKNSAGSWNALLMSTKPE
+>2_199
+MSSNFDFLAPVWPRVHENAVRAESYLHADPRSACFYARRTVELVVEGIYRLRNLPEPYKA
+DLAARINADAFLHEADPRIVQKLNVIRQRGNDAVHKLPDIDPRTAAFVLTELHHVLLWAA
+FRHSAAGPALDMQARFAPALAPQAAPLTREEVVQLNDLIEKKDAEAAAALAASEQAREQL
+EADLAAARAELTAAKEAAGAVVDPRDYTENDTRDLFIDQLLNEAGWPLTAARDREFPVTG
+MPTPTGDGFVDYVLWGADGKPVALVEAKRTTASVQLGQDQAARYADALEARFGRRPVIFY
+TNGVEHYLWDDAAGYPPRQVRGFYTPAQLDTLIQRRAGRRPLAQTPVKAEIAGRPYQERA
+IRAIGEAFENKRRATLLVMATGTGKTRTAVALVDQMARAGWVKRVLFLADRQALVKQAAD
+AFVEHGFAGTTVNLLKNRHGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAH
+RSVYAKYGEIFRHFDALLVGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLV
+PPRGVSVGTAFLRRGIRYDQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDR
+VLSTLMEHGHKVADGERLGKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYP
+EAMLDDFKTPGKAPHIAISVDMLDTGVDVPDVVNLVFFKLVRSKTKFWQMIGRGTRLRPD
+LYGPGRDKEDFLVFDWCQNLEFFNQDLPESDGSTQKSLTQRLFEDRLALVVALDALDDDG
+GAPAAVGPEERAVRRTAAEELQAAIARLTLENVLVRPHRREVEEFQRPEAWTSLSAQAAE
+RARALAGVVTGLPGEDVDAKRFDLLIVRRQLADLSGEGGTAERIRATVQSLAENLLSKDA
+IPAVKEQIILLEAVAGEDWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQ
+LEEVDVVRPTPGVDIERFWAKVSEPLRRNESSLALQKLRHGKQLTKQDLESLEQLLRSIG
+AEDVHLAAAKSEGEGQLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQAQIRFLGHMVEEL
+TANGVLDAGRLFESPYTDDAPEGPFGLFEEAQVYSLRERLDLVRASAMVPGPEANADGDE
+ARGVVA
+>4_182
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87351f280ee0522353d78c945c14ed1d8a6ca0e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000201.fa
@@ -0,0 +1,34 @@
+>0_39
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>1_2003
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
+>2_342
+MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL
+LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM
+LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA
+WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF
+TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD
+>3_285
+MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG
+DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA
+GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES
+VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI
+VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS
+SRPGADPPMRDELAD
+>4_34
+MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG
+DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA
+GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES
+VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI
+VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA
+SRPGADPPTRAELAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd066a27ff23503a58f8ab527b4725fa69dc0973
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000202.fa
@@ -0,0 +1,39 @@
+>0_40
+MGGVDTAQQTTAQDTAQDPASTTPRTVTVTGAAGNIGYALLFRIAAGGMLGPDTSVRLRL
+LEIPAALGAAEGTAMELADAAFPLLADVEVTDEPARAFDGVQHALLVGARPRTKGMERSD
+LLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPDVPAERFTALTRLDH
+NRAVAQLAARAGVAVTDVAGVTIWGNHSATQFPDLTHARVRVDGTWRPALEVVDPVWAGE
+EFVPRVARRGAEIIEVRGASSAASAASAAIDHMCDWTLGTGVDADGASRRTSAAVVSDGS
+YGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVAELEAERDAVRGLGL
+L
+>1_2004
+MRRAGVSSAGERGHDGGVDTALQTTAQDTAPDPVSTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VPAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
+>2_341
+MRARRRAGLFSAGVRGYDGRVSTVSAPSRAPRTVTVTGAAGNIGYALLFRIAAGGMLGPD
+TPVRLRLLEIPAALRAAEGTAMELADAAFPLLADVEVTDDPAVAFDGVQHAMLVGARPRT
+KGMERGDLLEANGGIFGPQGRAINDHAADDVRVVVVGNPANTNALIAAAHAPDVPAERFT
+ALTRLDHNRAVAQLAARAGVAVTDVDGVTIWGNHSATQFPDLTHARVRVAGAWRPALEVV
+DPAWAAEEFVPRVAKRGAEIIEVRGASSAASAASAAVDHMRDWTLGTGAGAGGAGTDAGP
+RWTSAAVVSDGSYGVPEGLVSSFPVTSDGGAAWRIVPGLAPDESLLPGTGGRLAATVAEL
+EAERDAVHGLGLL
+>3_284
+MTQDTLRTPATVTVTGAAGNIGYALLFRIASGQLLGPDTPVRLRLLEIPAAVRAAEGVAM
+ELADSAFPLLASVDVTDSADAAFDGTTHALLVGARPRTAGMERADLLRANGGIFGPQGAA
+INASADASVRVVVVGNPANTNALIASAHAPDVPAERFTALTRLDHNRAVSQLAARAGVGV
+ADVDGITIWGNHSATQFPDLTHARVRMSGDDGAPVWRPALEVVDPAWAAEEYIPRVAKRG
+AEIIEVRGASSQGSAASAAIDHMRDWSLGTGVDADGAPRRTSAAVVSDGSYGVPEGLISS
+FPVTSDGSGAWTIVPGLEPDESLLPGDGGRLAATVAELEAERDAVRALGLI
+>4_35
+MRRAGVSSAGERGHDGGVDTAQQTTAQDTAPDPASTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VQAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a56bc6b3753f4e9233597e989016368c49a013f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000203.fa
@@ -0,0 +1,30 @@
+>0_41
+MPALSLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIVALRDARDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVVVDTATDDVLIAHPMRVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLMARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPADVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>1_2005
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
+>2_340
+MPALPLPPRRPRLIATDLDGTIIGYRHTRSGYLSPRTVAALQEAHETGVEVVFVTGRPLR
+WLGALSEQLGQVGPVICSNGAVVVDTATDEVLLHHSMDRDAVWDAVGRLRALDRSATFGA
+ETLDGFFWESAFSEWGELEEGFRTAQRLEGVLPAHVDVVKLMARSSTMDPDVFLAAAREE
+LGALLNATHSAPGVSLVEMAAPGVHKAATLAEFAARRGVDARDVVAFGDMPNDTEMLAWA
+GLGLAVASGHESLLAVADAVVGECDDDGVAQAIELLLELPAE
+>3_283
+MSALPASARRPRLIATDLDGTVIGYAHTRTGRISPRTVAALRRAHAEGIVVVFVTGRPLR
+WLGPLRAQLGEVGPVICSNGAVVADTATDEVLLHHALDRAAIDHVVRRIRALDPAATFGA
+EALEGFFWEDAFASDELGQTRAASLEAALPGDATVVKLMAKSGGIEPDVFLAAVRELGDG
+LVTATHSAPGMSLVEMSAPGVHKAATLAAFARGTGVEAADVVAFGDMPNDAEMLAWAGLG
+LAVASAHASLRAVADGVVGACDDDGVAAAIEALLALPEA
+>4_36
+MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR
+WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA
+ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE
+LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA
+GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1366cc62625ec6bd86ef82937bcd78997f95456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000209.fa
@@ -0,0 +1,20 @@
+>0_52
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>1_2016
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLTAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
+>2_324
+MVSTDMDTTTQTPDERTLLRAAGLRVTRPRVAVLTALGECPHADAATVLAAVRRELPAVS
+HQAVYDSLHTLTDVGLVRSIQPAGSTARYEIRRNDNHHHLVCRDCGTVVDVPCHTGQAPC
+LEARTDHGFLIDEAEVYYWGLCPSCRADPGAAAS
+>3_265
+MSTVTVEQPEESALLRSVGLRVTRPRVAVLQGLRRHPHADAGSLLSAVREDLPQVSHQAV
+YDCLHVLTDAGLVRSLQPAGSPARYELAAHDNHHHLVCRGCGDLVDVPCQTGVAPCLHAP
+EDHGFLIEEAEVYYWGLCPDCRSGGYTTTSDGTPAPAPPAP
+>4_47
+METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY
+DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE
+GHGFAVDEAEVYYWGLCAGCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40c6bcce58555360b19d30ed965c66c9a723f1c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000215.fa
@@ -0,0 +1,45 @@
+>0_61
+MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA
+GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL
+LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
+>1_2025
+MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG
+MERFELV
+>2_315
+MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR
+ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ
+RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS
+GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR
+LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF
+NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV
+PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV
+AILENHQNADGSVTVPVALRPYLGGMERFELV
+>3_258
+MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV
+VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM
+GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR
+LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA
+RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL
+RPYLGGLERFELV
+>4_55
+MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA
+QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV
+LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL
+GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA
+DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL
+LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR
+RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG
+MERFELV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32610df2f4bfac493479d005c5d00d255e0b9847
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000216.fa
@@ -0,0 +1,30 @@
+>0_62
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
+>1_2026
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGID
+AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGLGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPTAA
+>2_314
+MEKKLVCLDVDGTIVDHDGHLHEPVREAVKAVVAAGHHVVIATGRSRGATLPVAQSLGIE
+AGYMVCSNGGVTLRLDPALEDGYEVTDCRTFDPRSVLSQLRSRLPGAKYAVEVPDGSFLS
+TERFQDMSFGVAAEGTTFEELKNTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLHVAPEHTVAVGDGRNDLEMLAWAGRGVAMGQAVREVK
+EAADEVTASVDDHGLADVLWSLVPEADRPEGVRVQEPAAA
+>3_254
+MTKKLVCLDVDGTIVDHDGRLHEPVREAVRAVIEAGHHVVIATGRSRGATLPVAESLGID
+SGYVICSNGGATLRLDRALEDGYEVTDLRTFDPQSVLAQLRDRLPSAKYALELPDGSFLS
+TERFQDMSFGVAAEGVGFEELMATTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASALEALRTVLHVDVADTVAVGDGRNDVEMLRWAGRGVAMGQAPDEVK
+EAADEVTGGVDEHGLATVLRTLL
+>4_56
+MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRAATLPVARSLGIG
+AGFMVCSNGGVTLRLDPELEEGYEITDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS
+TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT
+AWLDVAAAGVTKASGLEALRTVLKMAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV
+AAADEVTGHVDEHGLATVLRSLLEEPAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf2627e989616189fb498842e899387038e1542d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000220.fa
@@ -0,0 +1,40 @@
+>0_67
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARRVALAAAAREAGQGGAAPGAGTAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWA
+GDEFTRLRVDPPGRDPRVVSLDLDTLAALPAAVRHRVIARAARAAGGQAPPRERILAVDT
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>1_2031
+MPRPEARDPGPTPAGGAGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGSCRADAGPG
+RAGNRPRGLVALSGGADSLALAVACAVLVGTRDGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARREALAAAARDAGQGRAAVVLTAHTAD
+DQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAGLTWFED
+PHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWAGAEVTR
+LRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAVDALVTGAR
+AGCTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>2_306
+MPSGSAAPPALESWPPRGRWPEPLHRAVAALRPVLAAHDGGALIGLSGGADSCALAVAAA
+ALRGTRAGAALGPVGAVVVDHGLQAGSADVAEAAARVARTLGLEPVLVRRVAVREAGDGP
+EAAARRARRGAFADAAREAGAGLVLTAHTADDQAEQVLLGLARGSGTRSLAGIPAGGALP
+GGTALARPLLGLTRADAEAICRWAGVRWWEDPHNADPALLRSRVRTRVLPALEDLADGLG
+PGVREGLVRTAAIAAEDAAALEQWAACALAECRVRGEAGPGPGAEPGDDPGAGTGRSEAP
+GRGDVVVRLDLAAFAALPPAVRHRVLGLAVVEAGGPRPTRERTLAVDALAVPADPGAGGP
+RGPWSCPAGWK
+>3_249
+MSSPFVRDVVAVPGAPTLPALAGPWPPRSRWPEPLHRAVESVRAVRAEHPGPVLVALSGG
+ADSLALAVACAVLAGTRAGERLGPAGAVVVDHGLQDGSAAVAAAAARTARALGLAPVTVE
+AVTVTPAGDGPEASARSARRTALARAAEGVGEGTPALVLTAHTADDQAEQVLLGLARGSG
+TRSLAGIPAHGALPGGVALARPLLGLSRADTEAICRWAGLTWFTDPHNADPALLRSRVRT
+RILPALEDPDTGLGPGLRAALVRTAAIAAEDAAALDAWADDALARLRLPAPETDRPAPVL
+LDLDALAALPAAVRHRVHARAARAAGAGTPSRERILAADALVAAAHAGGGSAGPVELGHG
+VTVRRVAAGEGGVGGRKEGGPSGCARLAYIPRPADR
+>4_61
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGRRFGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLAPVTVTRVEVARTGDGPEADARRARRKALAAAAREAGQGDAVPGAGAAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVVRPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDVGLGPGVRAGLVRTAAIAAEDAAALDAWA
+GDEVARLRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAADA
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09303073403f217161e4deb89404488df8dc6872
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000226.fa
@@ -0,0 +1,20 @@
+>0_75
+MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL
+QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH
+>1_2039
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
+>2_299
+MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR
+RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL
+QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD
+>3_241
+MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR
+RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL
+LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD
+>4_69
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000233.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cadd0ed877ab9f9164fb3b220c828d17e0f251ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000233.fa
@@ -0,0 +1,20 @@
+>0_84
+MSTAHEPFRDATPHSGAHTPPPTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>1_2048
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
+>2_288
+MSTPYEPIRDATPHAGAHTPPPTQAEFRAEHESLGEMFKSLSSRLSTLVSQEIALAKAEA
+TESAKKAGTGAGLLAGAAVGGFFLLMFLSLALMWALGSAMHLGWAALIVAVLWGVCAAVL
+ALMGKKHLEKIKGLPQTQETLQEIPETLNPAKETR
+>3_234
+MSHATPNGGAPRHADPAAHQSTPAAGAHTPPPTQAEFRAEHESLGEMFSSATEKVSLLMR
+QEIALAKAEATDSAKKAGKGAGMFAGAAVGGFFLLMFLSLALMYALGSLMPLGWAALIVA
+VLWGVVAAVLALQGKKNIEKIKGLPQTQETLQEIPETLNPAKETR
+>4_79
+MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA
+TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL
+AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d929b8155d493dfa978b724ac289132861b4632
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000237.fa
@@ -0,0 +1,20 @@
+>0_88
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV
+SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG
+>1_2052
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTDVTDPELLEKNLFPMVSEEQMEKSLAKLAAEVG
+>2_284
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTAVTDPELLEKNLFPMVSEEQMEESLAKLASAVA
+>3_230
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV
+SLTYDWTDVTDPELLAKNLFPMVSEEQMEESLAKLASEVG
+>4_83
+MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD
+VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV
+SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72cf94579601aee60479a1cb1885837a01b31463
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000246.fa
@@ -0,0 +1,20 @@
+>0_98
+MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE
+EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGTGVGHLIIEELLDRARAVGVERVFCLT
+FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL
+>1_2062
+MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE
+EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLIIEELLDRARAVGVERVFCLT
+FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL
+>2_273
+MPADRQITLRSARTGDVPAIRALVEPLAQERVLLQKEAVAFYEAIQEFVVAEDADGSLAG
+FGALHVMWQDIAEVRTLAVSRDHRGAGVGHLILEELLRRARVVGVERVFCLTFEVEFFRR
+HGFAVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRTL
+>3_220
+MPAAPVVTVRPARTQDVPAIRALVSPLAERRLLLQKEAVAFYESIQEFMVAEAEDGSLAG
+FGALHVMWQDIAEVRTLAVADAWLGAGVGHRILTALLERAREVGVARVFCLTFEVEFFRR
+HGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRSL
+>4_93
+MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE
+EPDGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLVIEELLDRARAVGVERVFCLT
+FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4af337316f6789f1b64ddc31c8eb851bf41dab9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000250.fa
@@ -0,0 +1,40 @@
+>0_103
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>1_2067
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>2_268
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG
+>3_210
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG
+>4_98
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecb83a89d7054a71600ba7df65bbd0cf4ab8939c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000257.fa
@@ -0,0 +1,29 @@
+>0_110
+MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
+>1_2074
+MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
+>2_258
+MPTPPTTSIETLRSGHPVVWSRPAAERPGTDLVLVLHGYGSNEVRAANRFFPMLPERCTG
+LAVRGGFEIDAAATEGPGDPGAHGWFLLDLMLQSDFAQVVAAAHRVFDVLASEEVAQARF
+RTVSVLGFSQGMAMATTLIRLRPEAFACGVGLSGFVVDNELLAVLDSPPEGPGPRPFFWG
+RDVEDPVIHPDAVAHTRAWAEEHTLLTVRTYPGVLHGIGPEAVRDVRIFLDHSLRAATPD
+T
+>3_191
+MSTGSAPESEPLASGGHAVWSRPEHERAGTDLVLVLHGYGSNEVRAARRFFPMLPERCTG
+LALRGPFEIDAAAVEGPDDPGAHGWFLLDVLLQSDFAQVIAAAHRVYDALADDAVADAGF
+RSVSVLGFSQGMAMATTVIRLRPEAFACGVGLSGFAVDNELLAVLDSPAEGPGPRPFFWG
+RDAQDPVIRPDAVAHTAAWAEEHTLLTARTYPGILHGTGPEEARDVRIFLEHVLGGA
+>4_115
+MSPTPTPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPDRCTG
+LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF
+RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG
+RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77ec683c7fb2cdd71cc42777d9b95ba1005f67d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000270.fa
@@ -0,0 +1,30 @@
+>0_129
+MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS
+QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL
+YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF
+QREGYTHVSPPERAAFRAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL
+CSPALARTVTDAWIDREERKGKGASDHAPVVVELG
+>1_2094
+MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS
+QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL
+YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF
+QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL
+CSPALARTVTDAWIDREERKGKGASDHAPVVVELG
+>2_237
+MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVAHHGTS
+QWNGVAIASRVGLSDVQRGFPGQPHFGKGGIDPQEESRAIGATVGTEAGDGVAPVRLWSL
+YVPNGRALDNEHMPYKLEWLRVLREHVAQRLAEEPQTRLALTGDWNIAPQDEDVWDIEMF
+VREGYTHVSPPERAAFHAFEETGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL
+CSPALAETVTDAWIDREERKGKGASDHAPVVVELG
+>3_171
+MKIATWNVNSLRARADRVEAFLDRQDVDVLAIQETKCRDENFPWELFERAGYEVAHNGTS
+QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL
+YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF
+QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL
+CSPALARTVTDAWIDREERKGKGASDHAPVIVELG
+>4_137
+MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS
+QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL
+YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALAGDWNIAPQDEDVWDIELF
+QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL
+CSPALARTVTDAWIDREERKGKGASDHAPVVVELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90342c4f92adfcf4855e148ccd06fb73cadc57ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000273.fa
@@ -0,0 +1,25 @@
+>0_132
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>1_2097
+MGGMTDAQTPTVPTPEQDRERLKQLIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIEFDAVGGLTMGADPVATAMMHQAGTVGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
+>2_234
+MGGMTDAQTPTVPTPEQDRERLKELIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGVQFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRDVVVLEDTSTTGGSALTAVEGVRRAGGRVQAVAVIVDRATGAAERVAE
+EADVPYLYAFGKDELGLD
+>3_168
+MTAEHTSVAPTPEQDRERLRELIKELAVVHGRVTLSSGAEADYYVDLRRVTLHHEAAPLI
+GRVMLRLLEENGIEFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGMGRQ
+VEGPGVEGRRVVVLEDTSTTGGSALTAVEGVRKAGGDVQAVAVIVDRATGAAERVAEEAG
+VPYLYAFGKDELDLD
+>4_140
+MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA
+PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM
+GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE
+EAGVPYLYAFGKDELGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4132f06c7ffa9d7eec8cfde981c53e32ef3522c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000277.fa
@@ -0,0 +1,30 @@
+>0_136
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>1_2101
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>2_230
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS
+>3_164
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG
+>4_144
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8629f5acc7da442e9c7028448dc317cdfea8e4d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000280.fa
@@ -0,0 +1,45 @@
+>0_140
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>1_2105
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>2_225
+MTTQPHHSTPASAEQLQHDWDHNPRWAGIERTYSPDDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGDFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYHERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
+>3_802
+MTEQTVQQIAQEIQKDWDTNDRWTHIERTHTAEDVAKLRGRVQEEHTLARRGSEKLWEQL
+TSEHAKGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYPANS
+VPAVVRRINNALLRADQIEWSEGIKTVEDYLVPIVADAEAGFGGPLNAYELMKGMIASGA
+SGVHWEDQLASEKKCGHLGGKVLIPTGQHVRTLNAARLAADVAGVPSVIIARTDAEAATL
+ITSDVDERDAEFITGERTAEGFYKVKNGVEPCIARAKAYAPYSDLIWMETGTPDLELARK
+FAEAVKSEFPDQMLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYTFQFITLAGFHALNH
+SMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAISTAVNPESSTV
+ALKESTEAGQFH
+>4_148
+MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW
+TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP
+ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT
+AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA
+ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL
+ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA
+LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS
+STVALAGSTESGQFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4791ff829948e15389b0d4206429ae199fa14994
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000281.fa
@@ -0,0 +1,55 @@
+>0_141
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA
+>1_2106
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
+>2_224
+MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT
+DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS
+WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY
+DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL
+YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT
+AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT
+EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL
+VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV
+ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE
+EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA
+>3_801
+MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR
+RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW
+LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL
+HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV
+RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER
+GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK
+VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI
+KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS
+TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA
+YERFLSAEARRRAGHGA
+>4_149
+MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT
+DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP
+GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID
+FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE
+LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI
+LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH
+RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF
+DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG
+AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG
+PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30cf27885bbb76e87977c869ec71992a3a6fce15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000288.fa
@@ -0,0 +1,45 @@
+>0_171
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD
+>1_2118
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYELFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIQD
+>2_212
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNATPVIGNGVVVNLEALFEEIDGLESRGHSCAHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEVAEYFLGYAERLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIESIPVCVAYDVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGAREFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIDG
+>3_158
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPLIGNGVVINLEALFEEIDGLEARGHSCANLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATFLDVDHGTYPFVTSS
+NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRMTGGEFGVNT
+GRPRRTGWYDAVLAHYAARVNGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPIFEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDEV
+VQVRGLIED
+>4_168
+MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL
+SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL
+GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV
+TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS
+NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT
+GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ
+TEFHHAKPVYEHFDGWAEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV
+VQVRDLIED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8383c72c821c6d228a61d806d6218683be42716d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000294.fa
@@ -0,0 +1,45 @@
+>0_177
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>1_2124
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT
+>2_206
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>3_151
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS
+>4_174
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..193c82e59e2dbbd6781a1f85b32954ba741ff43f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000302.fa
@@ -0,0 +1,30 @@
+>0_189
+MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH
+RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW
+TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA
+GRWLVRGFVVVVIVGLPLALWLGAFAAR
+>1_2136
+MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH
+RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW
+TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
+>2_192
+MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR
+WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV
+NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR
+WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR
+AGRLLVYGFVAVFMVALPLATWIGAYLAR
+>3_140
+MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW
+GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN
+RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW
+TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT
+GRLLVYGFVALFVIGLPAALWIGAFLNR
+>4_189
+MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH
+RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW
+TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e625ed09c02697c4dc00113f1f041a20e0dd394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000303.fa
@@ -0,0 +1,70 @@
+>0_194
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST
+>1_2140
+MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR
+LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL
+NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV
+VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA
+VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE
+HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT
+AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG
+IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS
+PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY
+FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH
+PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA
+KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD
+AGPGAVRSASSAST
+>2_180
+MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP
+DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP
+ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE
+DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT
+TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET
+KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE
+DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP
+TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV
+DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS
+PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS
+TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE
+ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG
+QIAQVLADRPGR
+>3_134
+MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+TIGDTTSLQNEWCIPQIAEVVAARR
+>4_196
+MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA
+ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER
+PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR
+AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF
+SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI
+PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW
+THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH
+FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW
+ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP
+TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV
+WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL
+AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT
+ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f248d35b9d16c724d8bbae90c482388c602cc98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000305.fa
@@ -0,0 +1,30 @@
+>0_196
+MSAALTTPAATTGPEARERSGHDDGDTGARRRQRPRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>1_2142
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
+>2_188
+MTVLDRPGGRTAVGLIVPALLLLLWWALTAAGVFSGVQLPPPAWVAEAAVDLAARGTLWH
+HIAISVQRVLVGFLIGGALGLLVGSVLGLSRWADALLAPTIGALRAVPSLAWVPLLILWM
+QIGEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAYGYHGVRLLGTVQLPAVVPA
+MFSGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKISDW
+LLGFVERWAVRRWA
+>3_130
+MSTALTTPAATTGPEARERSGHDDGGTGARRRQRSRVLDRPGARAVVGLAAPAVLLVLWW
+AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA
+LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA
+LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM
+GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA
+>4_198
+MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV
+GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI
+GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF
+SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL
+GLLERRALRRWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c438d146096cdc7c1dd36320c4a7cbff58da8ca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000308.fa
@@ -0,0 +1,19 @@
+>0_202
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>1_2146
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD
+EGPLTR
+>2_171
+MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK
+NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD
+EGPQTR
+>3_117
+MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK
+DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA
+>4_202
+MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK
+KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD
+EGPLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c39d9a3b84c9b3e37978832a9d89acdae231652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000312.fa
@@ -0,0 +1,17 @@
+>0_206
+MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR
+>1_2150
+MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR
+>2_159
+MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ
+GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT
+RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA
+>3_110
+MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG
+AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA
+AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA
+>4_206
+MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0581c2e89f8cfe026d2111a02010df0c624d7291
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000315.fa
@@ -0,0 +1,34 @@
+>0_212
+MPEPHTAPAPSETLPPAVVALPADVWRAHARAHRERIARRTDPLVALRMRGQKHPVQDFL
+FGYYTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGATPRGEWKHYRRVEAGEVAGAV
+VDGRPVGGWLVDVAAVLADRASGVAFTRELLARTAERAPRLGCFGLHEWAMAYRSDVHGV
+RHSQLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMRKMEQ
+PGCLHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDLTGVDDLSDGRGG
+YAAVRIEEPAGRAEYARRQREFAARGQSLRVRLLAVLDAAAGAAPGARPDTEWTSSARP
+>1_2176
+MPEPRTDPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAGGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDP
+>2_150
+MAGTCLHTPPPSPAAPRTAPTDPTAVVVLRPEEWLARSAAHRERIEARTAPLLELHGRGE
+RHPVQDFLFGYYTHSPAALARWHPGAGVVLADPDGAAAAAEAERDGAPHRGGWRHLRATE
+PGEIPGAEPDGRPTVGWTVDADAFAADRATGIAFTAELLERTAARPARLGCFGLHEWAMA
+YRSDLHGVRHSRLPLRLGAEGTDAVVESQRIRCTHFDAFRFFAPEARGLNEGADGVLPTR
+AGMRDMEQPGCLHAGMDLYKWAYKLLPWVSSDLVADCFDLAWDIRALDMRASPYDLRGVT
+DLAGGDYPPVRIETPEGRAEYVRAQRGFADRGQALRARLLAALAPLLGDDARG
+>3_108
+MTSAAPSPVPLVLAPEDWRARARAHRERIAARTAPLMARRTRGEPHPVQDFLFGYYTLTP
+GALQRWHPGAGVVLADDDGAAATAEAAELGTAPRGEWRHWRRVEPGEVVGVVLDGREVGG
+WTVDVPAFLADRASGVAFTRELLERTAGRPARLGCFGLHEWAMAYRSDVHGVRHSQLPLR
+LGAAGTDAVVEDQRIRCTHFDAFRFFAPEAVPLNEGAEGVQPTRAGMRDMEQPGCLHAGM
+DLYKWAHKLLPLVDSDLVADCFDLAWDIRRLDMEASPYDLTGVDDLSDGLGGYTPVRIET
+PEGRAEYARRQRGFAERGQALRARLLAALEAGARAAGDRRPTEDPSTPDPEEHHG
+>4_213
+MPEPRTAPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY
+YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG
+RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS
+QLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC
+LHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEAAPYDLTGVDDLSDGRGGYAA
+VRIEEPAGRAEYARRQREFAERGQALRARLLAVLDAAVGAAPGTGPDAEWTSSSARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0878dad1a61f562faca60130f652d7a56d6b858a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000318.fa
@@ -0,0 +1,25 @@
+>0_217
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>1_2181
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>2_145
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF
+NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>3_103
+MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF
+NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
+>4_218
+MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF
+NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ
+LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE
+YADEVTLGRAFEGRRLISG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..699e670a65efaca36b1608ce5de130021d38771b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000319.fa
@@ -0,0 +1,107 @@
+>0_218
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA
+RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD
+ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA
+SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG
+DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR
+PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA
+WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA
+EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP
+VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG
+FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA
+TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG
+GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA
+AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL
+EERPNDA
+>1_2182
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN
+AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER
+PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE
+ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF
+QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD
+RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP
+RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE
+EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP
+APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR
+AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS
+DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG
+GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS
+ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV
+GRAVVERVLGGRLLEERPNDA
+>2_144
+MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV
+SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL
+PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG
+SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP
+PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP
+EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS
+SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR
+QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA
+PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ
+AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD
+SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG
+RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP
+VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA
+TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA
+GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP
+RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA
+REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE
+ERANSA
+>3_102
+MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC
+LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR
+YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP
+PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV
+SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL
+PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA
+RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA
+LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP
+SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV
+AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS
+EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS
+AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD
+EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE
+AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE
+TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG
+PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD
+PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR
+EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA
+GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE
+PGL
+>4_219
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77a118cf5ade264df3fb80981eae4a45963c6905
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000321.fa
@@ -0,0 +1,50 @@
+>0_221
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAAG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD
+AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVVLRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
+>1_2185
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD
+AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFLTRNLRNGMVRRVVLRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
+>2_142
+MTFEDLIGTLNDVIWSLPLIYLCLAVGLYFTVRTMFLQFVNIPDMIRQLREGEDSKDGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWAMALLGAATSFIESTLGQIYKER
+DRDTGEYRGGPAYYFTKAYSHKPWGKALVVYGVLFAIVTIFATSYFLPGVQANGVAAAVE
+QAWNVEPWIVAVAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIVLALIILVLNADQIP
+VVFGSIFSSAFGMDAVFGAIVGLAIQWGVRRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYEGESEAGAVIFEGGSLPATASVGPAYVQSG
+FDAMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFITRNFSNPLFRRVALRALQGLI
+LVSVAYGAVATTGAAWGLGDIGVGSMAWLNIIGILLLQGPALKALKDFRAQKRQGLDPQF
+DPRPLGIHNATFWEERADGRITPGVAGTAPTPVVDADGGSPRA
+>3_99
+MSFADLVTEINDVIWSPALIWLCLIVGLYFTVRTMFLQFVNIPDMVKQLREGEDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYRHTAAGGAFKVYAILFAIVTVFATSYFLPGVQANGVAAAME
+QAWSLPPWVAAVGMVILLAFIVLGGVKRIATFAVYVVPIMAIAYIILALVVLFMNWEQIP
+EVFGTIFSSAFGTHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVFEGESETGRVLFEGGTLPVTASVGPAFVQSG
+FDAVFAGFGPTFVAIALAFFAFTTIVAYYYMAEVNLVYLTRTLRNGTVRRVALRLLQALI
+LVSVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKKQGLDPQF
+DPRPLGIKNADFWEHRADGLITQGVGGLSTDVRADTADGAGSHRA
+>4_222
+MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS
+SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER
+DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG
+EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIILALIVLFLNFDQIP
+EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF
+VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDGSGSGLLFEGIVSPTASEGPAFVQTGFD
+AMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVALRFLQALILV
+SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP
+RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07b8339cf35471794dc06c9d7faae4aed73d8434
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000322.fa
@@ -0,0 +1,55 @@
+>0_222
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE
+NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
+>1_2186
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE
+NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
+>2_141
+MANVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRTHGGIEWVHTRHEEAAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAALEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHAMRGKDRIEYD
+NPYDVGLTGLLGFSSGYHALKDAETLLILGSSLPYRQFYPEDATVIQVDVRGDQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNASSSFLKKARRHYAKTRKDLDELAAPDRRTVHPQYVA
+RVLDEAASEDAVFLPDVGSPVVWAARYLTMNGRRRIIGSMTHGSMANAVTQAIGAQAVDR
+TRQVVAMAGDGGLAMMLGELLTFVQNGLPVKTLVFDNDSLNFVELEMKAAGLVPYATDLQ
+NPDFAAVAEAMGLKGFRVERSKDLPAVMAEFLAHEGPALLVVKTERQELTIPPSIEFEQA
+KGFALYALRTVLDGKGTQLVDLAKANLRQLF
+>3_98
+MATVAKHIVETLSASGVRRMYGVPGDSLNALTEALRQHTDMEWVHTRHEEAAAFAASAES
+QLTGELAVCAGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQELF
+RECSVFVEHVSDVSQMPQLLRIAMRAAVEQRGVAVLVIPGDVALQDLDAKPEVIRATRSH
+VVPDEDSLREAAEALNSCKRITILAGSGAAGAHDEVVALADRLQAPVVHALRGKDHIEYD
+NPFDVGLTGLLGFASGYHAMKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVS
+VDIPLVGGVRETAQALMPLLKGNSSSAFLKKALKHYDKSRKGLDSLATPSRGTIHPQYVA
+RLLDEAADDDAVFIPDVGSPVIWASRYLTMNGRRRIIGSMVHGSMANGITQALGAQAIDR
+SRQVVVMAGDGGLAMMLGELLSFVQNRLPVKTVVFDNDSLNFVELEMKAAGFVPFGTGLQ
+NPDFAQVAEAIGIKGFRVDRAKDLPDVMREFLAHDGPALLLVKTEPQELTIPPSIELEQA
+KGFALYALRTVLDGKGTQLIDLAKANLRQLF
+>4_223
+MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES
+QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF
+RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR
+VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD
+NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA
+VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA
+RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP
+TRQVVAMAGDGGLAMMLGELMSFVQNDLPVKTLVFDNDSLNFVELEMMAAGFVPYGTDLQ
+NPDFAAIAEAAGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA
+KGFALYAMRTVLDGKGTKLLDLAKANLRQLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8bb03680f9735ca2d4ec03f7d08cf7d115d2518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000323.fa
@@ -0,0 +1,30 @@
+>0_223
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDRTKLAMVSLEKTVGADQTEYERVRDDVAAGVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>1_2187
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAARVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>2_138
+MSTPSPIGLLLDVDGPVASTQTRTVPDGIVATLVRLAGRGVPVGFNTGRSADFLLHSVIG
+PLRAAGLPADAPFFAVCEKGAVWFPFSAVPAGTLPEVTVDAPAPAWVRTDPAMALDPGLR
+ERIWELNRERAGDLQFVDRTKLAMVSLEMRVGADQAAYEAVRDDVAAGVEEMLAERGLAD
+EVRVDPTVISVDVEHRSSGKDLGVDRCRALMAEAGVPVPGRWFTAGDSRTDYAMADRLHA
+IGLAVEHLDVRPADGIPATPYPVLTAADLAGRGVGNAEDVHERAGESLLRWVERDLLD
+>3_96
+MTSPSPIGLLLDVDGPVASTETRAVPEGIVTTLVRLAAARVPVGFNTGRSADFLLHSVIG
+PLRAAGLPEDAPFFAICEKGAVWFPFSDVPAGDLPAVTVDAPTPGWVRTDPAMAVDADVR
+DAIWEINGERAGDLQFVDRTKLLMVSLEKTVGADQDAYVQVRDDVAAGIEDLLRERGLAE
+DVRVDPTVISIDVEHRTSGKDLGVDRCLGMLAEVGVAVPERWFTAGDSRTDYAMADALHA
+MGAPVEHMDVRPADGIPERPYRVLTAADLAERGVGQAEDVHERAGESLLRWVERDLLA
+>4_224
+MRTPSPIGLLLDVDGPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHSVIA
+PLRDAGLPDDAPFHAVCEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAAGVEGLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLTVEHMDVRPADGVPEKPYGVVTAAILAERGIGDAEDVHERAGESLLRWVERDLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d2d842ea56a0c0747722dd1bf188aecd2754c8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000324.fa
@@ -0,0 +1,35 @@
+>0_224
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>1_2188
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
+>2_129
+MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT
+PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV
+SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL
+GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA
+WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD
+GGDDPVDGRR
+>3_94
+MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT
+SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI
+VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW
+VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG
+LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG
+GDPVDGVR
+>4_225
+MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT
+PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV
+SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL
+GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA
+WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD
+GGGDPIDGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f656cb3f2a90a3791453cd9409d898fbc5610392
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000327.fa
@@ -0,0 +1,35 @@
+>0_228
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLSDRLWEGTDLADWGRRLGLPHEPADAHGTLAELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRVGKVNLMAPT
+WWQLRTLVDAGEDVHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL
+>1_2192
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGETSVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLADWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPHGQSPERMSSEAASHGWASPAELLRRFRAGEVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLMAFRAAAQVEESK
+DNIL
+>2_125
+MSPAAPSADPADGDRPDVPAVPASSLMLVRPEQDGDTSVFALRRAGSMAFSAHATAFPGG
+RVDPADDLPDALWEGTDLAAWGRRLGLPHEPVDALGTLAALDPAEGAGRVLAAAVRETFE
+ETGVLLARDTATGAPVDPDRVAALPEDLRDAVERHEVDFGDLLRDEGLRPDAGALVPWSR
+WITPHGGPRRYDTFFFAVHLPAGQSPERMSSEAAEHGWASPAELLRRFRAGEVNLMAPTW
+WQLRTLDDAGEDVHAGRSRFEPLEGVMLVAGQGPAFSHADEYLRDLAAFRAAAHVEESKD
+NIL
+>3_90
+MDAAQTSSSETLPVEATPARAAASLLLLRDGAAGLEVFHVHRAGTMAFSAHATAFPGGRV
+DPSDDALPVPGADLAAWARRLGLEDRPVETQPEDDPARVAARFLAAVVRETFEETGVLLA
+RAADGGPVPPEAAAALAGRREDVEAHAADLGALLAEHGLAADVSGLRAWQRWITPLSVPR
+RYDTAFFLVAVPAGQDPDRLTTEATEHGWARPADLITAFQAGDVNLMAPQWAQLRALMDL
+PDVEAALRAGAAAEPVPVVQLASEASPEERTREFSHAAEYREHLRSFRTHDRVQDTPDNV
+L
+>4_229
+MSPAAPPAEPSAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLAEWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRAGKVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8ab6094110e82446a224fbc9c4d4191adc9012e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000331.fa
@@ -0,0 +1,35 @@
+>0_232
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS
+>1_2196
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS
+>2_119
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR
+>3_86
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG
+>4_233
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2846e44dab57266ee6c15703f722d5d169e84fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000332.fa
@@ -0,0 +1,40 @@
+>0_235
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG
+>1_2198
+MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG
+>2_116
+MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA
+ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY
+VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL
+AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA
+AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS
+AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL
+VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS
+>3_85
+MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR
+AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG
+FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF
+ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA
+PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL
+EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT
+VEEVSDEAVAAHFGPGEDAPLRLR
+>4_235
+MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW
+AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP
+YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH
+LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD
+EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE
+AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK
+DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0825689eda218f056d31c882803fd4bb725e23b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000338.fa
@@ -0,0 +1,40 @@
+>0_247
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>1_2212
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>2_104
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV
+TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV
+PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK
+YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA
+ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG
+KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>3_72
+MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV
+SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV
+PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK
+YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE
+AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG
+KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA
+EGTSVQVDLRGRGEPFTVVPLPFYTRAR
+>4_246
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..206754eca3ba8da14efb06b70109cbd068bc6202
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000339.fa
@@ -0,0 +1,30 @@
+>0_248
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>1_2213
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
+>2_103
+MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG
+GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM
+ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY
+QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA
+YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG
+>3_71
+MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD
+GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE
+QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD
+ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG
+DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG
+>4_247
+MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG
+GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM
+ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY
+QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA
+YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2eb4dd0c882003128ff75f05fec20dba6636aa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000342.fa
@@ -0,0 +1,30 @@
+>0_254
+MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA
+>1_2218
+MPQTGHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA
+>2_91
+MSQTAPASQNHDAVPALALAIAGSEATGGAGAQADLKTFQELGVFGIIALTCIVSFDPKD
+DWNHRFFPVPTEVLEHQLEAVQQDYPELLRTVKLGMQGSPEVIRTSAAALRRQEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVHSVDDLVAAARRI
+HEVSGAAVLAKGGMHLPGPDAVDVFVDADTVEVLSAPKIGEAGVSGAGCSLAAAVTAELA
+KGATPLEAARRAKEFVRSGIEQAVAGRTPFAALWQGGLRGA
+>3_62
+MTTTTTTPRSVAPALALAIAGSEATGGAGAQADLKTFQELGVFGILSLTCIVSFDPADDW
+NHRFFPVPQDVQAAQLEAILADYPDELRAVKLGMQGSPETIRTTAEALRGHAWDHVVLDP
+VLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMAVRTVEDLTAAARRIHE
+ISGAAVLAKGGMHIEGLDAVDVFVDADHEEVLATPKIGDSGVSGAGCSLAAAVTAELAKG
+AEPVEAARRAKAFVTAGIAQAVEGRTPFAALWQGGLRETPEAGR
+>4_252
+MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED
+DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL
+DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI
+HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA
+KGATTLEAARRAKEFVGAGIAQAVEGRTPFAALWQGGLRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc91b387e15c25dc338708b49ec250326cc42232
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000343.fa
@@ -0,0 +1,22 @@
+>0_255
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>1_2219
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA
+>2_90
+MLEFLTGTGLATSAGLNAYIPMLALGLLDRFTGLVDLPAGWTWLSADASLWILGVLLLLE
+VVADKFPGVDAVNDAVQTVVRPAAGGIVFASGVGTETTAVHDPGTLFGGSGWVSVLIGAG
+IALAVHLAKAGTRVGANTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLVVAVVVG
+LWLLARRFRARRTRGRAAAAAGGSEWTA
+>3_61
+MLALGLLDRFTPLVDLPPAWAWLSSDVALWVVGILLVLEVVADKIPAVDAVNDVVQTVVR
+PAAGGITFASGVGAQTVTVQRPDTLLDSQVWVPTLIGAAMALLVHLTKAGTRAAANTVTM
+GTAAPLLSTAEDASAVVLTAAALFLPVLVLVVLLAVLVGLWAVPRRFRAGRRGGRRATMA
+S
+>4_253
+MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLAADASLWILGVLLALE
+LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV
+VAVVVGLWLLARRFRDRRTRGRAAAVPGGPEWTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae316f451d462d645b42a0be4a7475eaa1b13381
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000345.fa
@@ -0,0 +1,25 @@
+>0_257
+MSAEQNSTQTPGHRTAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEALADGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHQASEHGVHAAFARQPEALQ
+ILTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>1_2221
+MSAEQNSIQTPGYRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPEALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>2_88
+MSTEQNSTQTPAYRAAHVPAGQDLGHRWSTRVADHEDPADRRAIRQIAELTFESSAEADL
+VEELAGGGEGWLPQYSLVAMTASIPGTDLQSDPMGYGTLVRAHVGEAEVLALAPHGVLPE
+HQGEGAGTAIVNALLQKAQGDGEKVVVVYGWPEYYAKFGFRPGVEHGVTAAFADQPEALQ
+VLTLQDDAEVPSGEFRYPPAFGAENAQVAGRA
+>3_59
+MSTEKGSTATPTYRAAHVPEGQDLGHRWSTRLAHHDDPADRRAVRQIAELTFESSAEADL
+VEELVASGEGWLPQYSLMAMTASIPGTDLYSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLEKAQKDGEQAVVVYGWPEYYAKFGFRPAAEHGVTAAFATQPEALQ
+VIALQEGAEIPSGEFRYPPAFGAENAQVAGR
+>4_255
+MSAEQNSTQTPGHRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAQVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPDALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac5bf255b719a9f58d573685d1d4dbd418abbe99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000346.fa
@@ -0,0 +1,25 @@
+>0_258
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>1_2222
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
+>2_87
+MARMSTPAEDTLTALIHLLDREGYDAVTADQLAREAGMSRASFFRNLGGKEEVVFADHAT
+LLAHLEELLRGTGLGVREALDEAVLQVFRHHTRDPERAQARARLLRGSQALRTRELLTSH
+RYEELFSAWLADALPDTPARGGVAVGLAAAVVAVHNRALRAWLHSPDDDAEAGLRADLAE
+VVARLTAEPSAAERTLEAVRRLLG
+>3_58
+MNPMTAVPEDTLTALIHLLDRQGYDDVTVDQLAREAGMSRASFFRHVGGKEEVVFADHEQ
+LLPRLEDLLHSTSLPLPTALREAGLQVFRHHVQHPERARARARLLRGSRALRTRELLASH
+RYEQLFSRWLAERLPDTPTRGSVAVGLAAAVVAVHNAALRGWLHAEAPDPTAAEAALGAQ
+LDEVILRLTREPGEAEVRLAAVRALLD
+>4_256
+MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA
+LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH
+RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE
+VIARLTAEPAEAERTLAAVRRLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b170be6f44c7fd654c56dac9edadfe0ecc1f179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000351.fa
@@ -0,0 +1,31 @@
+>0_268
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR
+>1_2234
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
+>2_67
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS
+>3_52
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA
+>4_267
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4067aed820e193ecfc99b1f7065d090cd1b2be32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000355.fa
@@ -0,0 +1,35 @@
+>0_274
+MAVPSPLPPRNGVNATRLRLPTSGWPTAQDYVLHRFGHVDPEGIRARFARGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLPD
+APDDGARGPGAPTDPILGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRRS
+NRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDP
+FYPDLLDLAPDDVARPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
+>1_2240
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVVLLP
+EAPDDGARGPGAPADPVLGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
+>2_61
+MAVPSPSPARNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFAAGEVVAADGTA
+LTPTTPLGVHDDLWYYRDVPHEDPLPVAHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGVDDLVPLHRLDRATAGVVMFSVDPATRGAYHLLFERRAVAKTYEAVSALPP
+DADDDGLVLGRFPLTVRSRIRKDKGVLRSVVEEVPAAASGRRAGAPVRTRRSNAAHAGAN
+AESRVEVLGVGESAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFYPDLLDA
+APDDFSRPLQLLSRSLRFTDPLTGREREFVSPAQLQERPR
+>3_47
+MAAPSPLPPRNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFARGEVVARDGSP
+LTPTTPLGVHEDLWYYRDVPHEAPLPFQHTLIHRDERLVVIHKPHFLPTTPGGRFVQETA
+LVRLRNELGIDDLVPLHRLDRATAGVVMFSADPATRGAYHLLFERRAVTKRYEAISALPP
+ARDHADDDAAAWLDRFPLVMRSRIRKDKGVLRSLTEEIPAAASGRAAGARVRTRKSNLSH
+AGANAETRIEVLDVGRSAGTLAGAPVVRFRLSPRTGRTHQLRLHLAALGLGIAFDPFYPD
+LLDAAPDDLARPLQLLSRSIAFTDPVTGEHREFVSPAELQERPA
+>4_273
+MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA
+PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET
+ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLP
+DAPDDGARRPGAPADPVLGRFPLTVRSRIRKDKGILRSVVEEIPPAASGRRAGAPVRTRR
+SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD
+PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..435b7cc2be7cf841697789dd6d2e882331b46166
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000366.fa
@@ -0,0 +1,50 @@
+>0_289
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>1_6
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG
+EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>2_47
+MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS
+PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA
+GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP
+LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH
+NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG
+EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR
+DAVLAIVRAER
+>3_25
+MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ
+TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN
+PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY
+LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA
+NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA
+KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY
+YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL
+ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG
+EAKDRATMETVRDAVLAIVRAPR
+>4_296
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..062558e9673924e6745869169f772ca8b8cee83c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000372.fa
@@ -0,0 +1,72 @@
+>0_296
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR
+>1_20
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
+>2_23
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR
+>3_19
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR
+>4_303
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5020a2c899f4d9a2a07eb9df14bb544a47d082f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000378.fa
@@ -0,0 +1,30 @@
+>0_303
+MVEKARRLRARTTPGSVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGGEPVTAVEMAERLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRWAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRSGGWPVLGGPHQWRRGELSVRWAAVAPSS
+>1_27
+MVEKARRLRARTTPGPGPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGDLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS
+>2_16
+MVEKARRLSASTTPGRVRGPQGHITRGTTAAQRMRRVDRWLTDVHGALLRRTDRPLAVDL
+GFGAEPVTAVEMFTRLRAVNPALELTGLEIDPARVARARERAGGVPGLSWAVGGFELPVP
+RPPTVVRAFNVLRQYREEDVPAVWALLCAGLAEDGVLVEGTCSEDGRRATWVDLRRDGPA
+SLTLALRLGSFERPSDVAARLPKALIHRHVPGEPVHRFLAEADAAWAAHAPLAAYGTRQR
+WLASVAALREAGWPVLGGPRQWRRGEMSVRWEAVAPSS
+>3_12
+MVQKARRLTLPDGGRARPGARGGPQGHVTRGTTAPQRMRRVDRWVADVHGPLLRRTAAPL
+LVDLGYGAQPWTAVEMLTRLRAVQPSAELVGLEIEPERVAHARATAPALPGLSWERGGFE
+LATSRPPTVVRAFNVLRQYREEDVPAIWDLMASRMAPGGVVVEGTCSEDGRRAAWVDLRA
+DGPASLTLAMRLGAFERPSDVAERLPKALIHRHVPGEPVHRLLADADAAWALHAPLGAYG
+TRQRWIAMVRTLKDAGWPVLGRESRWRRGELTVRWDAVAPGVG
+>4_310
+MVEKARRLRARTTPGPVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV
+DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP
+VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG
+PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR
+QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cfa143ce949d8304f608a0b43fdb365c251fd27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000379.fa
@@ -0,0 +1,25 @@
+>0_305
+MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV
+FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>1_29
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
+>2_14
+MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV
+FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP
+>3_10
+MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD
+EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL
+FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT
+TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA
+>4_312
+MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD
+EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV
+ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT
+TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88682580c98ba95941728466dcd4260ef7f7215b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000382.fa
@@ -0,0 +1,25 @@
+>0_308
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>1_32
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
+>2_11
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA
+LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ
+DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG
+GEH
+>3_7
+MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL
+GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV
+WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ
+H
+>4_315
+MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA
+LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE
+GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG
+EEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93383ab86688147daf5eed9cbb6b4f40ba134d70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000388.fa
@@ -0,0 +1,69 @@
+>0_317
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES
+TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV
+LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP
+>1_42
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP
+>2_0
+MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA
+GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP
+AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE
+ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV
+HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS
+PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV
+FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE
+AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS
+QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY
+GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL
+WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT
+NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC
+>3_1
+MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG
+DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL
+GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT
+HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES
+EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF
+LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW
+ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA
+VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV
+SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD
+EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW
+AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG
+VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED
+GQWQGQPAYLTLNVPPLTTLWLQPDED
+>4_324
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80cb23f11503bc93023ef599e9b6168e5be5b863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000392.fa
@@ -0,0 +1,48 @@
+>0_321
+MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD
+RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL
+RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL
+ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL
+DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW
+DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA
+AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA
+LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF
+>1_46
+MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG
+RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
+>2_2614
+MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE
+HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT
+DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA
+RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL
+HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL
+RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV
+GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR
+AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF
+>3_2425
+MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA
+VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE
+RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ
+SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT
+AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH
+RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW
+EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT
+VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL
+DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF
+>4_328
+MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV
+ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR
+AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR
+WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA
+EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER
+SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG
+TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG
+LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG
+HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a9609580aacf8fdeff5458fa8cce1067d2e4a37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000393.fa
@@ -0,0 +1,30 @@
+>0_322
+MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE
+PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPTG
+>1_47
+MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ
+RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE
+PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE
+PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL
+LADAPIG
+>2_2570
+MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR
+HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL
+LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT
+VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA
+LLGAGPRG
+>3_2424
+MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS
+PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN
+TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ
+PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA
+RELA
+>4_329
+MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR
+HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP
+VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP
+ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL
+ADAPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d57661426a013d39c638625a5231f46bd33f129
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000396.fa
@@ -0,0 +1,20 @@
+>0_325
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>1_50
+MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
+>2_2567
+MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL
+QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP
+DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA
+>3_2418
+MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL
+QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD
+GTREEDQYMAVEQDGEPVYGAELVESPPIGG
+>4_332
+MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL
+QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP
+DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc591ac97f2937ea58c44c59411cb043c05e056c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000398.fa
@@ -0,0 +1,45 @@
+>0_328
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>1_53
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>2_2564
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED
+>3_2416
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG
+>4_335
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99af681c3cebd7f560f99a5886a77149f2584b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000401.fa
@@ -0,0 +1,59 @@
+>0_331
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>1_56
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR
+>2_2553
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>3_2412
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR
+>4_338
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dedeb01f2b789ad8df6de7b35cca9aa07a209d64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000405.fa
@@ -0,0 +1,35 @@
+>0_336
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYAGDPTAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVCDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
+>1_61
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWTEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
+>2_2548
+MTVLIDPPAWPAHGTVFAHLVSDASLEELHAFARAAGLPERAFDRDHYDVPAHRCEELVA
+RGAVPVSGRELVRRLVASGLRVPARGRAEKRDAVLARRWAALFEGTGARAEAVDAAGRDL
+RERWAQPHRHYHDRSHLLAVLEAVDLLERAGADPGPEPRAVRLAAWFHDAVYAGDPAAPA
+GQDEADSAALAARMLAAPALAVPAAVVGEVRRLVMLTASHDPAPQDAAGALLCDADLEVL
+GRSPEAYRRYVQAVRRDFAHVPDADWARGRAAVLESLLGAERLYRTAPGRARWEAAARRN
+LEAELADLRP
+>3_2407
+MAVLIDPPRWPAHGTVFSHLVSDASLEELHGFAAAHGLSPRAFDLDHYDVPAHRHAELVA
+AGALAVDGGELVRRLIRSGLRVPARRRDGRAEPVLRRRWARLFAGTDASPDAVTAAGAEL
+LGRWSEPHRRYHAPAHLLAVLQAVDLLSAAGEDLGPHPLAVPLAAWLHDAVYTADPARGP
+GADEEDSARLAERLLAAPGLALGDDVVAETARLVRLTAEHRPAPDDAAGAVLCDADLEVL
+GRAPHDYEAYVDLVRADFAHVPDEAWRTGRAAVLEGLLGADRLYATAAGRARWEDPARAN
+LERELAAHRPALS
+>4_343
+MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA
+RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL
+LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA
+GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL
+GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN
+LAAERAALSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0a3e7d9f08edf4a7f6b78e1813c882240042e64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000406.fa
@@ -0,0 +1,15 @@
+>0_337
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>1_62
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
+>2_2547
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVGAMEAHLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAAQQYQDAEAANAAMFRH
+>3_2406
+MTIVQIDVEDLRAKSGAVEGSIARLQTEVNTMEANLRQLEGTWRGQAAANFQGVLTEWRA
+TQARVEESLGGIRRAMDLAATQYSDTEAANAAMFRL
+>4_344
+MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA
+TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb64cbd34b5902d724e8edb45373e2eb1dbbf48e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000409.fa
@@ -0,0 +1,20 @@
+>0_341
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQASNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
+>1_66
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
+>2_2543
+MPRRTAAPAPDPADPRRAHGSPGRRRDAGDTDDEEQVPHMPTGRIKFYDSAKGFGFAQTD
+EGEEVHVPSSALPAGVTELRGGARVEFGVAEGRRGKQALSLRVLDAAPSSVRNHRPRPAE
+MAVLMEDLIRWLDETSNGLRRGQYPQSGQAKKMAQVLRRVADDLEA
+>3_2402
+MPTGRIKFYDSAKGFGFAQTDDGEEVHVPAAALPAGVSDLRSGTRVELGVAEGRRGKQAL
+TVEVLDDAPSVVRNHRPSPEKMAVLMEDLIKVLDQTSNGLRRGRYPQRAQAQKIAAVLRR
+VADDLEA
+>4_348
+MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL
+SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR
+VADDLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7f3eb1fac82aec77a5a602b868147403e8a2534
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000410.fa
@@ -0,0 +1,20 @@
+>0_342
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG
+>1_67
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG
+>2_2542
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG
+>3_2401
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG
+>4_349
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c00471a8fdcd1c826e3a2f2d641b2a0e5a35538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000411.fa
@@ -0,0 +1,40 @@
+>0_343
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV
+AALLRCIDHVVERLG
+>1_68
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
+>2_2541
+MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG
+ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV
+ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+SALLRCIDHVVEQLG
+>3_2400
+MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA
+GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE
+ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG
+GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD
+NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV
+ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV
+TALLACIDHVVARLG
+>4_350
+MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS
+GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA
+PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG
+GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE
+NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV
+ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV
+AALLRCIDHVVERLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59c9eff2f21c6e8f258652357c879939845a3747
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000415.fa
@@ -0,0 +1,79 @@
+>0_349
+MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>1_74
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
+>2_2536
+MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA
+GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH
+SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN
+ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD
+NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG
+ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI
+VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI
+GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF
+SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES
+EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE
+AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR
+LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF
+GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD
+RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED
+>3_2395
+MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL
+TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT
+FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR
+LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT
+ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG
+PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT
+ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP
+ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV
+RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD
+LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT
+LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV
+FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE
+LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL
+ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV
+AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG
+>4_356
+MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE
+SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN
+KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT
+TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL
+RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG
+DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD
+AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV
+AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI
+LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ
+VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD
+FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH
+ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID
+WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS
+GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR
+LLLRYAPLTKVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..017521f9919c5919c7dd518947ff3652bf800c6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000418.fa
@@ -0,0 +1,25 @@
+>0_352
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>2_981
+MIRVLVADDEALIRGAVEALLALEEDLDVLPGVGTGDDAVAAARALVPDVCLLDLEMPGL
+DGVEAAREILRSVPTRVVIFTRHARPGVLRRALAERVSGFVPKSTPAEALADVLRQVAAG
+RRYVDPEIAASALSGERSPLTDRELDVLRAGRTAARVEDIAERLHLAPGTVRNHLSHAMG
+KLGVRTRHEAAERAWEEGWI
+>2_2533
+MNDIRIVLADDEKLLRTALATLLEMEGGIRVEEVAADGNEAVEAVRRIDPDLLVTDMEMP
+GLDGVAAVETLRETHPDLPVVMLTRHARPGVLRRALKAGVAGFVTKSAEPEEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
+>3_1153
+MRESADPAPSPASPPAAGLGPGAPLRLLLADDQALVRGALAALLDTEPDLTVVAQAASGD
+EVADAVETHDVDVALLDIEMPGVDGLEALRRIRDRGLGCAVLMVTTFGRPGYLERALAAG
+ARGFVVKDTPAEQLADAVRAVARGERVVDPSLAVDTLAAGPSPLTPREVDVLREALTGAS
+VRAIAGRLHLSAGTVRNHLSAAIGKTATSTRGEAATVARDRGWL
+>4_359
+MNDIRIVLADDEKLLRTALATLLEIEGGIRVEEVAADGHEAVEAVRRIDPDMLVTDMEMP
+GLDGVAAVATLRETHPDLPVVMLTRHARPGVLRRALKAGVTGFVTKSAEPGEIADVIRRV
+NSGQRWIDPDTTARAISDDCPLTDRELDALRATGEGYSVARIAQQLHLAEGTVRNYLSSA
+MQKTQTSTRHDAARFARRHEWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000420.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5853a0828afd19a09ca8cdb48285ad5b8ed18465
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000420.fa
@@ -0,0 +1,33 @@
+>0_356
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
+>2_7
+MDGADVDGTADAVTEPALLHAEALECGYAGVPVTGRLDLVVRPGERVGVVGANAAGKSTV
+LRTLVGDQEPVAGRVRLEGLPVLPESAAHRRALSVLTDEDAYFPTLTVAEHLTLVALGHG
+VPEPDRVVDRELDFFALREAADAPPSRLSSGQRRRLLLAAALLRPFRLLALDEPEQRLDA
+GMRERLTARLAALEPASALVLVTHDPDVLAGAATRCLIVDGRVREAAVAEGAAWIRERT
+>2_2530
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEIMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGELTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
+>3_1156
+MSNAPALATRGLTRRFGPVRAVDGVDLTVPAGEVLALLGPNGAGKTTLLDMALGFSPPSD
+GTVRILGSDPVAAVRQGRVGAVLQTGGLLEDLSVRETVAMVAGCHRRHIGVSAALERAGL
+TGLAGRRVKKCSGGERQRLRFALALLTDPELLILDEPTAGMDVRARHDFWDTMHAEADRG
+RTIVFATHFLPEAEDFADRIVLMREGRIHADGTPAELATGGSVTLTGRWAGGGGDPDAPA
+RLAAALGLPRDAVQLEPQHLSPGRLRVRVPAGGRVTGDDVARHLLNERLVEDLAITHASL
+DDVFLSLTDAGQSAPSEPQESLA
+>4_362
+MQNTTLLPAPTAVDSRTETIVEIHDLRVDYGDFTAVDGIDLEIRRGEFFGLLGTNGAGKT
+TTIEVMEGHRAPTAGSVRVLGQDPSDRTLRRRVGIMLQESGFAPDLTVRETLALIGRLTR
+RDDDVDRVLDLVDLRRRRDTRTGQLSGGEKRRLDFATAIFGSPELIFLDEPTTGLDIEAR
+DALWHVVDRLRDEGATILLTTHYLEEAQERADRIALMHSGRIHRQGTVAELTSAFPSTIS
+FRLSGEPTVPFEDATIAPGGAVTIPTTNLQEDLYRLLVWSRSRDVELEGLNVGAEGLESL
+FRALNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..388e99392a1d8374d4548b9611f1625ff021996f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000425.fa
@@ -0,0 +1,50 @@
+>0_362
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASLFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIAATDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGAVAEDAATE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>1_86
+MTDTTVPLIILALYIVFVVGVGIYARRKATSDSSRDYLTGSGDVGVWVNGFAIFAAFATG
+GTMLGNIGLSYVGGWGYITAYNAGVALGYVITTFFLAKTLKNMNVATVPEFIRKRFHGRT
+LNILVPIILMATLVAYVVAQMKVGGLLGEQLFGFPYEWSVIVVGLVYIFYTFYGGMRAVT
+LTDFVQGLLMISVVVICGGIAFGQHGGPANLYEMAVAIRPKWEGTEQFPLISYIGAFIIW
+ATVNAVLPHTVMRIFAAKNERQGRASLAIGLGLYVLTAIATTIFVVAAVIIVQGEEELAS
+ADSTFLIFLAEQTPSWVAGLAFAGIFAAVMSSVSAMLLALGGAFAYDLVAELRPSMSDRS
+KRRLTSISVLGFGILTLVLSLNPPELLTLLYTAAMGMLASGLFFPTLLGIWWKRMNSSGA
+LAGLIVGVGSYLFLLWGTGMPSLSQVTVSIPLSLLACIVVSLMTKPPTDAEMERITIAHE
+REFLIQGQDDLIETAERH
+>1_95
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSALKERLGAEFFSWDGIGVQSIVTYFVIYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIVYGVAGAVIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPIFRGEATASEDGATAEDEIPE
+TAAELASNRGWVLLLGAVVLGLAIVVPNVVAALTIAYDILVGGLFVAIVGGLVWQRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDPAVRAQV
+>2_2516
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTIGLFALMLPLSLANAGGWSAMQERLGAEFFSWDGIGVQSIVTYFVIYTLGLLVGQ
+DVWQRVFTARSPRVAQVGGATAGLYCIVYGVAGALIGMAARTVTADIATTDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATAAEDGATAEDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTLGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTRPTDP
+AVLEAWRVRSRHGVDAAARERL
+>4_368
+MTLNLTIVAVYLVGMLAFGWWGKTRAASSEDYLVAGRRLGPVLFTGTMAAVVLGGAATVG
+GVGLGYEFGLSGAWLVAAIGVGVLILSVAFAPILARLKIYTVSQMLRLRYGRGGASHASS
+FVMLAYTLMLAATSTGAYASIFVVLFGWDRWLSVLVGGGIVLAYSVLGGMWSITLADMAQ
+FLIMTVGLFALMLPLSLANAGGWGAMQERLGAEFFSWDGIGVQSIVTYSVVYTLGLLIGQ
+DVWQRVFTARSPRVAQIGGATAGLYCIIYGVAGAVIGMAARTVTADIATQDDVFAWVAQN
+LLPVGVGGVALAAAVAAMMSTASGAIIAASTVMRTDILPILRGEATASEDGATAGDEAPE
+TAAELASNRGWVLLLGAVVLGLAIVVPDVVAALTIAYDILVGGLFVAIVGGLVWKRGTGT
+AALWSMVVGTVGTLGTMGWLELNAAEPFEGVFANEPIYVGLAASAVVYVLLSLMTPPTDP
+AVLEAWRVRSRHGVDAVAGASLTRNPGACDPPMPARWSGQTMRRRAILPQAPPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28a354776e4ebf25e2aa69aed01cb3bb70141752
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000426.fa
@@ -0,0 +1,25 @@
+>0_363
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>1_96
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
+>2_2515
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI
+VLWTLVGHA
+>3_1717
+MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV
+AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG
+GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA
+LVLWILAGRT
+>4_369
+MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV
+TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR
+GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV
+VLWTLVGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18bdf911ca93f7de4b17ff45276b9e4e2158e633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000429.fa
@@ -0,0 +1,34 @@
+>0_368
+MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA
+IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
+>1_101
+MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADEDGAYLTRGDGPERPLAEVARPAPAGGERAQNLVTSYPAGEA
+IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
+>2_2511
+MSATVPSPAALRRIALDAAGAVSADLAAAFRRPSAAGPGPEAKSTHHDLVTVHDRRTEAR
+LVAALTTAVPGSAVLGEELGGRDGAGEAARLTWIVDPIDGTSNFAHGFAMFSVSVAATVD
+GEVVAGVVLDPVSGLAFSADDHGAWLARPGEAERPLADVARPAPAGGERAQNLVTSYPAG
+EALALEGEDALRRFGRLVSAHATVRRTVSGALELAYTAAGWADAALYVDTKPWDVAAGQL
+ILRRAGGRWLTPDPAAPLSGRLVDDGPRAHTCPFALAVAPGREVPTTAAVLGDIVASRAA
+DHV
+>3_2382
+MVSSDSGPRSAAGSPLAPSPARLRAIGLEAARAVAPALAAAFRTPDAAAATKRNHHDLVT
+AHDRATEEALVATLTAAVPGSAVLGEETGVTAPPADAGVPRVRWIVDPIDGTSNFSHGFD
+LFSVSIAAEVDGEVVAGVVLAPAAGLEFSADDAGAWLGEAPLPLRAAPDGGERALNIVTS
+YPAAEALAREGEAALRRFAQLVDAHATVRRTVSGALELAFVAAGWADVTLAVDTHPWDVA
+AGQLLVARAGGTLVAADDAGPAPALVPHLAPHLLAVGPGRRAPTARAVLAGLVADRAAE
+>4_374
+MSPALPRPAELRAIALDAARAVAGDLATAFRSPTATGPEAKTTHHDLVTVHDRHTEARLV
+AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE
+VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA
+LAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL
+RRAGGSWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH
+V
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17d13bde6a5c4e0c91690ed376dbe21ebd06d855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000431.fa
@@ -0,0 +1,20 @@
+>0_371
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>1_104
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>2_2508
+MTGPRAVEVRIPLRWADMDAYGHINNIAVVQLLEEARVAAFGVPANTGAGGGEAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVEAVKAASVHVGYALHDGVDDTLCAT
+ASSVMVFVDGETGRPVRVTPEQRAALQG
+>3_2379
+MTETTTSSAARDGAGRWVEVSVPLRWADMDAYGHINNIAVVQLLEEARVAVFGVPANTGA
+GGGGAPPVDLLEGVPEGVRTFVSEHTVKYRAQMPYRPVPLRVRVGVAAVKAVSVEVAYEL
+YDGVDGTLCVTARSVMVFVDGASGRPVRLTAEQRAALAG
+>4_377
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e5ef496b6276289c09b23ee95d8993b48668649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000439.fa
@@ -0,0 +1,55 @@
+>0_380
+MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST
+GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV
+EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV
+VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL
+ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP
+AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF
+TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD
+PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA
+VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV
+RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG
+>1_113
+MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVTLYLTGARHFFHG
+>2_2500
+MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA
+VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL
+QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS
+VRDEEVVAAAEAAGVTLYLTGARHFFHG
+>3_2369
+MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV
+TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV
+ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR
+RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ
+PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA
+VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL
+EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE
+ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE
+VVDAANAAGITMYLTGARHFFHG
+>4_386
+MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV
+TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV
+DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR
+RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ
+PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA
+VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL
+EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE
+AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG
+QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE
+VVAAAEAAGVSLYLTGARHFFHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..376192350689d21d9ba5a7d622e7a2f9c820a4fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000441.fa
@@ -0,0 +1,25 @@
+>0_383
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>1_115
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKQALLAHEAAHAG
+>2_2496
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR
+LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTAAKRALLAHEAAHAG
+>3_2364
+MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE
+LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR
+QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG
+SYLYGSAAKAALLAHEAAHAPA
+>4_389
+MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR
+LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW
+RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY
+GTDAKQALLAHEAAHAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f30e55073ac0e9ebf485f0109ce0e3306219f85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000442.fa
@@ -0,0 +1,50 @@
+>0_384
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP
+VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>1_116
+MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR
+>2_2495
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF
+EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS
+RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES
+HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP
+VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR
+>3_2363
+MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG
+APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL
+SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF
+EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR
+VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS
+RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV
+VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS
+PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF
+GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR
+>4_390
+MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ
+APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL
+ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF
+EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR
+VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS
+RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF
+LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES
+HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP
+VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f18c5330c1a6fca5261a2a8f0d09a3eea7c8a6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000443.fa
@@ -0,0 +1,60 @@
+>0_385
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>1_117
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
+>2_2494
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>3_2362
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD
+>4_391
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb1808ddac444719a1412304cd5e03bf6c425286
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000451.fa
@@ -0,0 +1,45 @@
+>0_399
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>1_129
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
+>2_2483
+MTQTPDINTQPLSEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTALMDHGDTL
+MGLSLAHGGHLTHGMKINFSGKNYKIAAYEVEPDTYRIDMDKVREKALEAQPKVIVAGWS
+AYPRQLDFAAFRSIADEVGAKLWVDMAHFAGLVAAGLHPNPVPHADVVTSTVHKTLAGPR
+SGFILSTEEFKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLQGAQIL
+AERLTAPDMTELGISVLTGGTDVHLVLVDLRESQLDGKQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVAEIVAAALKPSPDVQALRARVVKLTEDFPLY
+DGLEGW
+>3_2352
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEQW
+>4_402
+MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA
+EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM
+MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS
+AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR
+SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL
+AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP
+RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY
+DGLEGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6896b77aee9eee715a688ad16e828bc1469563c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000452.fa
@@ -0,0 +1,35 @@
+>0_400
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVTPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>1_130
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDIQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVGLAGKHVLVIGRGVTIGRPAGL
+VFTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>2_2482
+MTAKVLDGKATAAALKEELRERVSALTERGHTPGLGTVLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEEILAVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRRHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTQNLDELLGQADVVIAAAGSAHMVRPEQVKDGVIVLDVGVSCV
+TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLSNVVEAAERAADAEDWAGER
+AEA
+>3_2351
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTLGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIRSIQKELPGDATEEQILDVVRELNEDPECTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER
+AGA
+>4_403
+MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV
+GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD
+GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL
+VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV
+TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAAEDDGRAGER
+AGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c83a27fe8c834ea9fae809bf39dd796e13dfcfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000453.fa
@@ -0,0 +1,35 @@
+>0_401
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD
+>1_131
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD
+>2_2480
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD
+>3_2350
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD
+>4_404
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e809ae1676a4caf379c50612d3771e14032adeeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000456.fa
@@ -0,0 +1,35 @@
+>0_405
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>1_135
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>2_2475
+MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV
+RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR
+LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR
+SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA
+PLVVDYRF
+>3_2345
+MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG
+RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR
+TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL
+PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT
+LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP
+LVVDYQF
+>4_408
+MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fccc4401d279c64280cd2d8912aacf0734eeb59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000462.fa
@@ -0,0 +1,30 @@
+>0_412
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF
+>1_142
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
+>2_2468
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF
+>3_2339
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF
+>4_415
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ec70d469e55f383e2144569172de1c63b89dd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000463.fa
@@ -0,0 +1,55 @@
+>0_413
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>1_143
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>2_2467
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP
+YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>3_2338
+MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP
+YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
+>4_416
+MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED
+NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT
+RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA
+YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL
+PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR
+SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT
+CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG
+IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE
+DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR
+GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bea21420b1a4a74012d2012624814e2b75eb1714
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000465.fa
@@ -0,0 +1,20 @@
+>0_415
+MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA
+VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL
+GFAIRHFSLALGGH
+>1_145
+MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA
+VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL
+GFAIRHFSLALGGH
+>2_2465
+MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTAMVRVSPEAYDA
+VIGAYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTKHHKTLLWIVLALWAVLTV
+GFAIRHFSLALGGY
+>3_2336
+MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTAMVRVSPEAYDA
+VIRSYKTWYFALGETALVAAILFHALNGLRIILVDFWKGGTKHHKTLLWVVLAVWAVLFL
+GFAVRHLSIAFGGH
+>4_418
+MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA
+VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL
+GFAIRHFSLALGGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc64dcb66ccab3d87815b3eb592fc8f7ab1ad698
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000466.fa
@@ -0,0 +1,40 @@
+>0_416
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>1_146
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>2_2464
+MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT
+TDHAQEVKKAVEALKAEGVDEVL
+>3_2335
+MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR
+DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL
+SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG
+LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT
+TEHAQDVKRTVESLKAQGADDVL
+>4_419
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26f95ef243174a5f5528435967a4e16d5cc8fee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000467.fa
@@ -0,0 +1,40 @@
+>0_417
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>1_147
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
+>2_2463
+MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG
+YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT
+AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG
+VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE
+VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA
+WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH
+>3_2334
+MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA
+EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH
+TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE
+GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI
+AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD
+EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF
+AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR
+>4_420
+MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG
+YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT
+AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD
+VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA
+VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE
+VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA
+WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7c22be2429259cd4008eefd99220c9835bc827e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000470.fa
@@ -0,0 +1,45 @@
+>0_420
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPATTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYVAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+ALTGAGGHAAAPSTGVQEAAAAAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>1_150
+MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTVLAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPPGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVHLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLVAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQAAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
+>2_2460
+MSQNPPQTPASEPVQPPGGAPVPAAGVTGADAPPAPERGSQESVLREILSGNAMVTALAI
+VLSLAISAVLIIVTSPDVIDAAGYFFARPMDTLSAAWTVVSDAYLALFRGSIVNYRADSF
+ADMIRPLTETLTVATPLIIASLGVAIAFRTGLFNIGGQGQFLIGAAFATVGGVYLDLPLG
+VHLLLVIVMGALGGLLWGAVVGLLKAYTGAHEVILTIMLNYVALHLVSYLLNTPFLRRAG
+TNNPISEQFPDSAAFPALLGDGFRLHWGFVMALVLTFLAWWMLERSTLGFRLRAVGANPA
+AARTAGISVKGGYVAAMAIAGALAGLGGVAHISGTEKVLTSGIAGQFGFDAITVALLGRS
+HPVGVLFAGLLFGALRAGGVTMQTQTGVPIDIVLVVQSFIVLLIAAPPLVRAIFRLPAPG
+SVRARANADVVTQPALAGAAVPGAAAEAVPAETGSATTSKGEGR
+>3_2331
+MSTAVASRPAGARTQEDGSALRRLASSNGAVTVLAVLLSLVISAVLIVVTDEDVQDAAGY
+LFARPQDALTAAWKAVSGAYAALFRGAVFNYEADTFTDMVRPLTETLTVATPLIIISLGV
+AVAFRAGLFNIGGQGQFIFGAMVATWTAVHLPLPFGLHLLVVLLAGVVGGVLWGAVVGVL
+KAWTGAHEVILTIMLNYVAVNVLAYLLNTPVLRRAGTTNPVSEFLPESGMFPKLLGDGYR
+LHWGFVLALLVTAFTWWLMSRSTLGFRLRAVGANPAAARTAGMSVKGTYVAAMAISGGLA
+GLAGMTHVSGTENALNTSVAGSYGFDAITVALLGRSNPVGVLFAGLLFGALRAGGVTMQT
+ETGVPIDIVLVVQSMIVLFIAAPPLVRGLFRLPAPGAARARRTADVVTQPAVAGAAVPGA
+AGLASVPSAQTQDAAATAVAADPADPVAGTGPHREKGQDL
+>4_423
+MSTAAPQRPAPESDPRARPAPADSALRRVLSGNGTVTALAILLSLLISGLLIIAVDEDVR
+DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII
+ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS
+VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL
+GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI
+SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG
+VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA
+AVTGAGGHAAAPSTGVQEAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..639ff3c5f2d6bb893dba36f6cdad5a95f23b0828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000473.fa
@@ -0,0 +1,45 @@
+>0_423
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERAKAALAGGW
+AVGELDDAAARTLRERSVILDRIG
+>1_153
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+TAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERARAALAGGW
+SVGELDDDAARALRERSVILDRIG
+>2_2457
+MTAQQQAEPFDAVEVIRAKRDRQTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEISRWTDAMIASGERMDFSGLTAPDGRVLPTADKHSTGGVGDKITLPLAPLVASYGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLTNEQMMRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTVALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAMLAGAGV
+TDVDPAQNLANGKAMDVWHRMIEAQGGDPRADLPTAAHTEDVVAEADGVLAELDAMAVGL
+AAWRLGAGRERQGQPVQAGAGVELHVRPGERVARGQKVMTLHTDTPERFARAKAALEGGW
+AVAEKGEAEAAALRDRSVILDRIG
+>3_2328
+MTTTSMPAQPAAPEAFDAIEVIRLKRDGHRLDPERIDWVVDAYTRGVVAPEQMSALAMAI
+LLNGMDREEIARWTAAMIASGERMDFSGLSAPDGRRLATADKHSTGGVGDKITLPLAPLV
+ASYGVAVPQLSGRGLGHTGGTLDKLESIPGWRADLTNDQMMRQLGEVGAVVCAAGAGLAP
+ADKKLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR
+TMVDLGRDAGVDTSALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM
+LAGAGVTDVDPAENLANGKAMDVWHRMIQAQGGDSHAELPAARHQETVTADADGVLTELD
+AMAVGLAAWRLGAGRERQGEPVQAGAGVELHARPGDAVRAGQPLMTLHTDTPERFDRARA
+ALAGGWAVTAADEAEAAALRSRSVILDRIG
+>4_426
+MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD
+RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA
+VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY
+ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG
+RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV
+TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL
+AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVAQGQKVLTLHTDTPERFERARAALAGGW
+AVGELDDVDARTLRERSVILDRIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ffc4000d80d5f0fad8431ec9691789ca103706d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000474.fa
@@ -0,0 +1,25 @@
+>0_424
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNFTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR
+>1_154
+MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR
+>2_2456
+MLEWIEETVLHAAAQWWMLPLTLALCLLDGIVPVFPSESVIVALAAIVRDGQPFSLWALW
+AVGFAGAFLGDILAYAIGRAVGVDRFRWMRTPRVRASVAVARHHLNGHGALLLFTGRFIP
+GGRVAINLTAGAIRYPLHRFVVLDLLSTAAWSAYSIMIARLTTGWLDNALLQIAVSVTGA
+ALVGVLLDRALKAVLRRRLGTGVKGLRQAEDEALR
+>3_2327
+MVQALEQAILAGASHPWALPLAALLCLLDGLVPVFPSESVLVALASIVEDGRPFPLAALW
+AAGFVGAFLGDVAAYGAGRGVGVTRFRWMRHGRVRRTIVMARRNLDSHGALLLFTARFIP
+GGRVAVNLAAGAMHYSPWRFVGLDLVSTALWSVYSIAIARLTVGWLDSTVLRMAVAVLGA
+ALVGLLLDRAVKALLRRRLARDGHRLGADEQAALR
+>4_427
+MLAWLEEAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW
+GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP
+GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA
+ALVGLLLDRLLKALLRRRLGSGVKGLTLAEQEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..257f96f97cd8c9317e1c788475774675e954c1d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000476.fa
@@ -0,0 +1,30 @@
+>0_426
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>1_156
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD
+PERALRTTVARVRAGDWSALRPSG
+>2_2454
+MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA
+PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL
+AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV
+RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG
+>3_2325
+MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR
+ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT
+PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH
+LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP
+ERALRGAIACVRAGDWDALRR
+>4_429
+MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA
+YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG
+LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL
+AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD
+PERALRATVARVRAGDWAALRPSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e500946a78f58b0365583cf5cd26307b717b76d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000478.fa
@@ -0,0 +1,51 @@
+>0_429
+MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>1_159
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP
+TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
+>2_2450
+MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP
+TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE
+RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS
+>3_2322
+MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV
+ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA
+YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV
+AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR
+PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV
+KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS
+ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA
+RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA
+AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG
+IALSLRG
+>4_432
+MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP
+TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT
+GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA
+WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP
+AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA
+SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG
+GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL
+PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE
+RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ef9d58b8b0908638e4368dca3a56838fd94c880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000481.fa
@@ -0,0 +1,35 @@
+>0_435
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVAGVDLTEPYGPDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGAHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWSDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
+>1_162
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVGGVDLTEPYGQDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTELDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
+>2_2435
+MSETSAAEAFGAPHATGTQHRLRRAGAEAVAVGLAGALRTYRVHGVDLTEPYGPESIPPA
+GNGIQMSPWPNRVAGARWELGGAEQGLDVTEPARGHAIHGLLRNTHFVAEASSEHAVTLR
+GEIHPQHGWPFRLTHRVTYELDADGGLTVTQELENHADAPAPVAFGAHPFLRIGDVPVPE
+LSLRVPADAWIRTGEDLIPVETLPVEGTDRDFRRGRPVGEDALDVCLTGLAPDADGRHRQ
+TLLAGDGRAVTLWSDHAFAYTHVFVTDRLPGRDVAVAVEPLTAPADALNSGEGLHRLAPR
+TRWSAQWGLTPHVPPHADEENRS
+>3_2319
+MTVPPAPDADAVFGAPRASGAQYRIARGGAEAVVAALAGALRTYRLDGVDLTEPYGPDMV
+PPAGNGIQMSPWPNRVAGGRWELDGAAQQLDVTEPSRGHASHGLLRNTHFTAESVAEDAV
+TLRGEIHPQHGWPFRLTHRVAYALDDAGALTVTMSLENHADAEAPVAFGAHPFLRIGDVP
+SAELTLQVPAREWIRTGEDLIPVETLPVDGGPQDFRSGRPVGAQGLDVGLTGLEADADGL
+HRARLLAPDGRSVTLWSDPAFTVTHVFVTDRLPGRDVAVAVEPLTAPADALNSGTGLHRL
+APGATLTARWGLVPDLAPAAPAAAPKEDAA
+>4_435
+MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLASALRRYRVGGVDLTEPYGQDVVPPA
+ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR
+GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE
+LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ
+TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH
+ARWSVQWGLTPHVPDHPHEEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..058ea09bdf9c6e59c68ea714c3e6b2d6e3e255b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000483.fa
@@ -0,0 +1,45 @@
+>0_437
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPDLSMGGVHITIDMETR
+GTEHSAQVLEALRAAGYSPAPLP
+>1_164
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPAELPVTLEEIERARATLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP
+>2_2433
+MTAGEVAQEQESVQTAADAAPVAGPRWVRPADAEPAWEGLPVSYEDVEAARETLRGVSEV
+SPLQLSRSLSRAVGTDVHLKCENLQRAGSFKIRGAYVRMAGLSEAERVRGVVAASAGNHA
+QGVALAAAKLGISARIYMPRGVALPKLQATKDHGAEVVLHGSTVDESLAEAQRWAAETGA
+VFIPPFDDPAIIAGQGTVGLEILDTLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTV
+RVIGVQAATAAAFPGSLEEGRVQVLESVSTIADGIAVGKPGNLPLQITAELVDAVVTVTD
+DEIAAALVHLLERAKLVVEPAGAVGVAALLAGRTADLGFELGSTVAVLSGGNIDPMLLLK
+SVQSGLSAAGRYMTVRIPLRDRPGELATISRIIADSDANVVRVDHTRVGPELSMGGVHIT
+IDMETRGPEHSAAVLEALREAGYSPVPIH
+>3_2317
+MTAGGAAPAPWLRPADAQEPTGDRLPVRLEDVEAARGVLEDVAEHTPVMLSRALTDQLGT
+PVHLKCENLQRAGSFKVRGAYVRMARLSAEERAAGVVAASAGNHAQGVALAAAKLGIHAR
+IVMPRGVALPKLQATQDHGAEVQLYGSTVDEALAEAQRYAAATGAVFIPPFDDPAIVAGQ
+GTVGLEIMDDLPRVDTVLVGIGGGGLIAGLAIAVKERARREGRTVRVVGVQAATAAAYPV
+SLREGRVQVLESVSTIADGIAVGRPGALPFDIVSGLVDAVVTVTDDEIAGAMVHLVERSK
+LVVEPAGAVGVAALLSGRARDLGFDLGTTAVVLSGGNIDPMLMLKSIQSGLSAAGRYMTV
+RIPLRDRPGELATISRVIAETEANVVRVDHTRVGPELSMGSVHITLDMETKGWDHCEAVL
+TALRESGYSPLRLT
+>4_437
+MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS
+RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA
+AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF
+DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ
+AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA
+LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL
+SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR
+GAEHSAQVLEALRAAGYSPAPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2eedab9f2c926bcaa84c67c09b1c482aaf13f1bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000489.fa
@@ -0,0 +1,30 @@
+>0_444
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT
+>1_171
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT
+>2_2427
+MQRPEAFYRLYERRLARGLDPERLPRHVGVLVDGNRRWARAFGATTQEGHQAGAERILEF
+IDWCDETGIPVVTLYMLSTENLGRPPEELEALLGIILATAERLAEPREGRRPVRVQTVGA
+VDMLPEEMARRLRAVEERTRDNDGVHVNVAVGYGGRQEILDAVRELLRDEHGRGRTAAEI
+ADAMTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGA
+>3_2310
+MRRPEVFYRLYERRLAGELDPERLPHHVGVLVDGNRRWARAFGATTQEGHQAGADRIIDF
+IGWCDEVGVPVVTLYMLSTENLARPAAELTPLLEIITTTTQRLAEPREDRAPVRVQPVGA
+VDLLPPRMAQQLRDVAERTRDNTGVHVNVAVGYGGRLEIVDAVRELLEEAAAEGRSAADV
+AAELTVDAISDRLYTRGQPDPDLVIRTSGEQRLSGFMTWQSAYSEFYFCEAMWPAFRRTD
+FLRALRDYGRRQRRFGS
+>4_444
+MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF
+IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA
+VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV
+AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD
+FLRALRDYGSRQRRFGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70c62d55f02c4c9bbec0b0a965bf8c28b6cf10eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000490.fa
@@ -0,0 +1,25 @@
+>0_445
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
+>1_172
+MSMHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQVVLIFLGRVII
+PGVGLIPRRLGGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLG
+SGLLTWVIGTPGVHIGASGIVYALIAFLIVYGIAVRRIGAVVVSVLVALTHLGSSLIGLL
+PAPGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
+>2_2426
+MSMHRPTPRLPERGAVPAARPAPSLAERVSGRLVAVIAPTLLLVAALWVVQIALVFFGRL
+VIPSLGLIPRSVTGLDGILFSPLLHAGWGHLIGNASALILLGPLAALISGRPLALLAAAW
+LGSGVLTWVIGSPGVHIGASGIVYALVAFLVVYGIAVRRVVPVVVSVLVALTHLGSSLIG
+LLPAPGVSWTGHLAGAVVGVLLGLWWGRGDRRPRHADI
+>3_2309
+MPLPDRRPADDAVPAPRPSLTQAAAQGLVRTVAPTAVLVAAMWVMFLVSIVGGSTLIGGL
+GLIPRRAAGLDGILFSPLLHGGWRHLVGNTTALLVLGPVAAAVSRRPLALLAAAWLGSGA
+LTWVIGTPGVHVGASGIVYALIAFLLVYGVVARRVLAVVVAVAVAAAHLGSSLLGLLPQP
+GVSWTGHLAGAVVGVGLALLWGRADRPARAPLGP
+>4_445
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0242ebfb8c7d757cda60274dc064423dc314813
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000494.fa
@@ -0,0 +1,25 @@
+>0_449
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>1_176
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
+>2_2422
+MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG
+QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV
+LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC
+DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV
+>3_2305
+MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA
+DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA
+TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR
+AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA
+>4_449
+MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ
+APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL
+GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD
+HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09e35dfa5904cad08181600a0de70943bc1526cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000496.fa
@@ -0,0 +1,35 @@
+>0_451
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>1_178
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>2_2420
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR
+>3_2303
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG
+>4_451
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000497.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2ecee0a198981e44f94994a446583966fcdbc6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000497.fa
@@ -0,0 +1,40 @@
+>0_452
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>1_179
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE
+RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
+>2_2419
+MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL
+TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH
+RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI
+SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP
+DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE
+ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV
+TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR
+>3_2302
+MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI
+AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR
+NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA
+AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD
+PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL
+RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV
+DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA
+>4_452
+MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV
+VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ
+RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI
+SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP
+DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP
+ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV
+TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45b8a1deeb2105d2ca541b58777450df5b8b4be2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000498.fa
@@ -0,0 +1,52 @@
+>0_453
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
+>1_180
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE
+TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP
+>2_2417
+MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA
+LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI
+RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN
+ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF
+SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL
+IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR
+RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL
+TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP
+LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST
+NGLCAPGR
+>3_2301
+MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR
+VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV
+HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL
+VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC
+GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD
+AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ
+QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI
+GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI
+PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ
+LVRIASTNDLCAPGG
+>4_453
+MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA
+LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI
+RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN
+ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF
+DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL
+IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR
+RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL
+TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE
+TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47e212bbd4a448e047bebd96aaa137f081da4561
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000500.fa
@@ -0,0 +1,25 @@
+>0_456
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
+>1_183
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLLGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLRPRGRHR
+TPDAGV
+>2_2415
+MLSDLWSRLTGLVSMLWREVAKFGTVGAAAFVIDSLVFWWMMTGPLEGSNVKAKIVAGVV
+ATLFSWVANRYWTFREKRSSNKTRELVMFLLMNAIGLGIQAGCVFIAQYLMGVTDPGGLF
+IAGNVVGLFFGTVFRYFAYRFWVFKEELDVEPGFANDIAIITGQMPVLRDEQLHPHGRHE
+ARGRPAERHVRRDDGPARHRAS
+>3_2298
+MPTDLWHRFTGLVSMLWREVAKFGTVGAAAFVVDSAVFWWLMHGPLEGSNVKAKICAGVV
+ATIFSWVANRYWTFRDKRQNNVVRELVMFLVMNAVGLGIQAGCVAIAQYGMGVTDPNGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEELDEEPGFENDIAVITGQLPVLHAHDEHVPGLQH
+RHPRHDVEDGSA
+>4_456
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af3f7f51f75a0ff7b5a1283cdc07545fd1b82c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000502.fa
@@ -0,0 +1,21 @@
+>0_458
+MEQTQRVEDAHHADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAAPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
+>1_185
+MEQTQRVEDTHRADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE
+TGTPAATVTALFPGDARPVEAVPVSQDWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF
+PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
+>2_2413
+MEHTQRVEDTHRAESAQAAAPRPRGVPSDWFLDPADPLAGADAATLEDQATALLSAHDLE
+DEAGTPSATVTALFPGDAGQPVEAAPVADDWAAIPGLVTEPVEGELAWQVDALCAQTDPE
+AFFPEKGGSTRDAKRVCEACVVKDQCLEYAMENDERFGIWGGLSERERRRLRRARA
+>3_2296
+MQNTQRVEDVARAERAPAASRSRGVPTDWFLDPADPTAGGRATAGLAAESLEDQATAFLA
+AHDLDDAGTPAATVTALVPRPAEAPAVDDALVPDAWQPVPGVVMEPAEGELAWQVDALCA
+QTDPEAFFPEKGGSTRDAKKVCAACDVRRECLDYAMANDERFGIWGGLSERERRRLRRER
+G
+>4_458
+MEQTQRVEDTHRADPAQAPAPRPRSVPSDWFLDPADPQADVSGVSLEDQATAFLTAHDLD
+GETGTPAATVTALFPGDARPVEAVPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEA
+FFPEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01e50d6855a2e84b779d64b6428d54c64f740b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000503.fa
@@ -0,0 +1,22 @@
+>0_459
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPTGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
+>1_186
+MARMTAPASSDPLDPLPFRAGDAAGAEPGVEGGPAKAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
+>2_2412
+MDRLAALEAPGLRHVTARVERIPDRLDERLRALRAGAERDEETLFARAERQGQDGVVITL
+FERPLRDAADPEDLDGAVYGVALSRCAEALGVDPQVLDPGWGRA
+>3_2295
+MARMPADPLAPLPPLPPARRDGRGPRPGLRRDVRGRGLRHPLPFGARAGRGRADALMDAV
+EKAVDRLAGLQAPGLRRVAARLERIPDRLDERLALQRARAVADEEGLFGRAERDGADGVV
+ITLFERPLTESADPADLEEAVYAVALSRCAAALGVDPQVLDPSWGRA
+>4_459
+MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPAGRGGRDRRGRGLRHPRP
+FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD
+EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS
+WGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c11d08ce86aca4ba22a0b77d536d49a5bc04edf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000507.fa
@@ -0,0 +1,55 @@
+>0_463
+MQNQSPVHESATELIGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPTTTSRTLLFLP
+LAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKAQ
+KSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGEV
+ISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVTV
+KIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVII
+TAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDAEAFTQWALDRELTLTPA
+EAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIED
+HAEDVEALYRR
+>1_191
+MQNQSPVHESATELVGMPPADSTITDLIVASCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL
+PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA
+QKGGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE
+VISCVSGASALSPDLVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT
+VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVI
+ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP
+AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE
+DHAEDVEALYRR
+>2_2408
+MPRVFEKVESGVATKAQKAGTGKVYQAARSTAITWSKALEEKKFGSGRGPSPALRARHAL
+FDRLVYRKIREALGGEVRTCVSGASALSEELVHFFRGAGVPIVEGYGLTESTAPATVNVP
+GAHRVGTVGLPVPGVTVKIAEDGEVLLRGPVMFSGYHGMPEASAESHAEDGFFRTGDIGS
+LDEHGYLRITGRKKDVIITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALVTLD
+EEELTRWSLDRERSLTPAEAAKDPAVLETIQEAVDRVNEDVSRAESIRRIRILDHAFTED
+SGYVTPSQKLKRAQVIEDYAEDVDALYRGR
+>3_2290
+MQHASPISESSTDLYGLPAEDTNITDLILSSCAEDPRASVYAVRNGAGAWLDVRFDAFLG
+QVRDVAKGLIAHGLQPGQRVALFAPTCYEWAVLDQAVWFAGAVSVPIYETSSAAQVAHIL
+GDSQTHAAAVGGDELAATTREAARQAGIDVTVFPMSEAALRVLARDGAAVTDEQLEAART
+TATLDDAASVVYTSGTTGRPKGAIITHRNFAAASINVLNFAAGVVDYHPGTNSRTLLFLP
+LAHVLAHAVQVICLYARIQMAHSGSTKTLQEDMASFHPTWLLAVPRVFEKLEAGIAAKAE
+DGGRGPVYHAAKRTAIEYSEALEAQTHEGGPGPSRALRARHAVFDTLVYGNVRKAFGGEV
+LSCVSGASALSPELVHLFRGMGIPIVEGYGLTETTAPATVNIPAAYKVGTVGLPVAGATI
+RIADDGEVLVKGPIVFAGYLRQPEATAESMDGDFFRTGDLGTLDEDGFLRITGRKKEVIV
+TAGGKNVYPTPLEEIIRQHRLVQHVVVVGDDRPYVGALIVLDPDELKRWSLDRERTLTLE
+EAVADEGVLAALQEAVDQANATVSRAESIRRIRVLDHELTEDSGHVTQSQKLKRAQVLAD
+YADEIEQLYRGR
+>4_463
+MQNQSPVHESATELVGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT
+QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV
+TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS
+LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL
+PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA
+QKSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE
+VISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT
+VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDGFFRTGDIGALDEHGFLRITGRKKDVI
+ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP
+AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE
+DHAEDVEALYRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c666c32d1872c92a9c49dacc3b6c4cca513e0603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000510.fa
@@ -0,0 +1,35 @@
+>0_468
+MAHASETPLAYRAPAQQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDIASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVA
+ALARAVSENTARVYGSF
+>1_198
+MAHASETPLAYRAPAPQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCTEHGWHMSFAGPV
+TFKANDELREALRTAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>2_2403
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEFPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAAEGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLVPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
+>3_2286
+MATTTSAQSASTQSASTEPGIPSAYRPPATPADLGDGPARDTREEKSGRKRRLEYPPAPE
+PLPVPVVDNHTHLDFRDGLVRVDVHQAMDAAEAVGVVGAVQVACDVESARFTVEAIEAES
+RLLGAVALHPNDAARLTARGEFEEAFAVIAELAEHPRVRAVGETGLDFFRTTDEAGHAAQ
+EESFRRHIRLARELGKALQIHDRDAHDDVVRVLLEEEADGGLPPHVVFHCFSGGPDLART
+CAERGWHASFAGPVTFKANDDLRDALRLLPRELVMVETDAPFLTPHPHRGRPNAPYLIPV
+TLRGMAEARGEEVAELAAAVAENTARVYGEF
+>4_467
+MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD
+FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA
+RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL
+GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV
+TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD
+ALARAVSENTARVYGSF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c88a75b3dac143278260c6650da3502d015c2c3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000512.fa
@@ -0,0 +1,34 @@
+>0_470
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEVSA
+>1_200
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
+>2_2401
+MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV
+QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE
+LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS
+GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP
+RTRGEALGIEAFARIAEHGPRRAAGEGSA
+>3_2284
+MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV
+LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT
+AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA
+VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA
+AS
+>4_469
+MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV
+LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS
+EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG
+PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA
+VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR
+AAEEVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9899c57597f9d59073076ea2d427a8ed8f82102
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000513.fa
@@ -0,0 +1,35 @@
+>0_471
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRHTLGLDPDSHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGVELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPPRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGLDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL
+>1_201
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL
+>2_2400
+MSEARAGLSGTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRVTVGPCPRQVSLVDSHDVPWDERNLAHRAAVHLRTALGLDEATHGVHLDVAKQVPVAG
+GMGGGSADAAAALLACSVLWETGHTRSELAELAAPLGADVPFAVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFGTLDELRRDGHVPEGAAHPEVNQEVVRALTAADPLA
+LATVMDNDLQTPAVALFPDLGDVLDLGLDEGALRGMVSGSGPTLLFVVPDEHSALSLATA
+VEERTGVRALPVHGPVAGAHVL
+>3_2283
+MSGLPGPSARHVTVRAPGKVNLSLRVGPPRPDGYHPVASVYLAVSLAETVTAVARPDGDA
+RITLAESTRQPSSVDTRDVPWDERNLAHRAALHLRQSLGLAPETHGVHLEVSKQVPVAGG
+MGGGSADAAAALLACSVLWDTGLTRSELAELAAPLGADVPFAVTGGAAVGRGTGSELTPV
+AARRPVHLVLVPADAGLSTPIVFRTLDELRSLGRAPEGQGEPAVDADVVRALAQADPLAL
+ALAMENDLQTPAVTLFPELSDVMDVGLDEGALRAMVSGSGPTLLLLAHSEQDAARLATAV
+QERTGVAALAVHGPVPGAHVL
+>4_470
+MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD
+GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG
+GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP
+VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE
+LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA
+IEERTGVRALPVHGPVPGAHVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a616170169e76fec0d9ce7811987ced059c29f8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000514.fa
@@ -0,0 +1,60 @@
+>0_472
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKPRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDEAGGPARGAGPVRGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAALGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLRAAELAEGD
+>1_202
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+PDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMADAGGPARGAGVARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
+>2_2399
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPTHTVRQAVVGDVEDHVWASDPKVRDVLGGLLDGLDLEQTV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKDRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWILARAERARQAAVVEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDSVSLAKTATARLGKDVLDLEHVGLSLGEKR
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLEPDSGRVKRGKTVVTATLTQDVKE
+LDEVAHLRVAEVMAREGSAFQVGDKEMSAGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDAAGASGGPARGAGAARGRNDVVGTCAGMGGPEEDTGP
+TEAERRLARKEMARLEKQMTRLRDSRSVLEARMAELGQAQDFDALTAASADLKDLDAQLD
+VLEEEWLQAAELTEGD
+>3_2282
+MAHLLGAENIGISFGTRTVLDGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVHVGVLDQRDVLDPQDTVRRAVVGDVEDHVWASDARIRDVLGGLLAGMDLEQRV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLAGHLNARWRPNDGGLVVVT
+HDRWFLDAVCTRTWEVHDAAVDPFDGGYAAWILARAERARQAQVTEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDTVSLAKTATARLGKDVIDLEDVTLTLGDRT
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLQPDSGRMKRGKTVVSATLTQDVKE
+LDEVADLRVAEVMAREGSAFQVGDREMSPGQLLEMLGFGPTRQWTAVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGRVRDLPGGVDQYLELRVLMDDAGGAAPAPGSSRGRGDAQGTCAGMVVDIPEVSEAER
+RQARKDMARLERQMQRLRESRGGIEARMAELGQAQKYDELGAATAELTAVDAELEDLEEQ
+WLEAAERDA
+>4_471
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKARDVLGGLLDGFDLDQPV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIQDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDDAGGPARGAGAARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42459c925ab3cac659651c050a09a3ce96a4b13c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000518.fa
@@ -0,0 +1,40 @@
+>0_480
+MPGAQGEDEAMSETTALRIRTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH
+RDADTARPWLQWHEDLVFLATSRTIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV
+GGAQRLVYAEAEDLRDVVDGLLAAPPTSVTPAWEALTEEELRASVGAAAPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVACLRAEGPVPEDAEARVRK
+AMDALVSAGLATAG
+>1_209
+MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH
+RDADTARPWLQWHEDLVFLATSRTIESARGTHLMFHAACLAAPDTGAAIVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALAALVPQTSSLSLLPRGLVTLCRVLDAV
+GGAQRLVYAEAEDLRGVVDGLLAAPPTPVTPAWEALTEEELSASVGVATPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDEPRTAADVVARLRAEGPVPEDAEARVRE
+AMDALVTAQLATTG
+>2_2394
+MPAAPPDPSAAPVREALRIGAGLDAVTVSGLTGAERDELLRSWARCGVETVELTEDADAH
+RGPEHPRSWLDWHENLVFLATSRAIESARGTHLMFHAACLAAPDTGAAIVLAAASGTGKT
+TATRRLGPHYAYLTDETAMVDPADLSVTPYPKPLSLLEPGGSRPKTQRGPDELGLGLTRA
+DAVLARIAVLDRVREAAAPVPARAEPMDVVTALQHLVPQTSSLSLLPRGLVALCTLLDAL
+GGVQRLVYAEADDLRPVIDGLLAAAPQPVDPAWEPLDAAELAASEGAAEPGAVRRAAAAD
+GILTADGRLVLLAGTTLTVLDGIGPAVWFALESPLTPERIVARLAEDGPVPADAAERVAE
+AVAALESAGLLVTTPQGAGPEADALRS
+>3_2277
+MTDPRRGGRAVRIPAGDGSTTAAGLDETGVRTLLDAWRRCGAEEVAAPAEGAAAYWEATG
+WDWFHENLVHSATTAAITAGVGRRLLFHGACLADPGTGSAVALVAASGTGKTTATRRLGP
+HYAYLTDETVIVAPDTLEVTPFPKPLSLLGPSGVRPKTQVSPDELGLGDAVPARLARLAV
+LDRVRDVDGPVTARAETMGLGDALIAVVPQTSSLARLPRGLRELCRVIDRLGGVQRLVYA
+EADGLRPVVDELLAAAPEPLEPAWEPLTPAELAASRETGDAAAGAARREAVDDGIVTDDG
+RLILLAGPQLAALEGLGPVVWLMLEEPLTNAQIVERLAAEGPVPDDAADRVADAVTALAE
+SGLVRI
+>4_479
+MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEVVQPPTHTDAH
+RGAHTASPWLQWHEDLVFLATSRAIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT
+TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP
+DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV
+GGAQRLVYAEAEDLRDVVDGLLAAPPTPVTPAWEALTEEELRASVGAAVPGAVSRCAVDD
+GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVARLRAEGPVPEDAEARVHE
+AMDALVTAELARTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5fa323302671ceb8874f824fa900d9a7c87c5d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000520.fa
@@ -0,0 +1,35 @@
+>0_482
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
+>1_211
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA
+>2_2392
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT
+>3_2275
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA
+>4_481
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b4be5f2536d454c4537be2544200dacd753c4eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000522.fa
@@ -0,0 +1,30 @@
+>0_484
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPIPDFDVTARKRRQDMTRTDLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGLLELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLRHRS
+DLGAPRTAETPTTGPNRTPGGAQ
+>1_213
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAGEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHAGDPDGEPIPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
+>2_2390
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEADLHVVVSTDSEEIAEVAR
+RYGADVPGLRPAELAQDETPTEPVVEHALAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VAQFRETGVDSLVGVVPVSPFLWRHAADPADPPVCDFDVAHRKRRQDMDRPDLRFRENGS
+LYVTRPWVYDELHNRLGGRIGMFELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLQRVP
+DRTQLHGTSTATLGDAL
+>3_2273
+MSILCVIPVRGGSRGLPGKNIRMLGGHPLVAWTIQAALDAEADLHVVVSTDSEEIAEVAR
+KYGADVPALRPAELARDDTPTEPVVEHALAAERARGVEPEAVMLLQATSPLRLPGTLDRA
+VAAFREPGVDSVVGVVPVSPFLWRHAADPAAAPVADYDVDGRKRRQDMDRADLRFRENGS
+LYVTAPWVYDERHNRLGGRIALLELDDLEGVDIDTELDFALAEQQMDQYLAVQKLLQTRP
+DLTRTAGGAL
+>4_483
+MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL
+RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA
+VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPTPDFDVTARKRRQDMTRADLRFRENGS
+LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP
+DLGAPRTAETPTTGPNRTLGGTQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9e78d874c580261c36fa8b2734a5a96c0a7fd4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000525.fa
@@ -0,0 +1,35 @@
+>0_489
+MTETPLAPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEAHVVVDGDVDGSEGMLAQLA
+AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHAGGS
+GGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRTLHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPIARKLIAL
+QVEAAAETGRTRPGRARRQF
+>1_218
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLGQLA
+AERPGLDLSWTVFPENRGRVGALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHSGEP
+GGAIGLYLNVLEPTPYQRAYGDTQDVLHREHAYALQADQQWRHWAGNVSVPRALHQQIGG
+YDPDYRQYGWEDIDYGYRLHAAGYPVVIRPELETRHHAAAVTTHSKAVRALHGTAARNLF
+VGKHGAAPLGTIGAPRGVWGAAVRLVAWGTTEATLTRSSALIDAVADHLPRGLARRLIAL
+QVEGAAEAGRAHPHRAQRSI
+>2_2386
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLAQLA
+AEYPGLDLSWTVFGENRGRVAALDAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ
+RGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRVLHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTSTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGLWGAAVRAVATLSTERTIQYSSAVIERAAAVLPAPIARKLIAL
+QVEAAAETGRTRPGRARRQF
+>3_2268
+MSDQTAYEASVIVPSRGGAGRLPRLIGALAAQEEAPPFDVHVVVDGDVDDSASALERLAA
+AHPDLPLTWTVFEENRGRVAALNAGADATTGRILIRADDDLEPGVHYIRDHVAAHAEGPG
+GAIGLYLNILESTPYQRVYGDAQDVLHREHAYALPADQQWRHWAGNVSVPRAVHEELGGY
+DPDYRQYGWEDIDFGYRLHAAGYPVRIRPELATSHHAAAVTTYSKAVRALHGTAARNLFI
+QKHGAEVLGGVDAPRGLWGAAVRLVALGATEGSLTRSSALIDAIADRVPITVARKLIALQ
+VEGASEAGRAYPERAQRPI
+>4_488
+MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEGMLAPLA
+AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ
+RGVIGLTANVLPDSAYQRVYGGAQDEAHRRHAYALPAEQQWRHWAGNVSVPRALHEELGG
+YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF
+IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPVARKLIAL
+QVEAAAETGRTRPGRARRQF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000527.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7481e31eff8781f57e22797cf41e3393d58206bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000527.fa
@@ -0,0 +1,31 @@
+>0_493
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGIRDILVITTPQDAEQ
+FQRLLGDGSQFGVSLTYVQQPSPDGLAQAFVLGEEHIGVDHVALVLGDNIFYGPGMGQQL
+RRHTDVEGATVFGYWVKDPTAYGVVEFDTNGKAVSLEEKPAQPKSNFAVPGLYFYDNDVV
+EIAKDLKPSPRGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFTDLNDASNFIHAVE
+SRQGLKVGSPEEAAWRQGLLTDDQLRERAERLVKSGYGRYLLDLLDSGR
+>1_222
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAQQ
+FQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDEHVALVLGDNIFYGPGMGQQL
+RRHAQVDGATVFGYWVVDPSAYGVVEFDDAGKAISLEEKPEEPKSNYAVPGLYFYDNDVV
+EIAKSLKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLELLESGR
+>2_2382
+MKGIILAGGTGSRLHPITHAISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAGQ
+FQRLLGDGSRFGISLTYVQQPSPDGLAQAFLLGEEHIGDDHVALVLGDNIFYGPGMGQQL
+RRHTEVHGATVFGYRVADPTAYGVVEFDGTGRAVSLEEKPTAPKSHYAVPGLYFYDNDVV
+EIARALKPSARGELEITDVNRTYLERGTLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGAPEEVAWRQGLLTDDELRERAEPLVKSGYGRYLLDLLENAR
+>3_2263
+MKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILAGISDILVITTPHDAEQ
+FQRLLGDGSQFGVSLSYVQQPSPDGLAQAFILGEEHIGDDRVALVLGDNIFYGPGMGQQL
+RRHTEVEGATVFGYWVADPTAYGVVEFDGAGKAVSLEEKPKEPKSNYAVPGLYFYDNDVV
+QIAKDLKPSPRGELEITDANRVYLERGMLNVEVLPRGTAWLDTGTFHDLNDASNFIRTIE
+SRQGLKVGSPEEVAWRQGLLTDDELRQRAEPLVKSGYGRYLLGLLDRADPIGRSSR
+>4_492
+MNPDRTALNLHHRIGPMKGIILAGGTGSRLHPITHGISKQLVPVYDKPMIYYPLSTLILA
+GISDILVITTPHDAEQFQRLLGDGSQFGISLSYVQQPSPDGLAQAFILGEDHIGDDHVAL
+VLGDNIFYGPGMGQQLRRHSEVDGATVFGYWVADPTAYGVVEFDGDGKAVSLEEKPAQPK
+SNYAVPGLYFYDNDVVEIAKELKPSARGELEITDVNRTYLERGALNVEVLPRGTAWLDTG
+TFKDLNDASNFIRTIESRQGLKVGSPEEVAWRQGLLTDNELRERAEPLVKSGYGRYLLDL
+LETGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9753915a1eb55e55213691fb672934a2476c0916
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000529.fa
@@ -0,0 +1,25 @@
+>0_503
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPVHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGTEYV
+LDYATVPVEADATDLPEVVTISIEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVNEVV
+EQDLGDESVQEEQAAESAED
+>1_233
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGNDYV
+LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVSEVV
+EQDLGDESVQEEQAAESAEGESEGSED
+>2_2372
+MSDKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPIHLLLPAQETTLAVRNPNALLT
+VVNEAGEEHLVLPKDIQRHALKDTVEHLDLIEVRRGEKVVVDVTVHVEGEVAKGNDYVLD
+HVTVPLEAEATHLPESVTISVEGREAGEHVYATDVQVPAGTTLQLEDEIVIATVSEVVEQ
+DLGDESVQEEQAAEGEAAEGESAEGESEGSED
+>3_2254
+MSDQIKLKVTRRTDFGKGASRQARRAGQIPAVVYGHGAEPIHLLLPAQETTLAVRNPNAL
+LTVVNEAGEEHLVLPKDIQRHPIRQTVDHLDLIEVRRGEKVVVEVPVHVEGELSTAVDAE
+YVLDYPTVPVEAEATDLPENVLISVEGREPGQHVYATDVQVPAGVTLQLEDEIVIATVSE
+VVEQDLGDESVQEEQAAESAEGAEGEGESEGSEESAEGESEGSED
+>4_503
+MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL
+LTVVSEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVIVEVTVQVEGEVARGNEYV
+LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQLPAGATLQLEDDIAIATVNEVL
+EQDLGDESVQEEQAAESAEGESEGSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4203592da8ea3a7bf008c30448200e5b203bda04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000543.fa
@@ -0,0 +1,25 @@
+>0_520
+MIPHDDGAAGLGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAAAGVDAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAS
+RQGVLHSGHWLGLVLPESGAGSGMAEEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGEDFTRLWEPSNAQR
+>1_254
+MIPHDDGSAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAAAGVEAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAG
+RQGVLHSGHWLGLVLPEPGVGSGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR
+>2_2351
+MRHDDGAAGPGVRPRLVLGSASPGRAEVLTRARVPFRVVVSDVDEAAVGAAAPEADPCEL
+AVLLAEAKGRDVAARVAAAGVDGPTLVLGCDSVFEFDGRAHGKPYEPEVAVARWRAQAGR
+SGRLHTGQWAGLLLPGEDGAVPDAETSTCVGADVRFAAVDEDTVRAYVATGEPLHCAGAF
+TIDGAGAALVESVDGDPNAVIGLSVVVLRAQCEELGLRFADLWEKC
+>3_2234
+MSTLPHGGGAPAALVLGSASPGRAQILRRALLPFRTVVSRVDEEAVGAASPGATPAELAR
+LLAEAKAEAVAGVVAAEGVDRPTLVLGCDSVFELDGQALGKPWEPETAIARWRAQSGRSG
+TLHTGQHVILLTPGTDAAGAPASGATVSAGVAFTDVDEATIRAYVATGEPLQCAGGFTID
+GAGAALVESVEGDPNAVIGLSVSTLRRQCSVLGVDLSALWGSSNCDA
+>4_523
+MIPHDDGAAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE
+LAGLLAEAKGRDVAARVAGAGVEAPTLVLGCDSVFEFEGRAHGKPYEPEVAVERWRAQAG
+REGVLHSGHWVGLVLPEPGVESGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA
+FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..707f66abdbc285d9cc9b36cdf2913039c3c2a921
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000545.fa
@@ -0,0 +1,15 @@
+>0_522
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>1_256
+MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
+>2_2349
+MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR
+AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ
+>3_2232
+MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR
+RPDRSLVRRGDLGLWARPGEDQWRRAAGRR
+>4_525
+MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA
+AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed602803f7e855460dcaa4a7e7e891a5529d7254
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000547.fa
@@ -0,0 +1,20 @@
+>0_525
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGLVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVLTDRRILQGAGIGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR
+>1_259
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTVRPLWRWVFRRTVVTDRRILQRAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTRTWPAPVPTGDLR
+>2_2345
+MRLEPGEQVMVRTRTHPRALLRPAAVLVTVAFLLGLAMGVLARPDLPGILTQNRALLETA
+AWAVAVLALLPGVLLPVLRWATRRTVVTSRRIVQRTGLGGGADVAMSLVSIADVQRRRRG
+SGAGDLHILFQERARQVHWRLRDVPEAARFEEALAHLTRQARVASWPAPAPTGGPR
+>3_2229
+MRLEPGEQVVVRTRSHPRVLVGTAARLTGTAFLLGLAMGLLARPGLPSPLRAAVPWLEAV
+VWAAAVVAVLVGVVRPLLRWATRATVLTSERLVQRPGLGAGPEAAMPLVSIADVQRRRRG
+ASSGDLHILFQDPLRQVYWRLADVPEAERFEQVLAETTRAARDRARPAMPAWGGVL
+>4_528
+MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA
+AWVVAALVLLPGTIRPLWRWVFRRTVLTDRRILQGAGVGGSGAAMPLVSIADVQRRRRGS
+GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3f555aaec577ea5fb0533fdda95cbd5c19b3e5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000549.fa
@@ -0,0 +1,30 @@
+>0_527
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>1_261
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>2_2343
+MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA
+AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR
+WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS
+SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG
+GRDNVTAVLVRIP
+>3_2227
+MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG
+HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL
+ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR
+NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER
+LVEAALWRGGRDNITAVLVRIP
+>4_530
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ebd48f0fb340baf683af6f88f68b04b6e828d4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000552.fa
@@ -0,0 +1,15 @@
+>0_531
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>1_265
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
+>2_2338
+MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS
+NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE
+>3_2220
+MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE
+NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE
+>4_534
+MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE
+NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9b687a30f381c62c2fb68cd9dc29a4d7c944360
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000553.fa
@@ -0,0 +1,50 @@
+>0_532
+MTETFDVNATIGADELVRLTALQMAERLRAGTTTSVELVQTHLDRIAAHDGDVRADAAGD
+RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS
+RMLEGWFSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG
+SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI
+GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRIGVVTDLPAEAF
+HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR
+VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA
+RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGVPGMSVPGGVVDGLP
+YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA
+>1_266
+MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD
+RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS
+RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG
+SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI
+GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRVGVVTDLPAEAF
+HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR
+VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA
+RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP
+YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA
+>2_2337
+MTQTFDATAELAADQLVRLTALQMAERLRAGTTTSVELVQAHLDRIAEFDGDPRADAAAD
+RGVRAYLHVNAEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVAVKDNIVTQGQPTTAAS
+RMLDGWMSPYDATVVTRLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDLDRVPGG
+SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI
+GPAARTVADAAALQQVIGGHDPQDSTSLAEEQADLAAAARGRDLAGLRVGVVTDLPADAF
+HPGIRAAFDEHVAALREAGAQIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR
+VVPDGGGTIEQVMGATRAAGFGDEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA
+RAFEQVDVLLTPTAPTPAFELGAKTDDPLTMYVNDLATIPANLAGIPGLSLPGGVVEGLP
+YGLQLMAPAREDARLYEAGAALERLVEDGRGGPVWAQAPELEKGAQRAATATTAGGRA
+>3_2219
+MTQTFDVNASLSADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAVDGDPRSDAASD
+AGVRAYLHVNTEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVALKDNIVTVGQPTTAAS
+KMLDGWMSPYDATVVERIRAAKLPILGKTNMDEFAMGGSTEYSAFGVTRNPWDGQRVPGG
+SGGGSAAAVAGFLAPFALGSDTGGSIREPAAFTGTVGVKPTYGAVSRYGVIAMASSLDQV
+GPAARTVADAAALQQVIGGHDAHDSTSLPEEQADLVAAAAGRDLAGLKVGVVTDLDAEGF
+HPGVKAAFDADVQALRDAGAEIVEVSCPHFAAALGAYYLIMPSEVSSNLARFDGVRYGHR
+VVPDGGGTIEQVMAASRAAGFGGEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA
+AAFEQVDVLLTPTAPIPAFRLGEQTKDPLTMYLNDLFTIPANLAGVPGISVPGGLVDGLP
+YGLQFMAPAREDARLYEVGAAVEKLVTEREGGPLWARVPEQHPGAARAAQTPAGGTK
+>4_535
+MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD
+RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS
+RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG
+SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI
+GPAARTVADAAALQQVIAGHDPQDSTSLAEAPADLTGAARGRDLAGLRVGVVTDLPADAF
+HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR
+VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA
+RAFEQVDVILTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP
+YGLQLMAPAREDARLYEAGAALERLVAQRRGGPVWAEAPELEKGAQRATTATTAGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..435d4b480042fecba4f8ede85ebfc1b4e69b2bd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000554.fa
@@ -0,0 +1,50 @@
+>0_533
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>1_267
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>2_2336
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG
+ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>3_2218
+MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT
+LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV
+ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG
+AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV
+GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD
+LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA
+SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD
+GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT
+RGQADAGRVREIVLERLGVA
+>4_536
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6778a66e99f5f19aa0696eb31b9b58ec8453dcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000558.fa
@@ -0,0 +1,43 @@
+>0_537
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVAGWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDVEDILADLERGFAAAARRGDDDAGERA
+>1_271
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLADDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
+>2_2330
+MVASASLYGGTQNLFKHTLAKVGIETTFVQDPDDVAAWTAAVRPNTKAFFGETLGNPRGD
+VLDVAAVADAAHAAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIV
+DAGTFDFAQHAERFPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSA
+ISPFNAFLVNLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRY
+LPKGAGAFVSFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQR
+AAGVTPGLVRLSLGVEDLEDILADLERGFAAAASAGERE
+>3_2213
+MSTQPTPRRGFSTTQIHAGTDAPHAFGATALPIYQTTSYDFPSAQVAADRFALADLGPIY
+TRIGNPTQSAVEEKIAALEGGVGALLLASGQSATTFAILNVAGAGDHVVASASLYGGTQN
+LFKHTLARVGVEVTFVQDPDDLDAWRAAARPETKAFFAEALGNPRGDVLDVAGVAAAAHD
+AGVPLIVDNTLTTPYLLRPFEHGADVVVHSATKYLGGHAAAMAGVIVDSGRFDFARDPER
+FPGFNEPDESYHGLVYARDLGVGSPLGANLAFVLKARVQLLRDYGSAISPFNAFLVNLGL
+ETLSLRMDRAVASALAVARHLEGHPQVESVSHPGLESSPWHARAQELLPRGAGAFVSFEI
+AGGAAAGAAFVDGLELHHHVANIGDVRSLVVHPASTTHAQLAEDEQRAAGVTPGLVRLSL
+GLEDVEDILADLDKGFAAAAAALDAADAAEQD
+>4_540
+MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL
+DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG
+GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTKAFFGETLGNPRGDVLDVRAVAD
+AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ
+HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV
+NLGLETLSLRMERQVANAAAVARWLEGRDDVERVVYAGLESSPWHERAQRYLPKGAGAFV
+SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV
+RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26e650381500078b1ab630e44ff3dc999ef52adb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000559.fa
@@ -0,0 +1,40 @@
+>0_538
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRTLAL
+>1_272
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL
+TEYGQVADTLKRTLAL
+>2_2329
+MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA
+LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP
+WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA
+ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER
+RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV
+GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL
+TEYGQVADALRDSLAL
+>3_2212
+MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA
+GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD
+TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ
+AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD
+YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL
+DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA
+ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL
+>4_541
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRALAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09c0720b118ea3fde9fe609cf33fa3a1d7d55ad1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000567.fa
@@ -0,0 +1,45 @@
+>0_550
+MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL
+TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP
+RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV
+KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV
+WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF
+EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA
+LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM
+IQAAELDVSGG
+>1_291
+MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQQAMIQAAELDVSGG
+>2_2307
+MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH
+AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV
+ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR
+RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA
+AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI
+GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK
+HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH
+LPDGWLDSRELNAEQKAMIAAAELDVSGG
+>3_2197
+MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP
+VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL
+YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT
+EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA
+RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE
+RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP
+NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE
+LDVSGG
+>4_551
+MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL
+RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD
+PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL
+FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY
+SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD
+LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS
+EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA
+EQKAMIQAAELDVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000568.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb9cb4145d935a4664cd9dbde24e9c97503cb7fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000568.fa
@@ -0,0 +1,45 @@
+>0_551
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>1_292
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>2_2306
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI
+>3_2196
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL
+>4_552
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5766c070549b02189c6e4d7dc6c92a33d7f5a493
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000573.fa
@@ -0,0 +1,50 @@
+>0_583
+MSSACGCEAPTPGAPEEPEEHRPWWRDAAILLPVLSGVAFIAGLVLEWSGAGLVATVVFW
+VGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEALE
+DKAMDRARAGLRALLKLVPETATIRQGGATVQVEAKDLHPGQVLVVRPGERIATDGIVRT
+GRSSLDTSAITGESIPVEVGPGDTVSAGSINTSGALEIDATAAGTDNSLTTIVHLVEQAQ
+TEKGARARLADRIAKPLVPGVLVLAVLVAALGSLFGDPELWITRALVVLVAASPCALAIA
+VPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLTTPGLTE
+DQVLGWAAALEQHSTHPLAAAIIAAAPDAPGAKAVTETAGHGITGRIDGATITVGSPRWL
+DPGPLAAQVQQLEDQGMTVVIIHRDGTVAGAIGVRDELRPEVPAVVTTLTGQGIGLTMLT
+GDNARTARAIAAQAGIGDVRAELRPEDKAAAVGQLTGTRPTAMIGDGINDAPALAAAEVG
+IAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIMNQNIVLSLLIIGVLLPLAI
+TGMLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALASLTDRQAQRSTVG
+>1_1718
+MSAACGCEAPTPTPGAPEEHEEHRPWWRDAAILLPALSGLAFLTGLVLEWSGAGLVATVV
+FWVGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEA
+LEDKAMDRARAGLRALLKLVPETATIRAGGATVEVEAKDLRPGQVLVVRPGERVATDGIV
+RTGRSSLDTSAITGESIPVEVGPGDTVSAGSINTAGALEIDATAAGTDNSLTTIVHLVEQ
+AQAEKGDRARLADRIAKPLVPGVLILAVLVAALGSLLGDPELWITRALVVLVAASPCALA
+IAVPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLAAPGI
+TEDQVLGWAAALEQHSTHPLAAAITAATPDTPAAEGVTETAGHGITGRLDGATVTVGSPR
+WLAPGPLAAQVQGLEDQGMTVVIIHRDGAVAGAIGVRDELRPEVPTVVTTLTGQGIDLTM
+LTGDNARTARAIADQAGIDDVRAELRPEDKATAVHQLTGTRPTAMIGDGINDSPALAAAE
+VGIAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIINQNIILSLLIIAVLLPL
+AITGVLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALEPLTDRQAQPATTG
+>2_710
+MRATTHTPVEELETDDEHETPWWADRAVLIPIASGVAFVAGLACEWSGAQSAALVLFWVG
+LLLGASTFVPGALRKLATGKLGIALLMTMSATGAVILGHVEEAAALAFLYSIAEALEDRA
+MDRARAGLRALLKLVPQSATVLTDGHSASVPARDLAAGQVMLIRPGERIATDGIVRSGHS
+SVDTSAITGESIPVEVGPGDEVSAGAINAAGALQVEATAPGTDNSLTTIVSLVERAQAEK
+GQRARLADRIARPLVPGVLVLAVLVALIGSLAGDPQTWITRALVVLVAASPCALAIAVPI
+TVVSAVGSASKFGVIIKSGAIFERFGDIGHVAFDKTGTLTRNQPTVTAVVPAADVTEQQV
+LAWAAALEQHSTHPLATAITHAAPHNPRRPGHHRGSRPRNPRHRRRRRSAGRQPPLGRPR
+RPHLPGP
+>2_711
+MLVGSPRWVDPGDLTYRVRDLEAQGMTVVVVHRDGAVAGAIGVRDELRPEVPEVITTLAG
+QGIDVTMLTGDNERTARALAAQAGISDVRAELRPEGKSAAVGELSVRRPTAMIGDGINDA
+PALAAADVGIAMGATGSDAAIESADIAFTGQDLRLLPQAIAHARRGRRIVNQNIVLSLLI
+IAALPPLAITGVLGLAAVVLIHEVAEVLVILNGLRAARTHQPTRGH
+>2_2313
+MVPVFSGVAFLTGLVLEWAGLEVPALVLFWIGLLLGASTFTPGAIRKLFKGKLGIGLLMT
+ISAVGAVILGYVEEAAALAFLYSIAEALEDKAMDRARGGLRALLKLVPETATIRRDGASV
+EVPAKDLAVGQLMLVRPGERIATDGIVRTGRSSLDTSAITGESIPVEVEPGDTVSAGAIN
+TAGALEVETTAAGTDNSLTTIVDLVEKAQADKGDRARLADRIARPLVPGVLILAALVAII
+GSLLGDPELWITRALVVLVAASPCALAISVPLTVVAAIGSASKFGVIIKSGAVFERFGVI
+RHVAVDKTGTLTRNEPAVTAVLTAEGVTEKQALAWAAALEQHSTHPLAAAITAAAPGAPA
+ADGVTEQAGHGIEGTLDGARITVGSPRWLDAGTLGEQVAGLEEQGMTVVIVHRDGTPVAA
+IGVRDELRPEVPEVVRTLAAQGIGVTMLTGDNARTARALAAQAGIGDVRAELRPEDKAAA
+IAELGEKGAVAMIGDGINDAPALAAADIGIAMGATGSDAAIESADVAFTGHDLRLLPRAF
+DHARRGRHIINQNLILSLLIITALLPLALFGVLGLAAVVLVHEIAEVVVILNGLRAARTR
+KSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1f300e2efb8fa9c941ba4dc692275a253604acb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000574.fa
@@ -0,0 +1,25 @@
+>0_587
+MTTPTIPTDHPIEHRVDTGPASEEAGMPVAARHRPFGVVLLVTGVVGWVASAILVLERLA
+LYENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVIATAMVVLSGARPG
+RGYWAGLQAGVTLGMGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFILLTARNLAHGVI
+PAPPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGL
+>1_312
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTMR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
+>1_1722
+MTDRLTEPTAPSAASPVSAAGPAPAPAWFTGRRAFGLVLLVTGAVGWIASATLVLERLAL
+YENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAMVVLSGARPGR
+GYWLGLQAGVTLGIGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFLLLTARNLAHGVIP
+APPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGF
+>2_2292
+MRTPATDTDSPVKTEPLTDLPTERAADPDPSAPAPVPAVARHRPFGLVLLVTGVVGWVAS
+AILVLERLELYEDAGHITSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAM
+VVLSGARPGRWYWAGLQAGVTLGMVFVAWLWFQALFVIHILCLYCMIVWAAMIPLFILLT
+VRNLAHGVIPAPPGVVRFATGWAGTLIAVAYVTVTGSVFVQFLPAFTGY
+>4_1949
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTVR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff00cc93f6ff9091c847f7b753d9ec30f57e9c7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000576.fa
@@ -0,0 +1,23 @@
+>0_611
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQLRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>2_392
+MLCILPLDQSLHQTRSDSDFYREFVDHPRVIRVLALSGGYTRAQATTLLARNHGVIASFS
+RALTEGLSTAQSPAQFNAVLDEAINAIATASRT
+>3_2140
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVMGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIQLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDD
+>3_2141
+MTLPERADFYREFVDHPRVIRLLALSGGYTRAQATTLLARNHGVIASFSRALTEGLSTAQ
+SPAQFNTVLDEAINAIATASRT
+>4_570
+MDSEKYQRVRNGAGFVAALDQSGGSTPAALHLYGIDKDAYSGPEEMFDLVHQVRTRIITS
+PSFDGERVIGAILFENTMNRQVEGSPTGDYLWNSKGIVPFLKIDQGLAPEQQGAQLMKPI
+PHLDDLLSRAVEKHMFGTKMRSVIKLPGDGVGSVVEQQFGLARQILVTGLVPIIEPEVDI
+RSPRKAEVEDQLKAAILAQLDKLGDDQSVILKVTLPERADFYREFVDHPRVIRVLALSGG
+YTRAQATTLLARNHGVIASFSRALTEGLSTAQSPAQFNAVLDEAINAIATASRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1778a7bf48123377579de0bb3c906fc452802db0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000579.fa
@@ -0,0 +1,35 @@
+>0_617
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>1_363
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>2_2269
+MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR
+GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA
+VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL
+SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI
+RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>3_2131
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>4_587
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000585.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd2777a2d23d4ace62e83f8e1861365345d4a152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000585.fa
@@ -0,0 +1,30 @@
+>0_626
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAERAEAPAAEAAPQGE
+>1_372
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVPYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAAPQGE
+>2_2261
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQGQEVIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMSKTPSAVWVVDTKKEHLAVDEAKKL
+GIPVVAILDTNCDPDEVTYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQSAAE
+PMAEWERELLEQHNAQQAEQAEAPAEAQAQAEEASAEAPAQAEEASAGAPAQAE
+>3_2117
+MSVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLTYIDRAYEFVKQT
+VAHGGTILFVGTKKQAQEAIAEQATRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEAI
+DFEDVAGSTHTKKELLLLNRELEKLQGNLGGIRDMARTPSAVWIVDTKKEHLAVDEAQKL
+NIPVVAILDTNCDPDEVAYPIPGNDDAIRSVTLLTRIVADAVAEGLIARQGGKSGDSSAE
+PMAEWERELLEQHNAEQAAQAEAPAAEAAESEAPAAE
+>4_596
+MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET
+VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI
+DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL
+GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE
+PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAEQAEAPAAEAAPQGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c17105de7e3ab0fa3f154d124b6ae6462500d488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000588.fa
@@ -0,0 +1,25 @@
+>0_629
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>1_375
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
+>2_2258
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSYTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRVVMPELTEERRKEYVKLVKSK
+AEEHKVSVRNARRKAKDALDKAVKDGEVGEDEGARGEKDLDAMTKKHVDLIEEMAKNKEQ
+ELLEV
+>3_2114
+MIQETLTSAQEQMERTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDVSALRNIEKALSDSEVGANPSNDGKVIRVVMPELTAERRKEYVKLVKNK
+AEEHKVSVRNARRKAKEAIDKLVKDKEIGEDEGARGEKDLDALTKKHTDLIEEMAKKKEA
+ELLEV
+>4_599
+MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT
+DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK
+AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ
+ELLEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6c453417947718d51e973657d71187b44ced6cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000592.fa
@@ -0,0 +1,46 @@
+>0_634
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
+>1_380
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAESDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR
+LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG
+GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL
+TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM
+SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ
+VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLAMV
+>2_2253
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGSEGETLEVGAPLVTFTVEGAGGDGGDTESGGRVPTLVGYGAAPDTGKPGRRARRGGSA
+GSATSAAPAGEPERGRAPSTSEEAPAGAARPQPEAAEPERADEAPEAQPASGTSGERPRC
+TPPVRLYARREGVDLTAVSGSGVGGVITRADVEAFLAGGGAPAAEPTASAAAPAEAGTSG
+GVRTLGGRPRTESVPVKGVRKATASAMVASAFTAPHVTEFLQVDVTETMELLAELKASRE
+YRDVKLTPMTLAAKACLVAMERTPDVNARWDQASGTILQQNFVNLGFAAATPRGLMVPNV
+KDAQAMSLTELADAIRELTGRAREGRLSPAELSGGTFTLTNVGVFGVDAGTPIINPGEGA
+IIAIGQVRRTPWEHRGEIVLRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTM
+V
+>3_2108
+MTRTVFRLPDLGEGLTESDLVTWRVSAGDDVVLNQVLAEVETAKAVVEVSSPYAGTVAEL
+HAQEGQTVDVGSPLVTFDLPGDDAAPSDGPAADGRVPTLVGYGAAPESGAPARRRRRPAS
+SAGESTPETGTSAEPAPAPAESAPAERPRSTPPVRLLARRLGVDLESVTGSGDHGVITRA
+DVDAAARAASDSAGSEAPAEADAAPGVRTLGGRPRVVVEQVRGVRKATAQAMVSSAFTAP
+HVTEFLTVDVTESMELLDELRRDRAFRDVKVTPMTLALRACVLAMERTPEVNARWNGQDG
+TIERRHFVNLGMAAATPRGLLVPHVKDAQALDLRGLAVEVAALTERARAGTLTPAELTGG
+TFTLTNVGVFGVDSGTPIIHPGEAAILCLGAVRTQPWEHRGQIALRQVVTLSLSFDHRLV
+DGEQGSRFLADVGAMLRRPGMTLALV
+>4_604
+MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL
+HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA
+APATSAAPVGEPARGQAPSTSEAAPAGAGRPQPEAAEPARADAAPEAVRGAASGERPRCT
+PPVRLYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAATPPQSDAESGSTGGV
+RTLGGRPRTEAVPVKGVRRATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFR
+DVKLTPMTLAAKACLVAMERTPDVNARWDEAAGTIVRQNFVNLGFAAATPRGLMVPNVKD
+AQAMSLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAII
+AIGQVRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d4218f169cc997d7b5dcd574ed8013fc55ead8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000596.fa
@@ -0,0 +1,20 @@
+>0_642
+MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR
+>1_388
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR
+>2_2244
+MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF
+MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET
+PEATR
+>3_2105
+MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV
+MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET
+PEVAL
+>4_612
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAPENP
+EATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000597.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f7461af6d96c684cac3a08019926a2267bc9354
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000597.fa
@@ -0,0 +1,50 @@
+>0_643
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAVLLIAGAGIMTVWTLALFGFDFNALLGAAVEKNPKGEA
+ILEPGLQYGASALTRLDFVSLGLALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>1_389
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>2_2243
+MSALTPLLQAAPEAVGSPAVNIGIFLAFVVVTLVIVIRASKTSSSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIAIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGVMTVWSLAMFGFDFNAMLGAAVELNPEGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERIMAAPGGQNSAAPLLAFELGGSILLGVISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHQLTPNEEVRIGKITVVVIGLLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGAPTSMI
+PGADFAIFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>3_2104
+MSTFALPLAAAVGDPVVNIGIFVAFVAVTLVIVIRASKKNASAADYYAGGRGFSGTQNGT
+AIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMADVL
+SFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNITDKGGQALVIVIVGVLMI
+VYVLVGGMKGTTYVQIIKAILLITGAGVMTLWSLALFGFDFNAMMGAAVQLNPQGEAILE
+PGLQYGKNFTTRLDFLSLGLALVLGTAGLPHVLMRFYTVPTAKEARTSVVWAIVLIGAFY
+LFTLVLGYGAGALIGPEKILAAPGGVNSAAPLLAFELGGSILLGLISAVAFATILAVVAG
+LALTAAASFAHDVWGSVIAKEPLTPEEEVRIGKITVVVIGVLAIVGGIAAQGQNVAFLVA
+LAFAVAASANLPTILYSLFWRGFTTRGAVWSMYGGLIASIVLIVLSPVMSGAETSMIPTA
+DFAVFPLKNPGIVSIPLAFVLGWLGSVTSKDVEDPDKQAEMEVRSLTGVGAEKPVAH
+>4_613
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNTSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERITAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57b68f94b665c55af3ac8edf61443632ca17b390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000602.fa
@@ -0,0 +1,60 @@
+>0_648
+MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR
+EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV
+KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR
+AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV
+APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANRLAPRDGEPWTAADTLKCVVVTAVV
+DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP
+AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV
+LEATAVREGDQAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY
+GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT
+VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV
+LAEVRDGR
+>1_394
+MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR
+EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV
+KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR
+AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV
+APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANQLAPREGEPWTAADTLKCVVVTAVV
+DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP
+AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFMWDGV
+LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY
+GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT
+VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV
+LAEVRDGR
+>2_2238
+MALRMSTLFLRTLRDDPADAEVASHRLLVRSGMIRRAGFGTFTWLPLGLRVLRRVEQIVR
+EEMDAIGGQEVHFPALLPKEPYEATGRWDEYGDGIFRVQDRKGADLLLAPTHEEMFTLLV
+KDHYSSYKDLPAYLYQIQTKYRDESRPRAGLLRVRDFVMKDSYSFTVDDAGLDEAYEAHR
+AAYERIFARLGLETVPVEATAGAMGGSRSEEFLHPCAIGEDTFVESPGGYRANVEAVTTV
+APAPLDEAAMAALPAPEVKETPVSTTIAALVDVANELAPRAEGVWTAADTLKCVVLTAVL
+DGDERRQFVVAVPGDREVDLKRLETTVAPALGLSGEPGVEAATEEDLRRHPSLVKGYIGP
+GAGPDGGAPVLGAESVSGLPFLVDPRIAAGTAWITGANADQRHVFGLVAGRDFGWDGVVE
+ATVVRDGDEAPDGSGPLTARRGIEMGHIFQLGRKYAEALDLKVLDQNGKQVVVTMGSYGI
+GVTRAVAAIAESHRDEKGLVWPRAVAPADVHVLATGKGAEVFEAAEQIVAGLEAAGLTVL
+FDDRPKVSAGVKFGDVELIGLPTSVVVGRGLADGVVEVKDRATGEARSVPVAEAVDAVVA
+EVRDGR
+>3_2099
+MALRMSTLFLRTLRDDPADAEVASHKLMVRAGYIRRAAPGIYTWLPLGLKVLAKVEQIVR
+EEMDAIGAQEVHFPALLPREPYEATGRWEEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV
+KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR
+AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV
+APAPLDEAAMAALPAAEVKDTPASTTIAALVDVSNELLPREDRPWEAADTLKCVVLTAVV
+EGGERRQFVVAVPGDREVDLKRLEASVGPALGLVGEPDLEAATAEDLKRHPSLVKGYIGP
+GAGPDGTPVLGAEDSVSGLPFLVDPRIAAGTVWMTGANADQKHAFGLVAGLDFTWDGVVE
+ATVVREGDPAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDENGRQVVVTMGSYGI
+GVTRAVAAIAERYHDEKGLVWPRAVAPADVHVVVATKGEDGVQAALDLAARLEERGLTVI
+VDDRPKVSPGVKFKDAELVGVPTAVVVGRGLADGELELKDRATGASRAIALDSAVDEVLA
+EVRPQG
+>4_618
+MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR
+EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV
+KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR
+AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV
+APAPLDEAAMAALPAAEVKDTPVSTTIAALVDVANRLAPREGEPWTAADTLKCVVVTAVV
+DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP
+AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV
+LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY
+GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT
+VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV
+LAEVRDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2043bf8c38439e5b795a3e13134b4e775a0a67cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000603.fa
@@ -0,0 +1,30 @@
+>0_649
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
+>1_395
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
+>2_2237
+MVAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPVQALATNKMGSVFGTATSAITYRRRL
+RQDLSTALPMAAVAFVAALAGAVVAASLPAGVIRPVILVALIAVAVFTAVRPGLGKTAGV
+GPERRTAVARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKIVNLATN
+LGALAFFIPAGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLVVVAALIVKVG
+ADTLAPLLL
+>3_2098
+MELFGPVELSVGIVLLVLAAGFSAGWIDAVVGGGGLLQLPVMLLVPGLSPVQALATNKMG
+SVFGTAASAATYARRVRPDLRTALPMAAVALLCSLGGAVVATVLPAAVIRPVILVALVGV
+ALVTALRPQWGLTQGLKHAGTAHALRALAVGAVVGFYDGVLGPGTGTFLILGLVGVLGYD
+FLQASAKAKIVNLATNVGALAFFLPAGHVVLGLGLLLGAANLTGGYVGARMAISRGTGFI
+RTVFLVVVCALILRLAWDVFAPLLG
+>4_619
+MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL
+RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV
+GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN
+LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG
+ADTLAPLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67fe55e76773d1fa803b114a928bb96010a05086
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000606.fa
@@ -0,0 +1,81 @@
+>0_653
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>1_399
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP
+GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP
+AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR
+PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP
+GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP
+RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK
+VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE
+ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL
+TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI
+DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA
+NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA
+ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD
+QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA
+TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG
+SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV
+REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV
+>2_2234
+MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS
+KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG
+EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR
+PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP
+GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ
+PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA
+RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP
+VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG
+KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI
+IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE
+VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC
+GIGLGSFNDIKEGDVIETFEMREKPRA
+>3_2094
+MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK
+PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA
+SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS
+KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP
+AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG
+GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA
+DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE
+AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG
+AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH
+AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL
+EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG
+RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA
+QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI
+HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA
+LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL
+KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV
+>4_623
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27c5b91d4a6b8a6fdfeefd918a7c8d9a657868e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000607.fa
@@ -0,0 +1,20 @@
+>0_654
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>1_400
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRTAEPDADADDAPRA
+>2_2233
+MADPARAGRLAQRIKVLVAEALRRSVKDDRVEAVTVTEVRVTNDLQHATVYYTVLGDEAT
+AAAAHEGIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGATYAGEADPYRTSEPGSEADDAPRA
+>3_2093
+MADPARAGRLAQRIKVLVAEALRRAVKDERVEPVTVTEVRVTNDLQHATVYYTVLGDEAV
+VAAAQEAIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGAQYAGDADPYRTSGDDDEQD
+>4_624
+MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT
+VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA
+KAREGASYAGDADPYRSAEPDADADDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e07667b9ca41a92af19e122a7ec5494d23aa128
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000608.fa
@@ -0,0 +1,31 @@
+>0_655
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>1_401
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>2_2232
+MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR
+AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL
+AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA
+>3_2092
+MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG
+LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV
+AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV
+DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT
+ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV
+ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR
+>4_625
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abde69995a3aa091f53e1667159707c57d90babc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000611.fa
@@ -0,0 +1,35 @@
+>0_658
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>1_404
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>2_2229
+MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS
+VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV
+VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG
+DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE
+AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV
+EKLVAQMTQDVEQARAILAATPSDR
+>3_2089
+MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV
+VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV
+VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD
+VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV
+WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE
+KLVAQMHQDVDQARAVLAAAPQPAGRV
+>4_628
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5885a7da90ea70f76285b078c01845e865fb2282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000612.fa
@@ -0,0 +1,30 @@
+>0_659
+MSAPEPGAPPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
+>1_405
+MSAPEPGAPPAVPNLPGRPARVRRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA
+DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
+>2_2228
+MTGPGPGVPRLPGRPARARREAGNPFADAGGEHYDAVRPSYPAEAVAWVLEGLGQGLDRG
+LDVVEVGAGTGLFTRSLTALPVERVRSVAAVEPAASMRAVLERDVAAGSDGRVRAVPGTA
+EATGLPEASADVVVAAQAWHWVDPAAGSAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTR
+IMHAGDVHAARPELRRFAAPFGAEEHARWTWTLPQTAADLHGIMASRAYWLRASETTRAK
+MSANLDWYLHEHLGHGPDEAIVVPYVSVAWQASST
+>3_2088
+MSERGLPDSGAAPRPAGGYVPALPSRPAITRTGGVNPFEVSPEQGEQYDAVRPSYPAAAV
+DWVLDGLGAGLDVVETGAGTGLFTRRLAERPAERVRSVAAVEPSEAMRAVLERDVAAGSA
+GRVRAVDGTGEATGLADGCADVVVAAQAWHWMDAERASAEAARVLRPGGRLAAVWNQLDV
+TVPWVHRLTRIMHAGDVHAAAPERRRFAAPFGPEEHARWSWSLTTTPAGLHALMASRSYW
+LRAREGTRARMTANLDWYLHEHLGHAAGEELTLPYVTVAWRAPAPAR
+>4_629
+MSAPEPGASPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAVVDRVLAGIADGA
+EVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE
+ATGLPAASADAVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI
+MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM
+TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..412e9637eb5243b9c240e3b2f2911a1b1171bc93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000614.fa
@@ -0,0 +1,15 @@
+>0_661
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>1_407
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>2_2220
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>3_2086
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
+>4_631
+MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV
+GRRRRMLGYLQKVDIERYRALIERLGLRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac82561c045e1278f228e7b6426ac6309f6ec6d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000615.fa
@@ -0,0 +1,70 @@
+>0_662
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>1_408
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>2_2219
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA
+>3_2085
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA
+>4_632
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98af8ed96833c005f063c0e1fe61f76e69b8c179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000617.fa
@@ -0,0 +1,30 @@
+>0_664
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>1_410
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
+>2_2215
+MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA
+GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP
+DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV
+LGLRTVASRPGLTYGLDGYLDLG
+>3_2082
+MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG
+ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF
+SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD
+ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL
+ALREVAGRPGLTYGLDAVLGLD
+>4_634
+MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA
+GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN
+FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP
+DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV
+LGLRTVASRPGLTYGLDGYLDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6d03b995b0c0bd8864da03f12f8cb077e6b7ea7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000620.fa
@@ -0,0 +1,55 @@
+>0_668
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>1_414
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>2_2210
+MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD
+EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV
+VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV
+GTWVNRKLRRRPMIIPVVLEA
+>3_447
+MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL
+IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP
+LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE
+AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA
+IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI
+PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP
+GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH
+LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL
+EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ
+DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA
+>4_638
+MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD
+LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE
+HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL
+DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF
+SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD
+EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG
+ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN
+VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV
+VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA
+GTWVNRKLRRRPMIIPVVLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22b3deeaf7e5b22df53d640281dc589cc8f0ca4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000625.fa
@@ -0,0 +1,15 @@
+>0_674
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
+>1_420
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
+>2_2204
+MRVSEFQRLMDEEFGPGRAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCELHDIPE
+ERRLGRDVPPKR
+>3_2075
+MTEFQRLMEDEFGPARAGLVADSLHLPGFDATASEALAAGADPKDVWRAVCDLHEIPAER
+RLGRDVPPTR
+>4_644
+MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ
+ERRLGRDVPPKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f71829185501994cdec6096edc4c8eef9163aafa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000626.fa
@@ -0,0 +1,36 @@
+>0_678
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
+>1_421
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
+>2_2203
+MSKTPDREKALEAALAQIDKQFGKGSVMRLGDQTQTPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKIT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLAQEIEERILTKLGIGVDPEAEADEAPALTAVPGDTAAG
+>3_2074
+MSKASATEKVATEREKALEAALAQIDKQFGKGSVMRLGERSQAPVEVIPTGSVAMDVALG
+IGGLPRGRVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTD
+ALLVSQPDTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMS
+QALRKVTGRLHQTNTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLK
+EAGSPVGNRTRVKIVKNKMAPPFKQAEFDILYGEGISKEGSLIDMGVEEGIVKKSGAWFT
+YDGDQLGQGKENARRFLKDNPDLADEIEHRIFTKLGIGADPQAEDDAEGETPALQAVAGD
+VAAG
+>4_645
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLRDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d56df59a0c2fd24a1b28ca2ce2d1606427dbfa2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000629.fa
@@ -0,0 +1,35 @@
+>0_681
+MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV
+AEALAVVAGDAT
+>1_424
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AEALAVVAGGAA
+>2_2200
+MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG
+VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT
+DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP
+RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS
+ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ
+ALAVVAGS
+>3_2071
+MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP
+PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP
+TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV
+AAALAVVAGDAT
+>4_648
+MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER
+EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP
+PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF
+MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP
+TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV
+AEALAVVAGDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e7328e306a50f375f91b3450dceeff15634c81a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000630.fa
@@ -0,0 +1,35 @@
+>0_682
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLNPELAEEAASDSMVLAHGLTDPR
+PALSVSMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGTDSWLVEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTA
+>1_425
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAERVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR
+PALSVSMGNPHTVVPLASFADLEGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTA
+>2_2199
+MTEKTAAAAAPTSDAAPRVPFTKGHGTGNDFVLLADPDGNVHLEAAQVAVLADRHRGIGG
+DGVIRAVPSRHVEEGRALLAAHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLSEKGLVD
+LAPGESITIGTRAGVKTVSRLAHGYAIDMGPWSYLDPELAEEAASDAMVLAAGLADPRPA
+LSVSMGNPHTVVPLASFEDLEGLDLTRAPEVDPAPSHGSNVEFVAAHEPLVREGVGRARM
+RVHERGVGETQSCGTGACAVAVAMRAWSGEGGSDSWLVEVPGGVLGVDFVAHPDGTEHVV
+LAGPAELVFDGELTV
+>3_2070
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQHVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLPDPR
+PALSVSLGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAVAVAMRAWAGDQGTDSWLIEVPGGVLAVDVVPGPEGAEH
+VVLSGPAELVFDGELTV
+>4_649
+MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI
+GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL
+VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR
+PALSISMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV
+RMRVHERGVGETQSCGTGACAAAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGTEH
+VVLSGPAELVFDGELTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a338e679e507864a38be7212b77f50a1dd1111e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000633.fa
@@ -0,0 +1,54 @@
+>0_688
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA
+AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAL
+>1_428
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
+>2_2194
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR
+TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV
+VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI
+VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL
+EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK
+PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP
+DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF
+AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP
+DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS
+>3_2065
+MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA
+LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA
+GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL
+TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL
+LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR
+EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI
+GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV
+DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR
+LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA
+QEAASA
+>4_652
+MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD
+AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ
+LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA
+QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ
+VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR
+DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV
+RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA
+AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA
+ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV
+VEADAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ca5b1ac46928308b4d3b53283df3ffb0aa56675
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000634.fa
@@ -0,0 +1,65 @@
+>0_689
+MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>1_429
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>2_2193
+MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR
+HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL
+PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK
+EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA
+ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT
+SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ
+DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD
+ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR
+FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA
+EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV
+AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA
+VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS
+>3_2064
+MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ
+AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV
+VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA
+WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV
+TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS
+VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD
+AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV
+APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP
+FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR
+RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR
+PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE
+RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH
+>4_653
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..194af3219bf3b6c73fd26b51398101f7f3e0518a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000635.fa
@@ -0,0 +1,25 @@
+>0_690
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRVTAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
+>1_430
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRISAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
+>2_2192
+MATTDEQPAPLTDRQRRIVQTIRDAIAEHGYPPSMREIGDAAGLASLSSVTHQLGRLEQH
+GYIRRDPGRPRALEVLLDVDGTPLGEAAPPAAAAPSGLPAIPAWHTGAEDADTVPVPWVG
+RIAAGGPVLAEQQVEDVMAVPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQETAE
+NGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRAL
+>3_2063
+MATSPTPPPGGAQPLTDRQRRIVRTIRQAIAERGYPPSMREIGDAAGLASLSSVTHQLGQ
+LERFGYLRRDPGRPRALEVLRDEDGAAAVADAAPGAPEIPSWHTGASEDATVEVPWVGRI
+AAGGPILADQQVEDVMAVPRRLTGEGDLFMLRVVGDSMVDAAICDGDWVVVRRQETAENG
+DIVAALLDDEATVKTLRRRDGHTWLLPQNTAYEPILGDHATLMGRVVTVLRAL
+>4_654
+MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL
+ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPTAAPSSRVSAIPAWHTGADEADSVPVP
+WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQD
+TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62c38e3c4dd33e09ef5a195b07f5995d0d4635b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000636.fa
@@ -0,0 +1,20 @@
+>0_691
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>1_431
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
+>2_2191
+MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA
+VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI
+PATR
+>3_2062
+MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA
+TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL
+NGLEGRDPELGQELYVPPTR
+>4_655
+MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA
+VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV
+PATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5900bc3462b6b940635f771b795ac8f8ec9fb34e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000651.fa
@@ -0,0 +1,30 @@
+>0_707
+MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>1_447
+MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV
+GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA
+>2_2170
+MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV
+GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI
+RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA
+>3_2045
+MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA
+GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV
+RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS
+LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT
+QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA
+>4_671
+MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV
+GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI
+RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS
+LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT
+QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45cbddba3f4a84b5d0218ef8c9e91779d3b2c0b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000654.fa
@@ -0,0 +1,20 @@
+>0_710
+MPRGAAHGAQAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
+>1_450
+MPRGAVHAVPVPRGVHMGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
+>2_2144
+MTAGSGAAAAAPRRRRPRWRDDRGAAVAESTMVMTLVVLLFAALLQAGLVIHTRNVMIDA
+ASAGARYGALADRVPEDGVQRARELLAAGVPGQSGARIVAEPTSQDGVPVLRVTISSSLP
+GVGFLPGPIPVEVSGHAHRL
+>3_2042
+MEPAARPAVQGRPGPDRRAGDRGSVVAENAMVTALLVLLFAAVLQVGIIVHVRNVMIDAA
+SAGARYGALADRDPAEGAARARDVLSASVPGQSGAQVRSEPTTVGGVPVVRVTITSSLPG
+LGFLPGPVPIEVHGHAFRY
+>4_674
+MPRGAAHDAPAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI
+DAASAGARYGALADRNPEDGVQRARELLSTGVPGQSGADVAAELTSQDGVPVLRVTVSSS
+LPGLGFLPGPIPVEVSGHAFRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..496d3dcc1e6f1098ed9be0e498cb4dfdf83de20a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000656.fa
@@ -0,0 +1,20 @@
+>0_712
+MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>1_452
+MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>2_2142
+MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL
+GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD
+LLAAAGPFAGMLPLSVPIQATGDSRTSLSR
+>3_2040
+MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA
+DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA
+TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR
+>4_676
+MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE
+ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..676470eb088ac698f8d00c35a7ca9cf3ecb478d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000657.fa
@@ -0,0 +1,40 @@
+>0_714
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>1_454
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
+>2_2139
+MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG
+EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI
+RWRAEQAKAAQED
+>3_2036
+MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS
+HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF
+EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA
+EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI
+RWRAEQVKAAQED
+>4_679
+MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS
+HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG
+EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF
+EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV
+DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA
+EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI
+RWRAEQVKAAQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2d530908c8e3029948c8eb1e6d00d5ec02e3305
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000658.fa
@@ -0,0 +1,35 @@
+>0_715
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL
+>1_455
+MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>2_2138
+MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA
+NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>3_2035
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>4_680
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45353807efb5c0a752859c043d60636c91b8bb78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000660.fa
@@ -0,0 +1,30 @@
+>0_717
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEGRA
+>1_457
+MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>2_2136
+MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG
+WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRAAGEES
+>3_2033
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
+>4_682
+MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG
+WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY
+TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV
+TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV
+FVHRIVEVGTDIEKRIEKRTVRASGEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24e54ae561c0a680ee5ee60a59d6a6747e940dd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000661.fa
@@ -0,0 +1,25 @@
+>0_718
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD
+>1_458
+MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>2_2135
+MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL
+GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD
+>3_2032
+MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG
+DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD
+>4_683
+MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL
+GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG
+DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI
+ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e381d65659567383f410bc54cd7dc07b6e68d079
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000663.fa
@@ -0,0 +1,30 @@
+>0_723
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGVVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEDSA
+>1_462
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFMRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGEEAEGGA
+>2_2131
+MERPENPANRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLVDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRISVSGVDDVADASLSFSSIEGWRER
+GAIREFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHEDVLARLRPSGGGED
+>3_2025
+MDQTWNAARDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVSDADRAAEESI
+RSTLSRARARDLILGEEFGGNLSRTGRQWVVDPIDGTKNFVRGVPVWATLIALLIDGEPV
+VGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRIQVSDVDRVEDASLSFSSIEGWRERGAV
+REFLQLTSDVWRVRGFGDFWSYMLLAEGAVDVATEPELALHDMAALVPIVREAGGRFTSL
+DGEEGPFGGHALATNGLLHDEVLRRLTPGQD
+>4_687
+MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE
+ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG
+EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER
+GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF
+TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7b992daeb65c2e636dad798f55e47704cb2b5d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000665.fa
@@ -0,0 +1,47 @@
+>0_725
+MTRPTRAAAHSPAPRPDAAETWPAPVARGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL
+HGVLESRDTALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV
+PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADAATV
+APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE
+VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD
+RWRRILPQFGASVALTVDRTDRSRGRLTVTGVVQDDGAPRITGAGEIADTAELAPTAAAL
+ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEEETSLGFPGTDASGPLSPAA
+LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR
+>1_464
+MTRPTRAATHSPAPRPDAAETWPAPMARGPVRGDVRLPGSKSLTNRHLVLAALADGPCIL
+HGVLESRDAALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV
+PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVVEEGEPGRLPFTTTTRADAATV
+APDGDVPEVAVDAAGSSQFLSAALLAAAGMPRGLRLRHTGEAVPSPEHVAMTVGVLRALE
+VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD
+RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGAPRITGAGEIADTAELAPTAAAL
+ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEDETSLGFPGTDASGPLSPAA
+LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR
+>2_2129
+MTRPTPAPEDPSEHPSERPVEPLAGDVVAWPAPAARGPVRGTVRLPGSKSLTNRHLVLAA
+VADGPVTLRGALVSRDSALMRAALESLGARFEDLPDGGLRVHPLPLGKPLEGEVEVDCGL
+AGTVMRFVPFVAALRPGRVRFDGDAGARVRPMAPVIDALRRLGVAVHEEGEPGLLPFTVH
+TPPDAATVAGGPRATEDGAPVPEAAVDAGASSQFLSGALLAAAAMPRGLRLRHTGATVPS
+PEHVGMTVAVLRSLGVRVEQPDATSWTVAPGGIAAHEAAIEPDLSNAGPFLAAAAVTGGS
+VTVPDWPTRTTQIGDRWRRILPAFGASVALTVDRTDRSRAALTVTGGTRPDGTPLVTGAR
+DVADTAELAPTVAALALLAEGPTRLTGIGHLRGHETDRLAALAAESARFGVEVDEQADAL
+GFPGTDASGPLTPAAAQTYHDHRMATFAAVVGLRVPGTAVVDVATTAKTMPDFPAMWASL
+VAPAAGADEAGAL
+>3_2023
+MTAPGPAAPSPTTPPCASAASRTPASAWPDPWPAPAAAGPVRGTVRVPGSKSLTNRCLVL
+AAISAGPSVLHGVLRSRDTDLMRTALTALGARFEDRADGAVVVQPLPVGVPLEEPVAVDC
+GLAGTVMRFVPAVAALRPGTVVLDGDAGARVRPMAPLLDGLAQTGTRVEFLGAEGFLPVR
+LTTGEELGAEAAIDSSASSQFLSGLLLSAARRPAGLTLRHTGAQVPSPEHVAMTVQFLRE
+HGVHVDTLEEGAWRVHPGAPAGVESAVEPDLSNAGPFLAAAAVTGGEVSVPDWPAATTQI
+GDRWRSILPAFGAEVSFTPDPTDDARGTLTVRGGVDEAGRPRIAGAGELAGTAELAPTAA
+ALALLASGPTHLTGIGHLRGHETDRLAAIAAEAGRFGVRVEESADALAFPGSDSSGPLRP
+AEARTYHDHRMATFAAVVGLAVPGTAVQDVATTAKTLPDFPALWTALVGGEPAHDRPERD
+EVR
+>4_689
+MTRPTRAAAHSPAPRPDAAETWPAPVAHGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL
+HGVLDSRDAALMRTALTALGARFEALSDGGLRVHPMPVGEPVAGDVAVDCGLAGTVMRFV
+PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADATTV
+APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE
+VDVAETSPGAWTVAPGRVPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD
+RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGTPRITGAGEIADTAELAPTAAAL
+ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGVTVDEGETTLGFPGTDASGPLSPAA
+LETYHDHRMATFAAVVGLRVPGTGIVDVATTSKTMPDFPALWTALVAPGDAAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dad51f206d3f4379b3dc466dd6512a2c1c6df37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000666.fa
@@ -0,0 +1,30 @@
+>0_726
+MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR
+>1_465
+MSAALLTHASRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR
+>2_2128
+MTTALMARPDRDVDWRVMSTDNNLPEIARPADAPEHDRADIDVAAEDEQQRRARFERDAL
+EFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADSPEVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAERGIKAQPKKTGRG
+AAKKTETSTKEATR
+>3_2022
+MAATLLERPVLTGSRGAAVDWPAMSTQNSTPEIARPADAPALDLPGIDVDAESEAQRRAR
+FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN
+TYINLYRKKQRQPLEADTDTVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI
+PEEFRLAVYFADVEGYAYKEIAEILDIPIGTVMSRLHRGRKQLRERLTDYAGERGMGPKG
+RTAQETSTQEEKR
+>4_690
+MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL
+EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY
+RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL
+AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR
+GGTKQTETSTKEATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..268f0b97071067a664034c05755be76221c413bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000667.fa
@@ -0,0 +1,15 @@
+>0_727
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG
+>1_466
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
+>2_2127
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR
+>3_2021
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG
+>4_691
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..472fdcf27bab110bc2d2877cded3d64f3f7d32ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000670.fa
@@ -0,0 +1,50 @@
+>0_730
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPAVTLTLAELGGTDGAPDKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQQTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
+>1_469
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPVVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
+>2_2124
+MRFLTSPTVDLTYNDVFLVPSHSEVTSRLDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPVEVIAEVVRRVKSAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDADGGLLGVVRPRDCEDVDRFASAASVMQPASVTLTPAELGEAGGADGGQALRAAF
+DRLNAAGQDMAPVVEPAAGSAAPALRGVVTAAGLLRSSLFTPSLDDAGRLRVGAALGVNG
+AVGDKAAALVEAGVDVLVVDTAHGHQQSMLDALAAVRALDAPVPVVAGNVVSADGVRDLV
+EAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECSAAARDLGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLIDTITSGVRSSLTYAGAQDLAQFRERAVVGVQSA
+AGYEEGRPVASSW
+>3_2018
+MRLMHEPAVDLTYNDVFLVPSHSEVGSRTAVDIAPDDGTVGSVPLVSANMTAVTGRRMAE
+TLARRGGLGVLPQDVPVDVVAKTVAAVKAAHAVADTALTVDAHATVLDVLHLVDRRAHGA
+VCVVDDDGRLLGVAGAEDCGDVDRFASVVSVMRTPSVLLSPADLEGPDAPRAAFEVLHAA
+GRPLAPVVEDPVADRPVLRGVVTGQGLVRSSLAAPALDASGRLQVGAALGVNGDVGSRAA
+ALLAAGADVLVVDTAHGHQRVMRDALAAVRALDPEVPVVAGNVVTAEGVRDLVAAGADVV
+KVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAAREVGARVWADGGVKHPRDVALALAAGA
+SQVMIGSWFAGTLESPGDLVQGSDGRRYKESFGMASARAVEHRTRDEDAFSRARKAMFEE
+GISSSRMYVDPRRPSVEDLVDGITAGLRSSLTYAGAANLAQFRERAVVGVQSAAGYEEGR
+PVPASW
+>4_694
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCVGVDRFASATSVMHPPAVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..340f2ea91a8c8cb60f3f9603acdecb1803a6e192
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000671.fa
@@ -0,0 +1,45 @@
+>0_731
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>1_470
+MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
+>2_2123
+MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE
+LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD
+LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF
+PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR
+RVERVRFDPAAAADKEARA
+>3_2017
+MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE
+LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS
+PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE
+LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ
+LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL
+PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR
+RVDRVRFDPRPVTEEARA
+>4_695
+MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS
+ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE
+LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS
+PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD
+LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ
+LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF
+PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR
+RIERVRFDPAAEDEETRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f5b1564240aecfb616d9a97352ac2dc741ac804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000680.fa
@@ -0,0 +1,29 @@
+>0_743
+MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDPDAVAAFGDAEVEALLA
+DPGIIRNRRKIEAAVANAQAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA
+HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW
+RRGASGIWE
+>1_483
+MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDADAVAAFGDAEVEALLA
+DPGIIRNRRKIEAAIANAQAVVGMRGERFTPLHPGSPGAGPAWHGDGDRPARGLAGLVWA
+HQPAATPRPETVAQVPSASEESRALARALKAHGCRFVGPTTCFALMEAAGVVDTHLLGSW
+RRGASGIWE
+>2_2111
+MTKEHRTDHDAGDDAGPAAPVRSAAGAAEPPAGVVVGEDGRARAPWADRDPLLRAYYDEE
+WGVPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREAFAGFDPDAVAGFGPERVEELL
+QDAGIIRNRAKVEAAIANAQAVVGMRDEPWTPLHPGSPGAGPGWDGPGDRPDRGLAGLVW
+AHQPAATPRPGTVAEVPSASDESRALATALKARGCRFVGPTTCFALMEAAGIVDTHLLSS
+WRRGASGIWE
+>3_2006
+MDEENSEAAGLVLGADGRARAAWAAADPLLRDYYDAEWGLPVTDERGLFERLTLEAFQSG
+LSWRTVLAKRPRFREVFAGFDPDAVAAFGAVEVEALMADAGIIRNRRKIDAALANARAVV
+GIRDEVFAPLHPGSPGAGPAWDGEGDRPGTGLPGLVWAHQPAQTPTPRTIGEVPSASPES
+TALAKALKARGCRFVGPTTCFALLEAAGVVDTHLVSSWRRGASGIWA
+>4_707
+MSAHHADDGLPAPVSTPAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFWEVFAGFDADAVAAFGDAEVEALLS
+DPGIIRNRRKIEAAIANARAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA
+HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW
+RRGASGIWE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ccabffc6e51740f9116b8969bb9d245af9229a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000681.fa
@@ -0,0 +1,60 @@
+>0_744
+MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL
+TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE
+RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP
+ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE
+WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV
+PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV
+ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT
+LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA
+HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC
+SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG
+DAVLARD
+>1_484
+MSVSEHTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL
+TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE
+RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP
+ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE
+WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLCHV
+PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV
+ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT
+LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA
+HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC
+SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG
+DAVLARD
+>2_2110
+MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL
+TVYRTMGPGSVPEHGLPAQRAEWIRARGDVEEYEGRDRDLLDDGRSAVRRGAASQEWAGE
+RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP
+ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE
+WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV
+PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYEHYDELCEIFARYDVAFSLGDGLRPGSV
+ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT
+LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA
+HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC
+SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTLRGAAD
+A
+>3_2004
+MSASHHTPVPPQSEAVPTAEENYPTHRLGWLEDAEHGIRVPVTHVHQDDSPDGTPNPPFA
+VYRTMGPGSVPERGLPAQRAEWIAARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGER
+RPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDAELVRSEVAAGRAIIPANVNHPE
+SEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTREW
+ILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHVP
+LSADRVTGIVSRGGSIMAGWCLGHHRENFLYENYDELCEIFARYDVAFSLGDGLRPGSVA
+DANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYTL
+GPLVTDVAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAAH
+AADVAKGHPGARDRDDALSTARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFCS
+MCGPKFCSMRISQDIRSEFGGESEQARIAEAGMAAKSAEFRAAGGSVYLPEPSMRRPEGD
+AALAAD
+>4_711
+MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNPPL
+PVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE
+RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP
+ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE
+WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV
+PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV
+ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT
+LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPDRDDVKTGVITYKIAA
+HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC
+SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTIRTASD
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a97decbb74e0513b7a75ede607b928e9df84ebb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000685.fa
@@ -0,0 +1,40 @@
+>0_748
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>1_488
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>2_2106
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVGLLAVFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAAFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPAGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTCAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHARLKEIA
+>3_2000
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDALAPLLHAGWKGWPLLVDLLAGFSDVGTGFRTEGSWIVAADPSDVLAWEHVLAHAS
+ALGRRVEPVAVRALRRAEPALAPGLAAGFDAPDDHQVDPRRAAAACLAALVAEAGPDGGP
+LPAGAGPAARLVSGTVTSADPVGSGVGLTLADGGILTADGAVLAAGLGHRGIGGAATAEV
+PLRPVHGDVLRLRVRPEQLLPGEDHLITRTVRGLVHGRQVYLVPRADGTLVVGASAREDG
+LAGTSAGSVLDLLADAAAILPAVRECELAEVTTAARPGTPDDAPRVEVVPGAPVVVATGF
+HRHGILLAPWAAGRVLDLLTALPKETA
+>4_715
+MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ
+FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS
+ILGRRVEPVSVRALRRAEPALTPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP
+LPTGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE
+VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED
+GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT
+GFHRHGILLAPWAAGRILELLHAHLKEIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a910909ae2e9bb87a0acbdc7d166e0520e68a322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000686.fa
@@ -0,0 +1,15 @@
+>0_749
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGEDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRELAAGDEVDVVTAVQGG
+>1_489
+MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG
+>2_2105
+MSTLTLTLNGEPAELAAATVRDVVAHVTGRAIGDDGAAADARRLGVAVAVGGEVVPRSAW
+ATRELTAGDEVDVVTAVQGG
+>3_1999
+MSALPLTLNGEPAELDGPTVRDVVEHVTGRTVRDDGAAADGRRLGVAVAVDGEVVPRSAW
+AARTLAGGEAVEVVTAVQGG
+>4_716
+MSTLPLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW
+ATRALAAGDEVDVVTAVQGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98ac6bfc7de65417b55e3dc3841cb8d15ba9ffc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000696.fa
@@ -0,0 +1,34 @@
+>0_760
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>1_500
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD
+REA
+>2_2095
+MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA
+GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR
+PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG
+DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA
+TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA
+EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL
+LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG
+ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG
+PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA
+PAPTPAPDGDDAADRAGREA
+>3_1987
+MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG
+RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA
+LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP
+STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA
+>4_727
+MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK
+GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG
+TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES
+RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA
+DPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4133dea1b4eba9e69a7c85f3c69e105b49acd11c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000700.fa
@@ -0,0 +1,15 @@
+>0_764
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>1_504
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>2_2091
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
+>3_1983
+MEISGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIN
+>4_731
+MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI
+LGLVFAFVIGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7b400753e9d93ebbe986836bb9bf2cb2f329191
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000703.fa
@@ -0,0 +1,55 @@
+>0_767
+MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI
+EQDQVAQEQITKQKR
+>1_507
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
+>2_2088
+MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE
+NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID
+DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT
+AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA
+SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG
+DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL
+FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR
+QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG
+SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT
+KQKR
+>3_1980
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP
+SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG
+RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE
+REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI
+GQDQVVQEQITKQKR
+>4_734
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..041e8d6febb92118a050aa7f93dbb66b9b01b478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000706.fa
@@ -0,0 +1,15 @@
+>0_770
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQAHGGFFSVDHDRVVIAATSARLGDAAAA
+>1_510
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQARGGFFSVDHDRVVIAATSARLGDAAAA
+>2_2085
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRAVDGGTV
+TAQAHGGFFSVDHDRVVIAATSARLGDAAAA
+>3_1977
+MAELNVEIVSEEKSIWTGTASAVSARTINGEIGILPGHTPMLAVLGDGEVVVRATDGGTI
+TAQANGGFFSVDDDRVVIAAATAQLGGAAA
+>4_737
+MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV
+TAQARGGFFSVDHDRVVIAATSARLGDAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..421461aca23b1c01599f95aa7d1396ea756e08f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000711.fa
@@ -0,0 +1,34 @@
+>0_775
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRQLAAALF
+>1_515
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
+>2_2079
+MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA
+ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA
+VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA
+ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED
+RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF
+>3_1971
+MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ
+LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP
+AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP
+VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA
+AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS
+EDPRVHASRRRLAAALY
+>4_742
+MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL
+VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA
+GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA
+EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA
+AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT
+VVGTDDPRVQASRRRLAAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f55538d54097774040df4947fe0bd844c4e6ae5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000716.fa
@@ -0,0 +1,25 @@
+>0_781
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>1_522
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>2_2073
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR
+>3_1963
+MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV
+GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG
+FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD
+HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD
+>4_750
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2603043257d3253a224616fddf8aefdd18e0be59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000717.fa
@@ -0,0 +1,45 @@
+>0_782
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>1_523
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>2_2072
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED
+>3_1962
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED
+>4_751
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a94319538f0ae23de26d507e8cf9a09da7cc84c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000718.fa
@@ -0,0 +1,15 @@
+>0_783
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>1_524
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
+>2_2071
+MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED
+>3_1961
+MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ
+SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED
+>4_752
+MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY
+VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eba0c8e2b5ab823efe070246c0b1e47ebe08e9b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000722.fa
@@ -0,0 +1,30 @@
+>0_787
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
+>1_528
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+VQAETLAAATEDRA
+>2_2067
+MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK
+GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR
+IQAETLAGAAGSAEAQA
+>3_1957
+MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP
+RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG
+ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI
+IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA
+ELSRIQAETLAGDVAGRA
+>4_756
+MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK
+GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI
+VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV
+PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR
+IQAETLAAATEDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16aa0827ce76a10e1379e5936405c8a3dc91e630
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000726.fa
@@ -0,0 +1,40 @@
+>0_791
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAVELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA
+>1_532
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFAEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASEAEQDLLRDALEAARAAEVRA
+>2_2063
+MLLLHTSDWHLGRSFHGTGLLEGQRQVLDALVDTVRERGVDAVLLAGDVYDRALPSADAV
+ALLDATLARLREAGAQVVLTSGNHDSAVRLGFGAGLLSAAGVHVLTDPARLDEPVLLEDA
+AGERAAVYGVPYLEPRHLGQAWEVDPTHTGVMTEAVRRIRADLEDRRAGSPTPLAGVVLA
+HLFAAGGDASDSERDIGAGGSSWPASPAPADPAGRDAGCGAEPEGLVGTLGQVPVTVFDG
+LDYAALGHLHGRQTMAEHVRYSGSPLPYSFSEAKHVKGGWLVHVHGGAVTEVEPVDWRAG
+RRLAVLADRIGPLLDSPEYAFAENRWVQATVTDPERPEKALERLRSRFPHLLVFRHEPEG
+GRPERVRTYAQALRQAPTDLALTTGFVDHVRGRPASAEESALLDDALTASRTREAQA
+>3_1953
+MLLLHTSDWHLGRSFHGTGLLDSQRRVLAQLVDTVRERGVDAVLLAGDVYDRALPAADAV
+TLLDETLAALRAAGSQVVLTSGNHDSAIRLGFGSALMAAGGVHVRTDPERLAEPVLLEDA
+AGERAAVYGIPYLEPRHLGEAWGVDPHHTAVMTEAVRRVLADLEERRAADGPLAGVVLAH
+LFAAGAEGTESERDIGEGPHTDAHGTAPEGLVGTLGQVPVSVFSGLDYAALGHLHGRQTM
+APHVRYSGSPLPYSFSEARHTKGGWLVHVAGGAVTEVESVDWDAGRRLAVLEDRIQPLLD
+SPGYAWAEDRFVQATVTDPERPEKALERLRSRFPHLLVFRHEPEGGHAARERTYAQALRQ
+APDDLALTTGFVDHVRGRPASEAERELLDEALTASRIGEAQA
+>4_760
+MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV
+RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP
+GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA
+AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH
+GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI
+EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA
+QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00afa09a0a9774ae74d90f475c6b68781c1f3b32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000729.fa
@@ -0,0 +1,50 @@
+>0_794
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>1_535
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
+>2_2060
+MPTPSSATTHDVVLIGGGIMSATLGVLLQRLEPTWSIALYENLDQAGLESSDPWNNAGTG
+HAALCELNYAPLGKDGTVDVTKALGINEQFWTSRQFWSSLVKDGTLQDPKTFINPLPHMS
+FVWGDAHADYLRTRYEAMSAQPLFAQMEHTEDPATIAEWAPLLIEGREDAGRIAASRVVG
+GTDVDFGSLTRQLVTAMAGAGADVRFGHKVTGLSRGTDGRWEVSVKNKAAGTEVVDRARF
+VFVGAGGGALSLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNRHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSIRPHNLTTMLDVAKDNMDLT
+KYLVAEVVKSQNKKVESLKEFYPEAEGGDWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HGDGSIGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGALKELIPSLGRTLNDDPALL
+AEVSASTDAALKLA
+>3_1950
+MWIPPDGVRRCTILALEHQEHIVSTPTSTTHDVVLIGGGIMSATLGVMLQKLEPSWSIAL
+YENLDQSGLESSDPWNNAGTGHAALCELNYSPLGKDGKVDTAKAKGINEQFWITRQFWSS
+LVKDGTLADPKNFINPLPHMSFVVGDAHADYLKTRYEAMSAEPLFADMEHTEDPDVIGEW
+APLLMDGRTGTERLAASRVPTGTDVDFGSLTRQLVTALAAGGADVRFGHKVTGLSRGTDG
+RWDVTVKNKAAGTEVRDRARFVFVGAGGGALGLLQNSGIPEIKGFGGFPVSGQFLRCTDE
+KVVNQHMAKVYGQAAVGAPPMSVPHLDTRFVNGKRSLLFGPYAGFSTNFLKSGSYLDLPL
+SIRPHNLPTMLNVAKDNMDLTKYLVTEVLKSNEKKVDTLHEFYPAADGSEWELITAGQRV
+QVMKKKGKLGGVLQFGTEVVSHADGSIAGLLGASPGASTAAPIMVKLLERCFPAKMAGWD
+AALKDMIPTLGRTLNDDPSLLAEVRSATDAALQLG
+>4_763
+MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG
+HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS
+FVWGDDHADYLRTRYETMSAQPLFAGMEHSEDPEQIRAWAPLLIEGRASGQRLAASRNTG
+GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF
+VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM
+SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT
+KYLVTEVLKSRDKKIDALHEFYPEADGAEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT
+HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL
+DEVRTVTDAALKLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2b4fae2b3127ea41c8a07bf9836e93028f9ffac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000734.fa
@@ -0,0 +1,41 @@
+>0_800
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRT
+HGPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEV
+DALAAQLTALTALCAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEVGAGH
+LAMVTLAPELPGALDAVGRLAGAGVVVAIGHTDASYETTRAAIEAGARMATHLHNACRPT
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDSMAAAGCGDGE
+FPLGPLRVRVHDGVARVVGADGAAGAIAGSTATVTGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLHHGTWVKAAAPAAAD
+>1_541
+MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVTAVGAGDPPRT
+HGPVHELGDALLAPGCVDVHCHGGGGHAVESGPDAARAAAAAHARAGTTTVVASLVTDEV
+DALVAQLTALAPLRAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEAGAGS
+LAMVTLAPELPGALDAVGRLAEAGVLVAIGHTDASYEVTRAAIEAGARMATHLHNACRPA
+HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGD
+FSLGPLRARVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPA
+DALGLPDVGRLRAGSRADAVVFGPELEVRGVLRHGAWVEAAAPAAAD
+>2_2083
+MRPGGHARARRITPPLADHHVHGGAGVDLATSGAEDVRRWLAELRAAGASVVLGSLPALV
+PADLAAALERLRPLWEDGALAGVHLEGPFLSPARAGAQHPDALCAPDSAAGRRVRALLRA
+QPRGFVRTLTLAPELPGAREVAAELEAAGTVLCLGHTDAGPAEVAAALDWPRPRAAATPV
+ATHLFNGMRPFHHRDPGPVPTLLAAARRGRLRLELVADGAHVAPELMELILEDPDLAAQT
+CLVSDAIAATGAPCGTVHRLGPAVVHAAPDAPRLGEPAEDGQGSKATGPEDGGRAPLAGG
+RRTLVEAVTALLDADLDADAVLRAAVHVPRRSLPETPAPELEDGALVWDEGRPLVALPAA
+RA
+>3_1975
+MTASALLRTTAPWVGADPGATPVRVSAVWSAGPDGALLVWAGLAERVPQELWETAVDAPA
+LRLSPALTSHHVHGGAGVDLATSPAADVRSWLAAQRQAGVGAVVGSLPTLAEDALAAALD
+RLRPLWAEGLLAGVHLEGPFLSPARAGAHDPALLLTPPSPAGRRVRALIAAQPEGFVRTL
+TLAPELPGADALTRELTGTGVVVCPGHTDADGATTRAWLQTADDARAAATAAGLPAPTPV
+ATHLFNGMRGFHHRAPGPLPALLGAARAGRARLELIGDGVHVDDEVLTAILGDPGLAPAA
+CLVSDAVAATGATRGTAHRLGSLPIHAAQDGPRVGADEPTGPAEAALAGGAADLPEIVGR
+LLHSDLDPDAVLRAATHVPARTLGGSHAVPVGTPETTEHAAPGGDVLVWAPDGAVTVLRS
+QAAPGGRHHD
+>4_769
+MPASVPHRPRAEQAPQAAASPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRTH
+GPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEVD
+ALAAQLTALTPLCAEGVLAGVHLEGPWLSPRHRGAHRAASLRAPEPEDVARLVEVGAGHL
+AMVTLAPELPGALDAVGRLAEAGVVVAIGHTDASYETTRAAIDAGARMATHLHNACRPTH
+HREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGEF
+PLGPLRVQVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPAD
+ALGLPDVGRLRVGSRADAVVFGPELEVRGVLRHGTWVKAAAPAVAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d81d694676a938e12f6ce5450cca195728f4c798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000735.fa
@@ -0,0 +1,60 @@
+>0_801
+MSTTPRDARAAVPQVPTPASRPTESARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAVADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAERTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGDVKEIIPDLVAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>1_542
+MSTTPRDARAAVPQVPTPASRPTETARVQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLVREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGTEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGYDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>2_2047
+MSTTPRDARAAVPPVPTPASRPEEQARPQERRPAVRPDTVEPRVPGEGNRVKPTLMTGSE
+GIIRALEELGVTDVFGLPGGAILPTYDPLMDSDQIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGSDAFQEADIVGITMPITKH
+SRLVTRPEDIPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRVDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDA
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPCARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLAAELATDTEALPDLADWWAVLRRLQDTYPMGWTETEDGL
+LAPQEVISRISALSGPEAAYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
+>3_1945
+MSTTPRATAPAASAGRDQRGPTRTETVEPRVPGPAAVVEPTVMNGAQGIIRSLEELGVED
+VFGLPGGAILPTYDPLMDSSRIRHILVRHEQGAGHAAQGYHLAGGRVGVAIATSGPGATN
+LVTAIADAHMDSQSVVFITGQVSSAAIGSDAFQEADIVGITIPITKHSRLVTRAEDIPAA
+LAEAFHIASTGRPGPVLVDVTKDAQQSEFEFSWPPRLDLPGYRPVLRGHPRQIREAARLI
+REARRPVLYVGGGVARGEAHEELRALAALTGAPVVTTLTARGVFPDSHPQHLGMPGMHGG
+VPAVAALQQADLLITLGARFDDRVTGHLPSFAPGAKVIHADVDPAEISKNRLADVPIVGS
+VKEIIPDLVAELGAGADLPDLAPWWATLERLRETYPLGFTAPDDGLMAPQQVISRISALS
+GPEAVYVAGVGQHQMWASQFVEYERPRQWLNSAGLGTMGFSVPAAMGAKVAQPQRTVWAI
+DGDGCFQMTNQELATCVINGIPIKVAVINNSSLGMVRQWQTLFYDQRYSNTDLNTGHGTA
+RIPDFVKLADAYGAAGLRCEREEDLDDVIRQALEIEDRPVVVDFVVSRDAMVWPMVPAGV
+SNDAIQIARGMTPDWDHED
+>4_771
+MSTTPRDARAAVPQVPTPASRPTETARAQERRPAPRPEIVEPRVPGEGSRVEPTRMTGSE
+GIIRSLEELGVTDVFGLPGGAILPTYDPLMDSDRIRHILVRHEQGAGHAAQGYHLATGKV
+GVAIATSGPGATNLVTAIADAHMDSQAVVFITGQVSSAAIGTDAFQEADIVGITMPITKH
+SRLVTRPEDVPQALAEAFHIAATGRPGPVLVDVTKDAQQGEFEFAWPPRIDLPGYRPVLR
+GHPRQIREAARLIREARRPVLYVGGGVARGEAHEELRALAELTGAPVVTTLTARGVFPDS
+HPQHLGMPGMHGGVPAVAALQQADLLITLGARFDDRVTGHLPSFAPGARVIHADIDPAEI
+SKNRTADVPIVGHVKEIIPDLVAELATDTEALPDLADWWAVLRRLQETYPMGWTETEDGL
+LAPQEVISRLSALSGPEATYVAGVGQHQMWASQFVAYERPRQWLNSAGLGTMGFAVPAAM
+GAQVGEPDRVVWAIDGDGCFQMTNQELATCVINRIPIKIAVINNSSLGMVRQWQTLFYDG
+RYSNTDLNTGHDTARVPDFVKLADAYGAAGLRCDRREDLDDTIRQALAIDDRPVIVDFVV
+SRDAMVWPMVPAGVSNDAIQVARGMTPDWDQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b9a237e3d4f969a37ad74b9f0ec644cf0c397c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000741.fa
@@ -0,0 +1,40 @@
+>0_819
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH
+RLV
+>1_550
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
+>2_2040
+MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG
+PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF
+LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE
+LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE
+LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS
+GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH
+RLV
+>3_1939
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT
+GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH
+RLV
+>4_778
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..286c7c184cfbac1b5087bb2855efbc20356a7f67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000742.fa
@@ -0,0 +1,70 @@
+>0_820
+MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT
+LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI
+VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG
+AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH
+>1_551
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
+>2_2039
+MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML
+ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD
+RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG
+RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI
+FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG
+FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG
+SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV
+SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG
+GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV
+APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV
+VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA
+TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY
+VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH
+>3_1938
+MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR
+GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL
+FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL
+YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR
+GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT
+LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF
+KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI
+VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG
+AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR
+RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH
+>4_779
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e0629157184d322e8c21e3c6f753f142f2ae8b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000743.fa
@@ -0,0 +1,14 @@
+>0_821
+MVAPRTTPGGAPAAEASPARRTWQAARWWVRQLSGEGKYDAYVAHHRAHHPERAPMTERE
+FWRAEYARQEANPGSRCC
+>1_552
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC
+>2_2038
+MAASGTCPTPTGGSAAEPAAARRAGDGTGPAAGSGLRAAWASARWWVRQLAGEGKYDAYL
+AHHRAQHPGVEPMSEREFWRDEYAKQEANPGSRCC
+>3_1937
+MAGIWASTRWWVRQLTGEGKYDAYLAHHRAHHPGEVPMTEREFWRDEYARQDANPGSRCC
+>4_780
+MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV
+AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba86b788d6abfcbe9f80e785219de087bbcd68f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000751.fa
@@ -0,0 +1,25 @@
+>0_831
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>1_562
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
+>2_2028
+MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI
+DAYERARPSYKPTTLPARTAG
+>3_1921
+MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS
+AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV
+ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI
+AAYEAGRPSYKPTTLPARTAD
+>4_790
+MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS
+GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV
+ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI
+DAYEADRPAYKPTTLPARTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac0d9054094cccea07ed0184f430c4b414f49eec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000753.fa
@@ -0,0 +1,30 @@
+>0_833
+MSGVDAQSPAAAGGRPTRTARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH
+ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR
+EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR
+SLRVLPRKTARIRVGAPVDLADLRDRPVTAGTLREGTGRMMGAITDLVAELRGEPAPEGR
+WDPTAGARVAEA
+>1_564
+MSGVDAQSPAAAGGRPTRAARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH
+ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR
+EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR
+SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR
+WDPTTGARVTGA
+>2_2026
+MSTVDPQTPAPAAGRPSRAARAGYVIPAAIVRPALRGLVSQVWEGTENLPETGAILAVNH
+ISELDPLSVAHMVYNQGLLPTFLAKAELWKVPGFKQALQATRTIPVERSRDGGRSLAAAR
+EALATGRAIIVYPEGTVTRDPDGWPMAAQSGAVRLALQTGAPLIPVGQWGIQELLPYGGR
+APRPFPRKTARIRVGTPVDLDDLRGGPLTATALRAGTERMMDAITAIVADLRGEPAPAGR
+WDPRTGRREPGA
+>3_1919
+MNDGERPIAQPSRGLRRGFVAPAAVVRPALRALVRQEWLHAERIPRTGAILAVNHISELD
+PLSVAHMVYNQGLLPAVLAKAELWKVPVLRRVLQSTRMIPVERSRDGGRSLAAAQAALDE
+GRVIIVYPEGTVTRDPEGWPMSARSGAVRLALQTGAPLIPVGQWGMQELLPYPGFRLSPF
+PRKTARVLVGEPVDLDDLRGGPLTAAVLRVGTERMMDAVTELVAQLRGEPAPAWRWDLRT
+GRREGAA
+>4_792
+MSGVDAQSPAAAGGRPTRAARAAYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH
+ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR
+EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR
+SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR
+WDPTAGARVIGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f89c238b84394a6876f11ffdd186b4dea5708fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000754.fa
@@ -0,0 +1,36 @@
+>0_834
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>1_565
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>2_2025
+MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL
+PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER
+GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG
+PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV
+HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA
+>3_1918
+MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV
+WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE
+GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT
+ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN
+SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA
+DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK
+SEGRHA
+>4_793
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c06df00e1dc95b7debc184748006a933cf0e7f83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000757.fa
@@ -0,0 +1,39 @@
+>0_837
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRTGTLGETVAQ
+>1_568
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAEQAAEGAQGPVAPGADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPAAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSGTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRAGTLGEAVAQ
+>2_2022
+MALLAVGIAAAVYVGGIARTIDQDTQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAE
+QAAEGAQGPVAPDRDEKADEQALDVLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQV
+MSIMRDMWVPIPGHGDHKVNAAYQYGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDA
+LGGVSVDNPAAFVSTGGIDFPAGTVQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAI
+VAAFLSRDTLSDPSRVQAAVEEFAPFLTLDDELGSSTLANLAWSLRDARDAPIVTSTVPS
+VGVGYTDTGEDVVWPDWAAIARLGEGIRTGTLGEAVAP
+>3_1915
+MSTAEPTATPRRRRRPLLIVLVALLVLLLAAGLTAALWLGGLGRTVDEGVQRFEGQALPE
+ESLRPAEPGSAAAPGSAADGRNASGVYSPSAPPPGTAPAGVDPATALAGPAGPAADEVAD
+GKAVDFLLVGEDSGVEGRDPNGRSDTLMWVHIPGDRSAVQVRSIMRDTWVPIPGHGDHKV
+NAAYQYGQIPLTVATVENMFQARVDHVVAVDMAGFQGLVDALGGITVDNPIAFTADDGHA
+YPAGAIQMDGATALVYARERYNLPRGDFDRVENQQRVVKAVFSKALSLDTLSDPGRVQQA
+VERFSPFLTLDSELHSGDLAALAWSMRNLRGSDIQTSTVPAAGVGYSADGQAVVWPDWAA
+IHEIGRQIRTSEAR
+>4_796
+MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARIIDQD
+TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD
+VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ
+YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT
+VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA
+PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG
+EGIRTGTLGEAVAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdf9558e6aa18546d32164e58df5502688a4662f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000759.fa
@@ -0,0 +1,70 @@
+>0_839
+MAAEAPVTDLPLSEVLGGKLPARLERELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDVPLPGTAQAYRDLHAPNDVAATGPARTALALRE
+ALLVQAALAWRRNRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRIALVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
+>1_570
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPHDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRPGGLLEALDARLPFALTPGQVAVGEQLSAELARD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+GTLGAGDGPATRVALVTGSLKTTARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRSLP
+ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLRHVDVIADAPLIAVAADAVTRVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
+>2_2020
+MGAEVRVTDLPLSEVLDGRLPARLDKELGLATVGDLLDHVPRRWIERGELTPIAALPWDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPAADGAPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTAYRGRITLNNPDFALLDDDVAPGDVDVRPVPLYRATGKLPSWTVRSAVARVL
+ADVDLTRIPELLTPRLRAEAAAALDLDAPLPDTARAYRDLHAPEEVEATGPARTALALRE
+ALVVQAALAWRRDRERAVPAVPRPPRAGGLLDALDARLPFALTPGQAEVGEQLAAELTRD
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLALMGPLAEA
+GTLGAGDGPATKVVLVTGSLKTQARREALLALASGEAGIAVGTHALLSDKVGFAELALAV
+VDEQHRFGVDQREALRRSNPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVA
+THVARMDHGPRVIGRVWELIAEHAAAGRQAFVVCPRIDPDDADPGHANVEEMAPRLRSLP
+ALAGLRIEAVHGRMDQAEQDAAMQAFARGETDVLVATTVIEVGVDVPNATVMAVLDADDF
+GLSTLHQLRGRVGRGPDAAVCLLATRLPDEHPSLRRLEVLAQEQDGMRIAQEDLATRGVG
+DVLGAAQSGLASGLRHVDVLRDAPLIAVAADAVGRIMAEGPGLSAHPALAAEVARWESEH
+LTAADYLEKG
+>3_1913
+MAADGVLDLPLGEVLSGRLPGRLEKELGLATVGGLLDHVPRRWVERGELTPIAALPVDAE
+VTVVARVEHVATRRMRSRAGFIVDVTVADPSVAGTAGASLSMAFFNGHDAQRRLAPGVTA
+MFQGKTSLYRGAVTLNNPDFALLDDDVAPGEVDTRPVPIYRATGRMPSWTVRSAVRRVLE
+TVDLDAIPELLTEPIRARATLALGLPETLPGTAEAYRRLHAPDAVEQTGPARTALSLREA
+LVVQGALAWRRSREKAVPAVPRPRRAGGLLEALDARLPFELTPGQRAVGEELAAELSGPH
+PMSRLLQGDVGAGKTLVALRAMAQAVDAGGQAAFVAPTEVLAAQHHRALLALLGPLAREA
+GTLGAAAQEGPGTDVVLVTGSQRSAQRRAALLKLASGEAGIAVGTHALLAERVQFAELAL
+AVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRTP
+VATHVARMAHGPRVIARVWEVVAEHCAAGRQAFVVCPRIDPDDADPAHANVTEMAERLRA
+LPVLGGLRIGEVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAVLDAD
+DFGLSTLHQLRGRVGRGQDAAICLLATRLADGHPSLRRLEVLEATRDGMRIAQADLAQRG
+VGDVLGAAQSGLASGLTHVDVIGDADVIGVAADVVADLMAAAPGLSAHPALAAEVSRWEA
+AHLTAADYLEKG
+>4_798
+MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA
+EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT
+AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL
+ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE
+ALLVQAALAWRRDRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARE
+APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA
+CTLGAGDGPATRVVLVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV
+VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT
+THVAQMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP
+ALAGLRIDAVHGRMDQVEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF
+GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG
+DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH
+LTAADYLEKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f752568f6f97fe478033a6c7cf14badc8929a22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000760.fa
@@ -0,0 +1,25 @@
+>0_840
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>1_571
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI
+LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL
+YLWQDER
+>2_2019
+MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC
+EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI
+LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL
+YLWQDER
+>3_1912
+MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC
+EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI
+LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL
+YFWQDEG
+>4_799
+MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC
+EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI
+LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL
+YLWQDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40a636b929ca609d3821834719e500b415d4ec45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000762.fa
@@ -0,0 +1,20 @@
+>0_842
+MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS
+LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD
+ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA
+>1_573
+MRRAVCPGSFDPLHMGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS
+LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD
+ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA
+>2_2017
+MRRAVCPGSFDPLHKGHVEVIARAANLFDEVVVAVSVNPAKRYRFSTEERIAMIETTLSS
+LAGVTVRPMGLGLLAEFCREIGADAIVKGLRNGTDLEFEAPMAAMNRHLTGVETVYLPAD
+ARYTHLSSSLIKEVHGLGGDVAELVPAAVLRGLDGEP
+>3_1910
+MRRAVCPGSFDPLHKGHLEVIARAASMFDEVVVAVSDNPAKRYRFSTDERLELIRASVQG
+LAGVSAEAMGPGLLAEFCREIGAGVIVKGLRNGTDLEFEAPMAAMNRHLTGVETVFLTAD
+ARYTHLSSSLIKEVHGLGGDVREFVPAVVHARLEATRP
+>4_801
+MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSSNPAKTYRFSVDERIAMIEATVSS
+LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD
+ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45c021a92e04712399206363302de25aad193009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000764.fa
@@ -0,0 +1,25 @@
+>0_844
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>1_575
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>2_2015
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>3_1908
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR
+>4_803
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51982eb076d2948df4e6e28fe434c7b74dc320c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000765.fa
@@ -0,0 +1,15 @@
+>0_845
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>1_576
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>2_2014
+MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
+>3_1907
+MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK
+GRKVADA
+>4_804
+MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK
+GRKVADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a7a6380af1a80aa2a6687d9f44da16a37b05c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000769.fa
@@ -0,0 +1,40 @@
+>0_849
+MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERVLRRVAGR
+>1_580
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV
+RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG
+AGGRDWVRRHADLPAVARRYERLLRRVAGR
+>2_2010
+MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER
+ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG
+EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA
+>3_1903
+MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG
+EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR
+ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT
+LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA
+THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP
+SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA
+RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA
+>4_808
+MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER
+VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL
+WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG
+VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV
+RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT
+VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG
+EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000771.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9973376cb424dc7b41bef7ccc0d70dc87d6e9d1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000771.fa
@@ -0,0 +1,29 @@
+>0_862
+MSADPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEILERKQSELVRERIAWSGGERPTGITAL
+>1_593
+MSAEPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR
+GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG
+CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID
+EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR
+AVTRGYNLYARAMAQGRTEEAQEMLERKRSELVRERIAWTGGERPTGITAL
+>2_1999
+MSGSRPLDPAVVLDEAGMTYTVRSSDTGARRAGIGGMLRGVRGVRTDQVQALAPLSLIVD
+RGESVGIIGTNGSGKSTLMKLITGEIHPTTGRVYATSTPVMLGVNAALVRQISGEDNIRL
+GCLAMGMTTAEAAEKRDDVVRLAGLDDQALQLPLKAYSSGMASRLQFAIATSVDPDILLI
+DEALNTGDAQFRARTRARIDELRARAGCVFLVSHSLTTLKQMCSRVIWIEQGILTMDGNP
+EVVTGNYARYTRHRSNGADEVAERLLAEARAGVKRVAVRWAGGQRPSGVIAD
+>3_1896
+MTDTTVDYALVLDRVSMTYRVPSSAADSVAALPAWRRGLARALRQPPRVPVHALHEMTLG
+LEQGRTLGLVGRNGSGKSTLSQIIAGKLAPSTGRVLATATPMMLGVNAALVPAMSGRQNI
+VLGCLALGMAKDEVMAKTPEIAASTGLGEAIDLPIETYSSGMSARLRFAIATSRDPEVLV
+IDEALNVGDSQFRARAKERMQELKRKAGAVVLVSHDNKTILDSSNKVLWLDKGRPVMEGS
+PQRVMDRYEQYNEMLAAQKVDEARAFVEDLRTTYRPRVVLPATDMHLPSVQEVEFSPRHA
+L
+>4_813
+MPNLTGLDNIRIGLLAMGLTPAEVHDRIPQVAELADIGKSIRMPMRTYSSGMRARLRFAI
+SVASQPDIIMIDEALATGDDAFRERSNQAMRDLIARSGTGFLVNHSAGVIREMCTRVVWM
+DEGAIIEDGDTLDVMQHYSYFMSALRKHGEEKALEARARYETTEAERIVALKGTTGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dea48c0199bf8d29995e105f2825618ea16c2e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000775.fa
@@ -0,0 +1,40 @@
+>0_869
+MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG
+STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG
+KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL
+REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>1_597
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD
+>2_1997
+MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG
+STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG
+KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL
+REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>3_1894
+MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE
+ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA
+LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV
+AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR
+AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN
+LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG
+GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA
+>4_817
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b874d0c5d362975f0d32cded7aeaedfd979fd6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000781.fa
@@ -0,0 +1,29 @@
+>0_875
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
+>1_603
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTVDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
+>2_1991
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQAPADAGERPVLLVPTPSGERFSQGLARELAQREHVAIACGRYEG
+IDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNPASLVEESHED
+GLLEYPVYTKPADWRGREVPPVLLSGDHGKVAAWRRAQQEERTRARRPDLWEALGRDG
+>3_1888
+MRIDVVSIFPEYMAVLDVSLLGKARREGLVDVHVHDLRDVTTDRHRTVDDTPYGGGAGMV
+MKPEPWALSLEAVAAASPMAAPAKPILMVPTPSGTPFTQATARELAQAEHLAFACGRYEG
+IDERVFGWAEDLFDVRLFSLGDYVLNGGEVAALAVIEAVGRLVPGVVGNPESLVEESHED
+GLLEYPVYTKPSMWRDREVPPVLLSGDHGRIAAWRRDQQEERTRIRRPDLWAAHHAGSAA
+ED
+>4_823
+MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV
+MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH
+VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP
+ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL
+WAAYDSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5db55077591b5753aa2b29ad6ecffb1962724d4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000784.fa
@@ -0,0 +1,26 @@
+>0_878
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>1_606
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>2_1988
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS
+>3_1885
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP
+>4_826
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ac2983ac633a3d12e92fee780b71df41f3e655b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000785.fa
@@ -0,0 +1,30 @@
+>0_879
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>1_607
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
+>2_1987
+MTGSERAPRAGARTAVRAGLDVEAGLAAPFLAAGGTDRVLVAGMDEVGRGALAGPVVVGV
+CAAWLPAEGEIPAVRDSKALTDRRRRALVPEIRAWAAAVALGEANPAEIDALGISAALGL
+AGRRAWAAVCAAAGQEPVALVLDGRDDWLTRSDPDAGPAPAPRPVPPVPTMLVKAEDRCA
+TVAAASIAAKVARDDTMIALHADHPAYGWAGNKGYGAAAHRAAILDHGAGEHHRRSWSLG
+LPAAPADEPPTLFD
+>3_1884
+MSPRPPVVRAGLDVEASLAEAAIGPGASALVAGMDEVGRGALAGPVTVGVCAARVPALGV
+VPAVRDSKALTDRRRRALASEIEAWAAGVVLGEASPAEIDRLGITRALALAGCRAWAGLL
+AALGEEPVALILDGSDDWLRHARGGGMDDVVTGPVPPAPHMMVKAEDRCATVAAASIAAK
+VGRDDAMIALSAAHPAYGWAGNKGYGAAAHRSALVELGVTEHHRRSWNLGVPGTGAEPDV
+LF
+>4_827
+MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW
+LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR
+AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA
+ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA
+PAQAPPTLFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000786.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d29fab61b09ab1a48a650ad199597645fc50d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000786.fa
@@ -0,0 +1,15 @@
+>0_880
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>1_608
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>2_1986
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD
+>3_1883
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT
+LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR
+>4_828
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03d902f7299115b093af1918fa6206a7d28e1636
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000791.fa
@@ -0,0 +1,20 @@
+>0_885
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>1_613
+MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
+>2_1980
+MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY
+AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG
+>3_1878
+MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG
+SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY
+AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG
+>4_833
+MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG
+TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY
+AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc411f6d7074ede6fba710f40fd8c07cca39a22f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000794.fa
@@ -0,0 +1,35 @@
+>0_888
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>1_616
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
+>2_1977
+MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE
+TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS
+AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD
+IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP
+>3_1875
+MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE
+TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS
+AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS
+DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG
+PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP
+>4_836
+MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE
+TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS
+AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA
+DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG
+PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD
+IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9668e4cbb4e7ccf461cf9631ad049be6d4343464
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000800.fa
@@ -0,0 +1,30 @@
+>0_894
+MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
+>1_622
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR
+>2_1970
+MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF
+SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG
+ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA
+LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV
+DLPLPAPTPATGPVPVVAGPAPGEEPR
+>3_1868
+MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA
+PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY
+SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA
+LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE
+RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR
+>4_842
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..549349f983f55d642d97688d52206ced40d29556
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000804.fa
@@ -0,0 +1,35 @@
+>0_898
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>1_626
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>2_1966
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDEQYRRFMNQVP
+LFEKMLADDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
+>3_1861
+MELLQPDAPRENLREFIDNLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYEERLSR
+EEYEIEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHLNPRTARTVA
+LSKPTERELGQWYFQRYIQHFPTAGEIVLFDRSWYNRSGVERVMGFSTDHQYDLFMRQVP
+VFEKMLVEDGVHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIKSNDKKRARLNAMRYFLSRFEYEGKDHDVVGVPDPLIVQRGRD
+AVGD
+>4_847
+MELLQPDAPRENLREFIDKLRDGGYTVSDGHTNDPDLIDPQGRAVETWKEDYPYETRMTR
+EEYELEKYRLQIELLKLQYWGEDTGQRHIIVFEGRDAAGKGGTIKRFTEHMNPRTARVVA
+LNKPSDRELGQWYFQRYIQHFPTAGEIVLFDRSWYNRAGVERVMGFATDEQYRRFMNQVP
+LFEKMLVDDGIHLTKFWFSVTQTEQRTRFAIRQIDPVRQWKLSPMDLESLDRWEAYTEAK
+EAMFLHTDTDHAPWISIRSNDKKRARLNAMRYFLSQFEYEGKDHEVVGTPDPLIVRRGRD
+AVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4d77cda555a720366e97ed4c4d466bbe8dff602
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000806.fa
@@ -0,0 +1,25 @@
+>0_900
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK
+PLVDPAEYVDPALWI
+>1_628
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
+>2_1963
+MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS
+QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK
+PLVDPAEYVDPAMWI
+>3_1859
+MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS
+QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK
+PLVDPAEYVDPAMWI
+>4_849
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54be9cfe1c0ebd70ae9e5608aec74845ae9ec988
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000807.fa
@@ -0,0 +1,35 @@
+>0_901
+MARILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELSPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANVQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>1_629
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>2_1962
+MAHILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEASG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQQIVASTPNSIWAQQFANQANVQAHYTGTGPEIWDATEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTELYDD
+VYAASLEESIETSRTLATQEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
+>3_1858
+MAKILDNITQAVGGTPLVRLNSLTEGLPGDVAVKVEFYNPANSVKDRIGVAIVDAAEKSG
+QLTPGGTIVEGTSGNTGIALAMVGAARGYKVILTMPETMSAERRVMLRAFGAEIVLTPGA
+DGMRGAVERAQQIVRDTPNSIWAQQFANEANVRAHYTTTGPEIWDATGGAVDTFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPSDSPILSGGQAGPHKIQGIGANFVPEILDTELYDE
+VYAATFEESIATSRALGAREGILGGISTGAIVSAALKEAAKPESEGKLIVAVVCDFGERY
+ISTALFEDVRG
+>4_850
+MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG
+ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA
+DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT
+GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE
+VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY
+ISTALFEDIRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..129eb40bee87fe27c08ce1e4bdbc0efe202d1bfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000808.fa
@@ -0,0 +1,25 @@
+>0_902
+MTDFPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQENYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>1_630
+MTDSPRTEPLGASDAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTSHDPTSLNRQGADVGTQYRSAVFAHDE
+AETRFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>2_1961
+MTDSPRTEPLGASSAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSDGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>3_1857
+MSETPETPSTPAAHAPRVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGHTPDPDYEA
+VCTGQTGHAEAVRVRFDEAQVPAEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDEA
+EADFFRSQLARAQELYEAPIVTTIEPAAAWHPAEWYHQDFYASRPGNGYCRVVIDPKLAA
+VRRRHAAWLTDGA
+>4_851
+MTDSPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f421701c2eab73cbd18a6f8461160c592762115
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000809.fa
@@ -0,0 +1,35 @@
+>0_903
+MAGMTVSRPAVPASPEHALAPPTLGQVLEVVEGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAKGRLLHTLIEHRIALL
+AAHTNADAVVGGVSDVLARAVGVTGALSPLTASAAGTGAEGIGRVGDLPEETDLAAFARA
+VHAALPATAGGVRVAGGPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASEA
+RETAASGDGRPALVDVSHWASESLWLEHGARALEAALVERGLGVTTLFSDHRSDPWDFLV
+GGERADEGSRA
+>1_631
+MAGMTVSRPTVPASPEHALAPPTLGQVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRVAL
+LAAHTNADAVVGGVSDVLARAVGVIGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAAPGEGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>2_1960
+MDRMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRDLAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+FAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR
+VVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+ARETAVSGDGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
+>3_1856
+MTVPDHPLQGAGEGACGRAVATDAVASDVPRLSDVLAAVERLWPARLAESWDAVGPVVGR
+AGRPVRHVLWAVDPVQDVVDEAVRIGADLVVTHHPLMLRGTTSVAAVGHGGAFKGEVVHT
+LIEHGIALVAAHTNADSAVGGVSDAIAWRLGLTDVSPLQPSAGGSGAEGIGRVGELPAPV
+PLVEFARTVAALLPATAGGVRVAGDADLPVRRVAVCGGAGDSLFDAVRAADADVYVTSDL
+RHHPASEAREAARHAGGRPALVDTAHFAGEWLWLADGAAALAEELARGGHRARMTVSELV
+TDPWDLHLPSGLAERTTS
+>4_852
+MAGMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV
+LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL
+LAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGVEGIGRVGDLPEETDLAAFAR
+AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE
+AQETAVSGGGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL
+VGGERADEGSHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15486567c412d0aad4b4be7a79bb438fe141acd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000810.fa
@@ -0,0 +1,30 @@
+>0_904
+MSEVTAPPAVQARLLELQELDTALDQARAAVHRLQADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGPKELQAMQHEDDTLTALLDDHEAAA
+LEAMEATDAAESRLSKGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
+>1_632
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARALELEEALPGLEDA
+ARTADRAGAEATEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMETADAAESRLAKGHAALEQARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
+>2_1959
+MSEVTAPPAVQARLLELQELDTALDQARTQIRRLKADPELARLRARAQELEDALPEVEDA
+ARTADRAGAEASEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDGTLTALLDEHEGAA
+LEAMEAADEAESRLAAARQALEQARAEVDARAAEVRREGQVVTQRGRDLTQRRTALAAVF
+PAPLLALYEKARERNGGIGAARLVGRRSQASGTELSPADVARIEALPPAAVARCPESGAI
+LVRG
+>3_1855
+MNRVTAPAAEQARLLELQQLDLGIGRAKTRLAQLRADAALADLQKAVAAAEEAAAEQEAH
+ERETDAAAAQASERATTTRARRDRTRAHLDAGDGGSKELTALQHELEGLESLLAEHEGAA
+LAAMEAADEAEEALARARAAVDEARAAVAARADEVRAEGRRVTEEGRELAALRAGLAGRL
+PADLLARYEEARAANAGIGATRLEGRRTGAGTELSPADLDAVLATPADEVAVDPETGILI
+IRA
+>4_853
+MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARAQEFEEALPGLQDA
+ARTADRAGAEATEKAAATRARRDRTRERLETGQGGSKELQAMQHEDDTLTALLDDHEAAA
+LEAMEAADAAESRLAQGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF
+PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI
+LIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb0b32a86c81500daaaaae35fd5b2ccf36fd13bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000815.fa
@@ -0,0 +1,25 @@
+>0_909
+MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>1_637
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA
+>2_1953
+MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF
+TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA
+GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT
+WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA
+>3_1849
+MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF
+TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT
+GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT
+WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR
+>4_859
+MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF
+TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS
+GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT
+WLPGTDEDPFGHEEIEDHEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6961a4b3fdcd2a7b5296226d5e427a0305832b11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000816.fa
@@ -0,0 +1,15 @@
+>0_913
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFRRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>1_641
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
+>2_1948
+MSVVKINAITVPEGAGPELEKRFAVRKHAVDAEPGFEGFQLLRPTAGEDRYFVVTTWATE
+EDFQNWKGGRMPAAHAAESEGRPAPVATGAELLEFEVVDLD
+>3_1848
+MSVVKINAISVPEGAGPELEKRFAVRKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHADEQGGRPTPVATGADLLELEVVDLG
+>4_861
+MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFKGFQLLRPTAGEDRYFVVTTWASE
+EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1669beebdd7e1322fdb781b7672d3e5eca50fb91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000820.fa
@@ -0,0 +1,50 @@
+>0_925
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY
+PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>1_647
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH
+R
+>2_1887
+MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV
+AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV
+TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS
+SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN
+VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA
+STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL
+TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV
+LRHPDRAVSPTCTQYLQHR
+>3_1837
+MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA
+KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII
+MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV
+WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT
+SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL
+LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR
+VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE
+AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER
+VWSQGDVVVLHHPTRPVSATCTDYLRHR
+>4_871
+MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG
+VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA
+AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV
+TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS
+SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN
+VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY
+PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT
+WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..554c55475da902d433b35cc906189dc4d4f75e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000823.fa
@@ -0,0 +1,35 @@
+>0_928
+MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQALAAASRTVPAARPAHSL
+HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV
+AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVTPAIYVDPAAETENRNMVW
+MKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPGMSAASLDHAMWFHRPARV
+DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMVRLPEGAAARRARVRGAAQR
+MAMRTVLRRSWRR
+>1_650
+MPQRHPRPRPGRAPARPASAPKDPTDVLRGILELTPAAPDPVTGQVRFTGTTPRQTHGRV
+FGGQVLAQALAAASRTVPAARPAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA
+SQNEKAILALTCSFQEPAGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSR
+PFDIRHVTPAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQH
+GVAWIQPGMSAASLDHAMWFHRPARVDQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVAT
+VAQEGMVRLPEGAAARRARVRGAAQRMAMRTVLRRSWRR
+>2_1883
+MPQRHPAPRPGRAPARPASAPKDPTDMLRGILELNRADADPLTGQPRFTGTTPRQAHGRV
+FGGQVLAQALAAASRTISADRPVHSIHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA
+TQNEKAILALTCSFQEPAEAALDHQVAMPEGVPAPEDLPSTADVLGRINHPIAQEWAWAR
+PFDIRHVTPAIYVDPAPEAENRNMVWMKTFTPLADDPALHVAALTYASDYTLLEPVLRQH
+GVAWIQPGMSVASLDHAMWFHRPARADEWLLYVQHSPSAQGARGLGTGSVFTRDGTLVAT
+VAQEGMIRMPEGAAARRARLQGAAQRFALRTVLRRSWRR
+>3_1831
+MSPKPPARPATAPQDPTEALRGLLDLTDAGPDPVTGEPRFEGRTPAQVGPRVFGGQVLGQ
+ALAAASRTVPTARSAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAIL
+ALTCSFQEPTGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVT
+PAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPG
+MSVASLDHAMWFHRPARVDEWLLYVQDSPTAQGARGLGRGHVFTRDGELVATVAQEGMIR
+LPEGHAATAAKAKNVVQRAAMKTVLRRTWRG
+>4_874
+MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQSLAAASRTVPGARPAHSL
+HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV
+AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWARPFDIRHVTPALYVDPAPETENRNMVW
+MKTFTPLADDPALHRAALTYASDYTLLEPILRQHGVAWIQPGMSVASLDHAMWFHRPARV
+DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMIRLPEGAAARRARVRGAAQR
+MALRTVLRRSWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..861bea9b579b16961908ae5a20bb15b92283aaa9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000825.fa
@@ -0,0 +1,80 @@
+>0_931
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA
+>1_653
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
+>2_1880
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA
+>3_1827
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA
+>4_877
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8501c239abdcc2202da93773aaca1046e99864a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000828.fa
@@ -0,0 +1,47 @@
+>0_937
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA
+AEQA
+>1_660
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGADEAAEQA
+>2_1876
+MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG
+REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV
+KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP
+VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK
+AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE
+ASEQA
+>3_1822
+MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG
+REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE
+LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ
+VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE
+RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP
+ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG
+ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV
+DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA
+>4_880
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000829.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88ded0b548ce2cdf5086a12f9b46cffdd414e349
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000829.fa
@@ -0,0 +1,25 @@
+>0_938
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
+>1_661
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
+>2_1875
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAKEA
+LEYGFIDHIADRAASVTGGGGVQG
+>3_1821
+MTDLTPRMTSVEPTQREDYLYNQLLKNRIIWLGSDVRDDNANAICSQLLLLSAEDPEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGAPGKRYATPHARI
+LMHQPSGGIGGTESDIRIQAQLILHMKQIMAELTAAQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDRIAQSAASVTGGGGVEG
+>4_881
+MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI
+YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV
+LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA
+LEYGFIDHIADRAASVTGGGGVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..684bb1d76b088b9d1da52a86cd4bc74ada627879
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000830.fa
@@ -0,0 +1,25 @@
+>0_939
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>1_662
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
+>2_1874
+MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN
+RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG
+>3_1820
+MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS
+ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN
+RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA
+>4_882
+MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS
+ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA
+AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN
+RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a5fd12044c2742c9fb2b592fa936d58554ebaf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000831.fa
@@ -0,0 +1,45 @@
+>0_940
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>1_663
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
+>2_1873
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV
+LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE
+ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP
+AEVERRRRGRSA
+>3_1819
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE
+LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE
+ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP
+AEVERKRRRRTA
+>4_883
+MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV
+LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE
+VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA
+DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK
+HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE
+DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD
+ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP
+AEVERRRRGRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000846.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb8c9ae151f5135a8a027d1bf59f73a8db5741c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000846.fa
@@ -0,0 +1,20 @@
+>0_958
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>1_681
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>2_1855
+MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP
+FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN
+LVHGSDSSLSAERELGIWFG
+>3_1800
+MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP
+FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN
+LVHGSDSTLSAERELAIWFA
+>4_901
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3da577c6a2b318281bfd12ed417a0e4b30ab944
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000850.fa
@@ -0,0 +1,15 @@
+>0_962
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>1_685
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>2_1851
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
+>3_1778
+MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF
+ALSAGTVSFGQRRGRKVVDIVAAGE
+>4_905
+MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF
+ALSAGSVAFGQRRGRKVVDIVPAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000851.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09fac985395ce4de5e5543292e76e583be7cfcc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000851.fa
@@ -0,0 +1,50 @@
+>0_963
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>1_686
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
+>2_1850
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGNGGNGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHRAGKHGESLVIPVPDGTVVKDEQGNIVADLVGEGASYTAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAAIS
+AARPKIADYPFTTLVPNLGVVQAGEVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGTLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLVALNKTDLP
+DGAAMAEMVRAELEGRGLRVFDISALARDGLEALKYAMAGLVTEARERVPEPEPAAPVEV
+PRRHRRKGEHAEFTVRREERNLEPLFRIRGEKPERWVAQTDFQNDEAVGYLADRLQRVGV
+EDALFKAGATPGDAVVIGDDASGVLFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDQRRAARAATRAEMEAERRSGLWTETYDRED
+>3_1777
+MAAFVDRVVLHLTAGNGGHGCVSVKREKFKPLGGPDGGNGGNGGDITLVVDHQTTTLLNY
+HHAPHRSADNGQPGMGDHRAGRHGEDVVLPVPAGTVVKDADGNILADLVGEGASFVAAAG
+GQGGLGNAALSSVKRKAPGFALLGLPGEERELILEVKSVADIALVGYPSAGKSSLIAAIS
+AARPKVADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGKGLGLEFLRHVERCAAL
+VHVLDCATLDPERDPLSDFEAIEAELEAYAVEPVFSQGGAGVVPLNERPRLVALNKTDLP
+DGREMADLVRAQLEERGLRVFDISALAHDGLESLKFAMAGLVEEARAREPEPEEAPVVEV
+PRRRRRGDQADFTVRREERNLEPLFRIRGDKPEKWVAQTDFQNDEAIGYLADRLQRAGVE
+DALFKAGARPGDAVVIGDDATGVVFDWEPTLSAGAELLAGPRGSDLRLEERTRATRAEKR
+AEQDQRRAARAATRAEMEAERRSGLWTGDPVEEEELD
+>4_906
+MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY
+HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG
+GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS
+AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL
+VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP
+DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV
+PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV
+EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK
+RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93b280fea24eb8dc2a20508356ef3c5b341f96f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000855.fa
@@ -0,0 +1,25 @@
+>0_967
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>1_690
+MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
+>2_1846
+MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC
+RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP
+>3_1773
+MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK
+SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT
+GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR
+VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP
+>4_910
+MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP
+WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF
+FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC
+RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000856.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1f777061be229e906f1779bfbf040136afb6983
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000856.fa
@@ -0,0 +1,20 @@
+>0_968
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>1_691
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>2_1845
+MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA
+EEHTRPDAAGEGAADDAAPHAS
+>3_1771
+MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE
+EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP
+EEATRPDDALDAAAQD
+>4_911
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAAAQDDDASASHAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b009b34da1b8bcf4477c2c42cb4b4c1fb4a0748
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000861.fa
@@ -0,0 +1,33 @@
+>0_978
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA
+>1_701
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR
+>2_1832
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ
+>3_1723
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD
+>4_922
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba7f3054f37b529e6e5f2cbe3319bbc483f1cc3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000866.fa
@@ -0,0 +1,15 @@
+>0_983
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>1_707
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
+>2_1825
+MTVTVYTKPACVQCNATYRALDKKGIAYEIVDMSQDPAALERVRGLGFMQAPVVVTETDS
+WSGFRPDKIAELAEAAAASVA
+>3_1714
+MTVTVYTKPACVQCNATYRALDKKGIAYETVDMSQDPEALDRVRALGFMQAPVVITDTDS
+WSGFRPDKIAELAESAATQVA
+>4_927
+MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS
+WSGFRPDKIAELAESAAASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..327cd6dc84a4fa94988c4386eb4d6e6916d856df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000868.fa
@@ -0,0 +1,70 @@
+>0_985
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>1_709
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>2_1823
+MTLTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVQRVYGVPFSEISVTEKYYEMVDDARIKKTKINARE
+FFQTLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLTYSHI
+GQDISCNLGSMNIAKTMDSPDFGQSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGL
+GQMNLHGYLARERVHYGSEEGVDFTNMYFYAVLFHALRASNKIAIETGERFGGFEDSKYA
+SGEFFDKYTDQEWTPATERVAGLFSDAGITLPTQEDWRELKASVMEHGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
+>3_1712
+MTVTEADLIQQAKHMPEAWQDLGYHELNAMLNLYGSDGKIQFEADHAAARQYFLQHVNTN
+TVFFHDLEEKLEYLQEKHYYEPETFAQYAPEFVKATFDRAYKAKFRFPTFLGAFKFYTSY
+ALKTFDGKRYLERYEDRVAVVALHLAAGDEALATHLVDEMISGRFQPATPTFLNAGKAQR
+GELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNVREQGAPIKHIQNQSSGVL
+PVMKLLEDSFSYANQLGARQGAGAVYLHAHHPDIHRFLDTKRENADEKIRIKTLSLGVVI
+PDITFELAKRNEDMYLFSPYDVERVYGKAFSEISVTEKYYEMVDDARIKKTKINAREFFQ
+TLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHVGQD
+ISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGLGQM
+NLHGYLAREHVHYGSEEGVDFTNIYFYTVLFHALRASNLIAQETGQKFGGFEDSTYASGE
+FFAKYTEQEWTPATARVAELFETAGIDIPTQDDWRELQAKVMEHGLFNRNLQAVPPTGSI
+SYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDTYAA
+ATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGCVSC
+ML
+>4_929
+MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV
+NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY
+TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK
+KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS
+GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG
+VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKISARE
+FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV
+GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL
+GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA
+SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEYGIFNRNLQAVPPT
+GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT
+YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC
+VSCML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e6b7b948a12c8dea01c9c4e7ca2c37b85ca3968
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000870.fa
@@ -0,0 +1,30 @@
+>0_990
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLNGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>1_714
+MTDITSTPATSVAGDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVVLPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHAEQTLTLRSWPAEGGL
+>2_1815
+MTDISSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQEHNALDGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVVGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>3_1704
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQAHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+PWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
+>4_934
+MTDITSTPATSVADDPLAFYVRLGEPTVDADGVRTSRVRSTVHAQGAWREEEMHMAAVSG
+LLLHEVAAHETTPGLRVGRLSYDILGTLWSGELEVVTRTLRPGRTIELVESVLHARGRTV
+LTLRAWLLSTSDTSAVAQLPDEPLPPRSQAQSHNALHGWGGGYIASLDGVILPGHGPGHG
+RVWLTTDREMVAGESTSDLVRLISLTDAANGIAPALPAKPGGWFFPNVDLQIHLYREPTG
+HWLGLAGQVTVGPDGVGLTSTVLHDDDGPFAHVEQTLTLRSWPVEGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09d1c71aef2b6ec6192f48f5db76a323816e3c7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000872.fa
@@ -0,0 +1,25 @@
+>0_994
+MTILPASPPPSVILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPDGVIVAE
+GIFAERMPAALDRAEVHYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAMAAGFTPRRKREIIADLT
+>1_716
+MILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA
+>2_1813
+MILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG
+TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL
+DRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG
+FTPRRKREIIADLTA
+>3_1702
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA
+>4_936
+MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT
+PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE
+GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD
+AARRAAAVAAGFTPRRKREIIADLTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000874.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00667176b4fcabe036f66881374f895dcf26da6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000874.fa
@@ -0,0 +1,40 @@
+>0_996
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>1_718
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV
+KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLPEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>2_1811
+MPQKVRGVVARAKDAPVTLETIVIPDPGPGEAVVDVKTCGVCHTDLHYVQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAQELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETVALDEVNEAFETMKAGDVLRS
+VVVL
+>3_1700
+MSQKVRGVVAMAKDAPVSIETIVIPDPGPGEAVVDIKTCGVCHTDLHYVQGGIGDDYPYL
+LGHEATGVVSAIGEGVTHVEVGDTVILNWRAVCGECRACKKGEPKYCFNTHNASQKMTLE
+DGTELSPALGIGAFAEKTLVHAKQCTKVDGVDSTEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRALTGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
+>4_938
+MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL
+LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE
+DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV
+KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV
+EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR
+GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS
+VVVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3acc7e98b0af285d475cad080c37f535f3b4dff5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000878.fa
@@ -0,0 +1,109 @@
+>0_1004
+MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY
+LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>1_726
+MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK
+HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG
+GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA
+ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD
+GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR
+RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG
+TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL
+RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN
+AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE
+GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD
+PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI
+ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV
+LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE
+VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM
+VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD
+RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR
+GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT
+AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT
+GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY
+LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR
+PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR
+>2_1808
+MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK
+EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD
+VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC
+VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD
+LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP
+VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA
+VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL
+LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL
+DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE
+LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV
+TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA
+TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM
+GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA
+EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG
+ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL
+AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL
+VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR
+RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP
+RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG
+VPADRRPIPVPHPDTWELLPTPER
+>3_1694
+MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI
+TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL
+VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP
+AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA
+VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP
+ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD
+RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN
+GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD
+AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD
+LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL
+GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG
+KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF
+HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH
+AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP
+VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR
+LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS
+TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA
+HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG
+CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL
+DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE
+RPAPAPSSRPIPVPHPETWELLPTPES
+>4_945
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7f24f5a6530c2f69773449afe44964f7c491af0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000880.fa
@@ -0,0 +1,25 @@
+>0_1006
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA
+>1_728
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA
+>2_1805
+MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT
+CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA
+ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP
+>3_1692
+MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK
+GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD
+ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN
+FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA
+>4_947
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6efd6a3267355c9f6697c78f6939cc30b5709eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000882.fa
@@ -0,0 +1,20 @@
+>0_1008
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVRVTGAVVAEIAAG
+>1_730
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD
+>2_1801
+MAKTGRGRGRAHGAATPAVAALETAGVPYTLHTFEVDLDAGGERFGVQVARAMGVPPERM
+FKTLMVAAPDGGLAACVVPVSGQLDLRAAAAVLGVKRLALADLALVERRTGYVRGGVSPL
+GQRHRHPVLLDSSALDAPVMYVSGGQRGLDLELAPADLAAATDAVVAPIAAR
+>3_1690
+MGRRKAADAAHGAATPAIRALVDAGVPHRVLSFDVHLDAVGERFGVQAAKALGVPPERTF
+KTLMVALPDGSLAACCVPVSGQLDLRAAATALGVKKVAMADLAVAERRTGYVRGGISPLG
+QRQRHPVVVDSSALDGDVLYVSAGQRGRDLELAPADLVAVTDAVVAPIAAR
+>4_949
+MGQRKKDRSARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6006d1b53af39da87aff2a87f5033ec88e062c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000885.fa
@@ -0,0 +1,35 @@
+>0_1011
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
+>1_733
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
+>2_1798
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL
+GRGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVE
+YTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSNTL
+PGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEANF
+PDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFADRL
+YDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK
+>3_1687
+MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL
+GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF
+VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN
+TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA
+NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD
+RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK
+>4_952
+MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000896.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed611e8edfc2c581c821cc98bd8b26e5a5cca20d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000896.fa
@@ -0,0 +1,29 @@
+>0_1035
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADELTFLDVTASTSDR
+ATTYEVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDAVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
+>1_763
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
+>2_1786
+MVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTADRATTYDVVTRTAEEVFIP
+LTVGGGVRTEEDVDRLLRVGADKASVNTAAVARPELITEITRRFGSQVLVLSLDARRTQD
+PGCASGYEVTTHGGRRGTGIDAVAWCREASERGAGEILLNSIDADGTRNGFDLEMIRDVR
+AVTRVPLIASGGAGVPEHFPPAVEAGADAVLAASMFHFGPDDMLARVKDALRQAGHTVR
+>3_1672
+MTVAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELAARYGAQGADELTFLDVTATTGDR
+ATMFDVVTRAAEQIFIPLTVGGGVRSVEDVDRLLRTGADKASVNSAAVARPELIGEIARR
+FGNQVLVLSLDARRTRDPGCASGYEVTTHGGRKGTGIDAVAWCREATERGVGEILLNSID
+ADGTRDGFDLEMIRDVRAVTTVPLIASGGAGLPEHFPPAVDAGADAVLAASMFHFGPDDM
+IGQVKDALRAAGHVVR
+>4_984
+MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR
+ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR
+FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID
+ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM
+LARVKDALRQAGHTVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b465f52218defabed200e0e03bc9e648a8232b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000898.fa
@@ -0,0 +1,50 @@
+>0_1037
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>1_765
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>2_1783
+MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV
+WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA
+LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG
+AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA
+>3_1670
+MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW
+SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL
+PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI
+NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA
+AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP
+DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM
+LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG
+TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA
+GIVADSDADAETAETVTKATAPLRAVLTAAELRGA
+>4_986
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..044e33532d8d4c86dd27c8816e2cf0cfe828a14a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000901.fa
@@ -0,0 +1,30 @@
+>0_1040
+MSVLQEIIDGVREDLEPRRRALPEARLSELVAATPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>1_768
+MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>2_1780
+MSVLQEIIDGVREDLAPRRRDVPEARLAELVAAAPAPRDAHAALLGGRTDPAGIRVISEV
+KRSSPSKGALAEIPEPAALARAYERGGASAVSVLTEARRFGGSLADLDAVRGAVDLPVLR
+KDFTVTEYQIHEARAPGADLVLLIVAALDDAELTGFLQLTESLGMHALVEAHTPEEIERG
+VTAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESDEQIKAYAAAGADA
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>3_1667
+MPETVLDSIVAGVLEDLAPRREAVPEARLQELIAQAPAPRDAYAALRDGRSDPAGIHVIA
+EVKRRSPSKGALAEITEPAALAASYADGGAGAISVLTEQRRFGGSLADLDAVRAAVARPV
+LRKDFTVTEYQILEARAHGADLVLLIVASLDDARLRGFRELAESLGMHALVEAHTSEEIA
+RGVDSGARILGVNVRNLKTLDVDPDRYAALAGDLPEDVVRVAESGVESEAQVRQYAAAGA
+DAILVGEALVRHGAPADALRAFRAASLTVR
+>4_989
+MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04cf35a9a124decbd94982b3435a4c34089f8f9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000903.fa
@@ -0,0 +1,30 @@
+>0_1042
+MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP
+VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGALARELAAGAVREG
+>1_770
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
+>2_1778
+MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS
+VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALGEGGPQAVGALARELAAGAVREG
+>3_1665
+MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD
+VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD
+RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV
+ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA
+DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES
+>4_991
+MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP
+VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL
+AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS
+VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR
+ALTDGGPQAVGTLTRELAAGTVREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb66443250d941beed029ec8ed4757da04eb0257
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000905.fa
@@ -0,0 +1,135 @@
+>0_1044
+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
+>1_772
+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
+>2_1775
+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
+>3_1663
+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
+>4_993
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000907.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b96b186ae1e7734bd57579202dbf5fbf6e1899e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000907.fa
@@ -0,0 +1,50 @@
+>0_1046
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEESRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGTVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPLGFWPARSPL
+>1_774
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSDNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAIMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGGDAAGGSSAASP
+QTREPVGFWPARSPL
+>2_1773
+MRHAKIIATFGPATASDETTRSIIRAGADVVRLNMSHGDHEVHAASFERVRRLSVEERRP
+VAIFADLQGPKIRLGRFADGPHHLETGDRFTITTRDVEGTAELVGTTHAGLPGDVRPGDT
+LLVDDGKVRLRAVEVTDTDVVTEVEVGGDVSDSKGINLPGVAVDVPALSEKDEEDLRWAL
+RTGVDMVALSFVRDAADIERVHAIMDEEERRIPVIAKIEKPQAVDNLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGRYPVETVQTMARIIESTETHGLEMIHPLGSRPRTRGGAITRAAVE
+VADQLDIPFLATFTESGDSARRLSRLRPRQPIYAFTHREHTHNILCLTWGVYPKMVSFQD
+STDKMTLQVEESLTSEGIAERGDLVVIAAGSPPGMVGSTNTLRVHRVGDDAGGGSSPARP
+VQKEPVGFWPARSPL
+>3_1661
+MRHAKIIATFGPATQTDETTRALIRAGADVVRLNMSHGDHEVHASSYERVRRLSVEEKRP
+VAIFADLQGPKIRLARFSDGPHELAVGDRFTITTREVTGSREIVGTTHKGLPGDVSVGDP
+LLVDDGKVRLRAVEVTDTDVVTEVVVPGKVSDNKGINLPGVAVNVPALSEKDEEDLRWAL
+ETGVDMVALSFVRDAADVTRVHEVMDEVGRRIPVIAKIEKPQAVDNLEAIVDAFDAIMVA
+RGDLGVELPLEDVPIVQKRAIELARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVQTVETMARIIESTETHGLDMIHPLGSRPRTRGGAITRAAVE
+VAGQLDIPFLATFTESGDTARRLSRLRPSQPIYAFTHEEHTHNILCLTWGVYPKMVPFAD
+STDKMTMQVEESLTSEGIAEQGDLVVIAAGSPPGKVGSTNTLRVHRVGDGVAADSSPVAP
+EDREPVGFWAAHSPM
+>4_995
+MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP
+VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV
+LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSNNKGINLPGVAVNVPALSEKDERDLRWAL
+RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA
+RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL
+DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE
+VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD
+STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP
+QTREPVGFWPARSPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b1628dd11290baf91080ac1fb6f85884496579
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000910.fa
@@ -0,0 +1,20 @@
+>0_1049
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>1_777
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
+>2_1769
+MTIAITVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGRGDV
+ETQADALPQAFVLTAIVIAFAITVLLLTLAVTGRDDDAVADGHEAPDPLEQSAADARFPR
+EELRAAAARLGREAEARDGGRA
+>3_1658
+MTVALTVGLLMAGAVYLFSKRELLRVILGMVLLGHAANLAILATGGTDRRALPFVDGGPA
+PAGAADPLPQAFVLTAIVISFAVTVLLLVLAVTGRADDAVAAPGERPDVREAAAADARFP
+LAERHAAARTLTGSLPAAPEAGATPEREERA
+>4_998
+MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV
+EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR
+EERHAAAGRIAQHYAGQGPEVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000912.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4c2f22cd6a90887200b6aa207658141b66ef249
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000912.fa
@@ -0,0 +1,20 @@
+>0_1051
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>1_779
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>2_1767
+MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD
+QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG
+LYADDADALRGEIHDMERRLLHAMRKQGVA
+>3_1656
+MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA
+RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD
+ALRAEIHDMEARMLHAMRRTGVAR
+>4_1000
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000913.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b27b01f9a53c22873b5c75eedeaebff533e9b0cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000913.fa
@@ -0,0 +1,15 @@
+>0_1052
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
+>1_780
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
+>2_1766
+MPVDYDWSHLGIDVAVALLAVAALVSAYRIVKGPLDADRAVSGDLLTFSILGMLVLFGVR
+MDNPFTFDLVLVAAIVAFLSGMSLARALTRGKR
+>3_1655
+MSGLLQDYDWSLAGIDLAIALLLVAALVSAVRILRGPLDADRAVSGDLLTFSVLGMVVMF
+GVRAQNPFTFDLVLVAAIVAFLSGMSLARALTRGKR
+>4_1001
+MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV
+RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..984f593541a0ebbed07e3a64c0876cba85b6853d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000915.fa
@@ -0,0 +1,20 @@
+>0_1054
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>1_782
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>2_1764
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG
+>3_1653
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR
+>4_1003
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81aab3f76b899350e18671b2c38e6608b60c64ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000919.fa
@@ -0,0 +1,25 @@
+>0_1059
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>1_787
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>2_1758
+MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA
+RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG
+GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD
+AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD
+>3_1648
+MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR
+RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV
+VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT
+GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA
+>4_1008
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e7ff369c61da9c223fb674e86fd235cdf55e3ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000920.fa
@@ -0,0 +1,25 @@
+>0_1061
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>1_789
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
+>2_1755
+MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV
+QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA
+DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD
+>3_1646
+MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA
+VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV
+VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV
+ADVVIVNDGDLDRLREITRRVWEGMAA
+>4_1010
+MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV
+QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV
+QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA
+DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec6c1ee52be7a42bd87a1cae140512cce5b45b0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000923.fa
@@ -0,0 +1,30 @@
+>0_1064
+MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG
+GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA
+LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>1_792
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
+>2_1751
+MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG
+GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA
+LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME
+RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA
+LVWVGLGAPALS
+>3_1643
+MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL
+ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET
+ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ
+AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL
+AGG
+>4_1013
+MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG
+GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA
+LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME
+RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV
+VVWLALGLTAPGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f1bd9f115eb7c617f6ef9f887c60c150e7dd2d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000930.fa
@@ -0,0 +1,35 @@
+>0_1075
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFHSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIEMADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVSIGEAMTH
+>1_803
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAVV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPEVRSALAATAARRLMVLNLRTGDQETTGLAHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
+>2_1741
+MTSPLTGQLPLPPGVGTAVRGPAGGMARPAIRVTALGGGHGLSASLTALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVDAEEAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGG
+LRTRRVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALAAIELADWVVLGPGSLYTSVLP
+HLLMPEVCQALDATAARRLMVLNLRTGDQETTGLTHADHLRVLHSHAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTD
+>3_1633
+MTGPVTGPSTSSLPLPPAAARGAWATTSGTVRPQVRVTALGGGHGLSASLAALRLVAGHL
+TAVVTVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVPE
+AEATLDGHALGNLLIVALWELIGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDLLAED
+DAGRLVRRHVEGQVALAQAAHDGRVVDVRLSPADAPATPEALAAIELADWVVIGPGSLYT
+SVLPHLLMPEVRGALEVTTARRIFVLNIDTGTQETTGMTHADHLKVLREHAPGLQLDVVI
+ADADAVADRAAVVQEARRLGARVAFSRVAHAANRLAHDPLRLAVAIDEAMSS
+>4_1025
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08ef39d7202eab64e2112d88e72c39b80ffaa3b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000932.fa
@@ -0,0 +1,25 @@
+>0_1077
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>1_805
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>2_1739
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA
+>3_1631
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA
+>4_1027
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c070148bde1ebf8656a5f54757f79c256043fce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000934.fa
@@ -0,0 +1,40 @@
+>0_1079
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
+>1_807
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALADEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
+>2_1736
+MPAQTLNDLLEAGVAGRTVLIRSDLNVPLDGETVTDDGRIRASLPAIRQLADAGARVIVM
+AHLGRPKGEPDPKYSLRPVAARMGELLGADVALAEDVTGPSARAAAEALADGDVLLLENV
+RFDARETSKDDAERAELAAEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAGELEVLTRLTQSPERPYAVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVRAYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLPVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAETVFWNGPMGVFEFEAFAEGTRAVAQALTEATAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALSGEGEA
+>3_1629
+MTAQTLTDLLEAGVAGRTVLIRSDLNVPLDGQTVTDGGRIRASAPAIKDLADAGARVVVM
+AHLGRPQGEPDPQYSLAPVARRLGEVLGADVQLASDVTGEDARAKAAALQDGQVLLVENV
+RFDARETSKDAAERGELAREMADLAGEDGAYVGDAFGAVHRAHASVADIAGLLPAYQGPL
+VAAELQVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLMEKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLETVRGYLERSGKDGAAEIVLPTDIVMASAFAKDAEHEVLPVDALTTG
+AHGADALGLDIGPGSAAAFGERIRGARTVFWNGPMGVFEFPAFAEGTRAVAQALTEATQA
+GGLSVVGGGDSAAAVRSLGFTDEQFGHISTGGGASLEYLEGKELPGVSALSGTDT
+>4_1029
+MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM
+AHLGRPKGEPDPAYSLRPVAARMAELLGADVALAADVTGDDARAKAAALQDGQVLLLENV
+RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL
+VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG
+HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA
+HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG
+GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e819cdc8cbf518d88f399c2d5d9ba641aa6b186c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000937.fa
@@ -0,0 +1,35 @@
+>0_1082
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>1_810
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
+>2_1733
+MKIRMHDTTTSQVAKRITQLREKGGVVALGRVLTLVISTDDAGIEAAVEAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVA
+WWPGVPPAVPSETALGRLAHRRITDTASAARAEPALWTLRQGHRDGDTDLAWTRLTLWRI
+QVAGIFDTLDVAALRSVTVDGAPDSPSTMLLAAWLTLALKVPVTIAHSKAGHGIRAVRLR
+CQDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTDQDCLAEELRRLDPDEVFGAVLHRGL
+PRTDLSPVQASER
+>3_1626
+MKIRMHDTTTSQVAKRLTALRESAGVSALGRVLTLVIVTDDAGIEAALGAANAASLEHPC
+RIVVLALGDPLAPTRLDAEIRVGGDAGASDVVVLWCQGEDAVADEPLVSGLLLPDAPIVV
+WWPGEPPAEPATTALGRLAHRRITDSATCRDAKETLQRLAAGLHDGDTDLAWTRLTLWRS
+QVAAILDNLDLADVRSVTVDGAPDSPSTLLLAAWLTWGLDRPVTIAHSKAGHGIRAVRLR
+GPEGDVVLSRSQSEVARLYQQGRPVQRISLPRRSDQDCLAEELRRLDPDEVYGDVLRVGL
+PRTDLAPVDASDR
+>4_1032
+MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC
+RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV
+WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI
+QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR
+CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL
+PRTDLSPVQASER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15b764ad544494622a684c615d5d3b26228ef908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000942.fa
@@ -0,0 +1,35 @@
+>0_1087
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>1_815
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
+>2_1728
+MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL
+YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGEPLMRFGA
+>3_1621
+MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW
+TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW
+AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGGPLMPAVTGS
+>4_1037
+MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR
+GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW
+VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW
+AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL
+YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL
+SITYLTLLFIALAVDPFVGAPLMHFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000946.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8480ca11ecaabe116f6b832776421dfaa3ae756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000946.fa
@@ -0,0 +1,25 @@
+>0_1091
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>1_819
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
+>2_1724
+MVYSDLPSHRAAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDA
+LVEVKRVTSARGAGRPSRRYVVTSHAQEHLPKDHLAVALHSLARLEELGGDEEVRRTARR
+AFRDVEERFAAAVDGRDTELQERTRILASVLDDAGFAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPQFCEEETELFARLLQVDVRRLSTLAAGAHVCTTHVPLGRD
+>3_1617
+MYSDSADPAAPAPGTRERVLERVLSHGPVSAAEIGGALGLTAAAVRRHLDALEEEGFVEV
+KVVSAARGAGRPSRRYVVAPQAQRRLGGDHLGIALQAVDRLVEVGGEGEVRRLAADALQP
+VEEAFQAAVAGREMGLEERTRVLADLLDDAGYAASIRHVGAGLAPTLRAEQLCQGHCPLQ
+GLPARHPEFCEEETALFARLLGVDVRRLSTLAAGGHVCTTHIPLGRA
+>4_1041
+MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS
+LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH
+AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH
+CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9facd014feeec5863f6e436720f60581e18502dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000947.fa
@@ -0,0 +1,50 @@
+>0_1092
+MTDQIVQRDSTETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>1_820
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGSVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>2_1723
+MTDQIVQRDPVENADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRNLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYNSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVESGGTMEWVDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PNTSSSIVSKSVARNGGRAAYRGLVQVTEGAKNSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGLSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
+>3_1616
+MTDQIVQQDSRGADPGVISEILEKNPELNAIGAYQYGWADSDAAGSSARRGLNEDVVKDI
+SAKKSEPEWMTKLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWDDLPE
+DIRNTYERLGIPEAERDRLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPEI
+FEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERTL
+IIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKRA
+VVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEGATGETLSVAFAGKDQHQDTGSKMVHMAP
+NTNSSIVSKSVARNGGRAAYRGLVQVNEGARGAANSVVCDALLVDTVSRSDTYPYIDIRE
+DDVTLGHEATVSRVSEEQLFYLMSRGLAEDEAMAMIVRGFIEPIARELPMEYALELNKLI
+ELQMEGSVG
+>4_1042
+MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD
+ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP
+EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE
+IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT
+LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR
+AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA
+PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR
+EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL
+IELQMEGSVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0558c1d6baefacccd31707abe13fcbe54166e4f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000951.fa
@@ -0,0 +1,34 @@
+>0_1096
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP
+DIRQCDTFRAPSLDI
+>1_824
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
+>2_1718
+MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS
+TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG
+PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST
+GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI
+QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI
+>3_1612
+MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT
+GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI
+QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE
+EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG
+EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS
+QQSPDINQCNTFQAATLDI
+>4_1046
+MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV
+GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW
+RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI
+VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF
+LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP
+DIRQCDTFRASSLDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ba111220296f7dddd22da2ad14896785a10c787
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000952.fa
@@ -0,0 +1,50 @@
+>0_1097
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>1_825
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
+>2_1717
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA
+>3_1611
+MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV
+SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS
+RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM
+NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG
+VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA
+>4_1047
+MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR
+TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS
+RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM
+LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM
+TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG
+VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN
+GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT
+QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE
+ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98df113c038652e19a27a411d92b2e6c9133b780
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000955.fa
@@ -0,0 +1,30 @@
+>0_1102
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE
+LVGGAEDFLGQD
+>1_830
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
+>2_1713
+MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA
+VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF
+AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE
+LVGGARDFLARGEG
+>3_1606
+MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA
+VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF
+VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE
+LVGGAQDFLGQD
+>4_1052
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70c7ccd5f52d23d3e6b8f81e8f3c5a1c31ab69e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000957.fa
@@ -0,0 +1,30 @@
+>0_1104
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA
+GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR
+>1_832
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
+>2_1711
+MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL
+LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY
+GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL
+LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA
+GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ
+>3_1604
+MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP
+NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ
+DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL
+MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL
+ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA
+>4_1054
+MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL
+LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY
+GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL
+LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA
+GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a187cef8cf168da613dfc90d5325fbe5aec811c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000958.fa
@@ -0,0 +1,30 @@
+>0_1105
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>1_833
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
+>2_1710
+MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA
+IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV
+VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ
+GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM
+VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG
+>3_1603
+MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM
+GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL
+ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL
+VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA
+>4_1055
+MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA
+MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV
+VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ
+GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL
+VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000967.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea0ba7ce328c1f1507c589bad7aeaa86127269c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000967.fa
@@ -0,0 +1,31 @@
+>0_1117
+MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA
+VGSANPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETALRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP
+>1_845
+MQTTQLSAPPSLARLYARAARQAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVSAWRGA
+VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETPLRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP
+>2_1696
+MRTTELAAPPSLAGLYARAAGQAAKDALTRRSRPAVLPEREVVVTGHRIPRAAVAAWRDA
+VGPADPAALPSVLVHTQVFGAAMELMADPEFPLPLPGMVHLTNTVLHRRPVPAETALRVT
+ARAVGLVPHHAGTAVDVAVTVEGPHPAGGEAVLWEGVSRYLAKGVHLTGLRPERPAREEF
+TAPARTAEWRLGAGAGRRYADVSGDWNPIHLTGVSARLFGMKGAIAHGMLLAARMLQGRE
+PAAGGFRWEIEFDAPVVLPGTVAVRYEPADGQGTRVIGWDGRRCRRHFTGRIAPLAD
+>3_1592
+MHTRTESSMPALAGLYRRAAGQALADAARRRTRPAELPDERLVVEGHRIPERALRRWQAE
+IGPVDPASVPSVLVHTQVFGAAMALMAEPDFPLPLPGMVHLTNAVEHRRPVAAGEALDVT
+ARAVGLVPHHAGTAVDLQVAVREAGETDDAPAAWEGVSRYLARGVHLAPLRPERPERPEF
+TPPAPTAQWMFDGGAGRRYAEVSGDWNPIHLSALSARAFGQRRAIAHGMLLAARMLNRRE
+PRAAAFGEGFGWDVEFHAPVVLPARVAVRYEAAADGSTRVSAWDPRRGRPHLDGRIRHAR
+P
+>4_1067
+MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA
+VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVPAETALRVT
+ARAVGLVPHHAGTAVDVVVTVEGPGDDGGEALLWEGVSRYLAKGVHLSGLRPERPARPDF
+VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE
+PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVYGWDARRRRPHFSGEITPLES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bcdea2fa68df94a5916502df69cb8ab1c4f3091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000968.fa
@@ -0,0 +1,101 @@
+>0_1118
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>1_846
+MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV
+EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR
+LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA
+AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR
+RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV
+HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR
+VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV
+PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF
+RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV
+LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA
+QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA
+LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA
+SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR
+VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA
+DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE
+VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL
+RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE
+GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY
+AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV
+TAVPRRSPGLDA
+>2_1695
+MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL
+RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE
+RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD
+VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL
+GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV
+DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH
+SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE
+LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE
+SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL
+APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE
+LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP
+ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG
+EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG
+TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH
+SWEAYADGLLEAAAGLARRQDGA
+>3_1591
+MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL
+DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL
+VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV
+AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR
+RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV
+WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR
+RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD
+VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL
+GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE
+AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA
+DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL
+VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS
+VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV
+TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG
+AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA
+DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD
+ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL
+GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH
+AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV
+AGLPRP
+>4_1068
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d244dfc4d726f982c47768604e42012b6b6e788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000972.fa
@@ -0,0 +1,30 @@
+>0_1122
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>1_850
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>2_1690
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSASDPGAAFTAITQIGTELAVLIYF
+WRDITRIIGRWFQALAGRLPHSDPDVRMGWLIILGSLPIAVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQAKPLERLTVRDGVLYGFAQALALIPGVSRSGGTITAGLAM
+GYTRSAAARYAFLLAVPAVFASGFYKLFQSLAEPGTQGPYGMGETFLATVIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLGLFALLGTGVISA
+>3_1587
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSAADPGAAFTAITQLGTETAVLIYF
+WKDISRIISRWFQALAGKVPHSDPDVRMGWLIIIGSIPIGVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRKGRQTKPLEKLTLKDGIVYGFAQALALIPGVSRSGGTITAGLAM
+GYTREAAARYAFLLAVPAVFASGLYKVAKVVTEPGQAGPYGMGETILATAIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLVLFVLLGTGLIAA
+>4_1072
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4858303636939b22a1971a880e823578bb890f15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000973.fa
@@ -0,0 +1,45 @@
+>0_1123
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
+>1_851
+MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR
+LR
+>2_1689
+MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY
+VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE
+VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG
+QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE
+CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH
+AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL
+RLR
+>3_1586
+MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY
+VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN
+VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG
+SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE
+CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS
+KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH
+ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL
+R
+>4_1073
+MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY
+VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE
+VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG
+QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE
+CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS
+KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH
+AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ebf9cde69eb76119b7307970560f51c517d93a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000978.fa
@@ -0,0 +1,55 @@
+>0_1128
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>1_856
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+TARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPRDPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGGDTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VMEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>2_1684
+MDQDAQGGPEQLERRLGEARELLRQSQAEAERLRHQLDSAQRHAARLSERRREAEAQTQT
+AARNNRRMVELLETTRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLVPGAQVLLDESSAIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVELRHGDAVTVDSRVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVATAGSADAARATLIARTVAALYDRGTGTALAE
+LTDVSGTTRALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVVA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>3_1581
+MTEDDTQDRAGVLPAGDDARRLAEARELLRQSQAEAERLRHQLASAQRHGAQLSERRRAA
+QAQLDVAARNNRRMVELLEATRTEMTSLKEALDDTTKAPFTFARLEAVHAARAPREGVET
+GAVVRAGADVVQNGRRLRVAVSPLLDAAALTAGAEVLLDESSTIVGEVEHSVSGQLLRVK
+ESLPDGSLVLAGAADEERVVRRAPALAGEVLRHGDAVTVDPRLEWALARVELSEVDDVLL
+EEVPDVTFDDIGGLGPQIERIREAVEVPFLHPDLYREHGLRAPKGIMLYGPPGTGKTMLA
+KAVANALSARSAEGGRSFFLNIKGPELLNKYVGETERQIRIIFQRAREHAAAGSPVVVFF
+DEMESLFRTRGSGVSSDVETTIVPQLLAEIDGVESLDNVIVIGASNREDMIDPAVLRAGR
+LDVKIRVDRPDARGAVDIMARHLDEEVPLHVDEVRDAGSAEQAREELIGAAVTALYERSP
+RTALAELTDITGATSTLHLADLVSGAVVADVVDRAKRAAVRDLLAADLDPAARGLRTRHL
+LDAVDAVLADQADLLGTVAPGEWARTSGWRGPRLAELRMLPGAGGRP
+>4_1078
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEIATLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSVRSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVVAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000980.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bcd88241a521a8cc690cc16951570f72e758459
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000980.fa
@@ -0,0 +1,25 @@
+>0_1130
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTLEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGIVRTDVDRADRL
+VARADALLGRVRAAVTG
+>1_858
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVAG
+>2_1682
+MIRDESIEAYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEVLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPVARSRRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCIRGGLTAATVTLETNLGPLRDEGVEGILRTDVDRADRL
+VARADALLGRVRAAITG
+>3_1579
+MIRHETVEDHLTRLASGEPTPGGGATGALVVAQGAGLVAMAARFSGREEVAVECERVIRD
+SLAISDEDEEGFAAVADAYTLPKDGDAARARRSAAVQAALDQAVRPPRAIVDAVDRTVGL
+AERVLDDANPHVLSDVGAALGCARAGAGAAVVTLLTNLSPLHDEQLGAELRAEIARADEL
+TSRIDALAARVRERIAR
+>4_1080
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a9d5f3d64ac441c2f1c6e6921ccc12cd2cbf306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000983.fa
@@ -0,0 +1,45 @@
+>0_1133
+MTDADRARRIFGLETEYGVQHWNPEGRALSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMATDGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARTFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFGRIA
+>1_861
+MTDADRARRIFGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVEAAPPTTRARVRADFVSRAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA
+>2_1679
+MTDADRARRIFGLETEYGVQHWNPEGRPLSPEEVVRYLFRPVVEWGHSSNVFVSNGSRLY
+LDVGSHPEYATAECSTLDELIASDAAGDLILHDLVTRAQERMAADGISGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGDGAAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTSLSEHTHLLRFGATDL
+MLRMIEAGFPLGDRVLAHPTLAVRQISHDLTGTARVALRDGDASALELQEHYLERARAFV
+AAEGAHHERVEEILTLWEDVLEAVRTGDRSRIEDRIDWAIKLRMLEDYRARQNLDWGSAR
+LAQLDLAFHDIDPDRGLFRLLLRRGAAARLLPEDAGRLAVDAAPPTTRARVRADFIARAR
+QRGLGYAVDWTTLKLTDHPLHAIAAKDPFDASSDAVDRLFERIG
+>3_1576
+MTTDARRIFGLETEYGVQHWNPQARPLSPEEVVRYLFRPVLEWGRSSNVFVRNGSRLYLD
+VGSHPEYATAECSTLDELIASDAAGDLMLLDLIARAEEAMAADGIGGRIYLYRNNADSSG
+SSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVIPAGVWPEGEGRAHFAFSQR
+ADFVQEGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEATTLLRFGATDLML
+RMIEAGYPLGDHRVAHPTLAIRQISHDLTGTVRVNLREGTASALDLQDHYLSRARAFVAS
+EGAHHDRVEDVLDLWGTVVDAVRSQDFGPIEETIDWAIKLKLLRGYRDRYGLDWDAPRLA
+QLDLAFHDIAPGRGLFPLLRERGGVRRVLPEGAARAAVDAAPPSTRATVRAEFIARARAA
+GMDYAVDWTTLKLNDHPIHAISTKDPFSTDATPVDRLFERVG
+>4_1083
+MTDADRARRILGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY
+LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS
+SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS
+QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL
+LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV
+AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR
+LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR
+ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000984.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1865377b000b14ac8dab0b5462b958b5f814e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000984.fa
@@ -0,0 +1,20 @@
+>0_1135
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>1_863
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>2_1676
+MSFGQRDYDRTKPEIDFPGENPPAELVVEDLIAGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMQVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>3_1574
+MSFGQRDYDRTKPEIDFPGDTPPTELVVEDLIEGSGPAVEPGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGIGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
+>4_1085
+MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF
+DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET
+LIFVCDLVSVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a89b704777f73eba6f0b1352d5a92d0a8a75bb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000987.fa
@@ -0,0 +1,30 @@
+>0_1138
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
+>1_866
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI
+>2_1673
+MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA
+ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK
+AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY
+LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP
+LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI
+>3_1571
+MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP
+VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG
+LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI
+TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL
+AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL
+>4_1088
+MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM
+AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK
+KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL
+YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI
+PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..294138f5b3c68f75b5dfc7d28d20af30da46344b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000988.fa
@@ -0,0 +1,90 @@
+>0_1139
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR
+RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM
+SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL
+VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>1_867
+MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLARVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHIMAGGRLYDLFAE
+DIAFEDAADRDGEALLNPELKRLGEEAERRFQRADWGRPGRQQHRDGRGGGTKGRARGGR
+HTGRDGGRGRTGSSALDRERPVSGRPGGHDGGPRRGPRLSTSRPEMIRVLDRDGLLPCIT
+FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS
+RGFAAHHAGMLPPFKEAVEDLFTAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH
+VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVARLASRRTYPLRSSFRPTYNM
+SANLLAQVGAEQARGILESSFAQFQADRSVVGLARELRSKQASLEKYEEAMQCHLGDFAE
+YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRSLGRAVVVFPAGNP
+QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG
+RPPAGGRSTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV
+LRERIAGRTNTIARTFDRVVGLLRAYGYVHEDAPSPRAALTERGEALRRIYGERDLFTSL
+VLQDPAMDGLTPEEWAAVAALLVYQGKGETEPGLVPMPTPRLARVAEAAERIEERLRTDE
+AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP
+GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED
+>2_1672
+MSHAPASATPPEEPQLSPAERFARAKAARHHAGSELGRFASRLGFPLDDFQRRACAEVED
+GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLSRVHGAENVGL
+LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE
+DIAFEDTADRDGEALLNPELKRLGQEAERRSERPDWGRPGRHRGRGGRDGGQRGRGGRGG
+DGRKGGRDADRRGRHGSHAMDREQPATGRVRGQEDGERRGPRLSTSRPEMIRALDREGLL
+PCITFIFSRTGCDAAVEQCLRAGLDLTTAHEKALVAERVEQAARLLPVEDLEILGYWAWR
+DGLSRGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFN
+GENHVDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLKSSFRP
+TYNMSANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEKAMQCHLG
+DFSEYLALRKELASAEKSGSQGRRRAQLAAVKESLADLAVGDVVELDAGRSLGRAVVVFP
+AGNPQNPRVGVVTDKAQLRRITVDDVTGPVEPVAGAALPQVLQVKTPTQRKDVAALMREA
+VRTGRPPAGGGRRTSGFRLREDPAAPRVEELRRALQRHPCHACQDREEHARWGDRWWGMR
+REVSVLRERIAGRTNTIARTFDRVVGLLRSYGYVHEDASSPRQALTARGEALRRIYGERD
+LFTSLVLQDPTVQGLTPEEWAAVAALLVYQGKGEAGHGVVPMPTARLAEVADAAERIEER
+LRADEAQARLEPTPPTDPGLVGPMHRWVRGASLRRTLEGADLAAGDFVRWARQVIDVLDQ
+LANVPGDARRSRACRKAADLVSRGVVATSLPAATAREADED
+>3_1570
+MAPHTHHDLPPEEPALSPAERFARSRASASRPGTELSRFAARLGFPLDEFQLEACREVEA
+GHGVLVAAPTGAGKTVVGEFAVHLGLARGRKAFYTTPIKALSNQKYADLAAVHGADRVGL
+LTGDTSVNPDAPVLVMTTEVLRNMLYADSEALTDLGFVVMDEVHYLADRFRGPVWEEVII
+HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVVVSEHRPVPLWQHVMAGGRLYDLFAE
+DVAFEAAADADGTPLLNPELQRMAQEASRRVERPDWGRTGHRGRGRGGPGGRGAGRGRGK
+GGPRGGREGASSGWDRERPHRADASPGDGERRALGLSTSRPEMIRALDREGLLPCITFIF
+SRAGCDGAVEQCLRAGLDLTDRREKALIAERVEQAAAALPPEDLEILGFWAWRDGLSRGF
+AAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGVNMPARSVVLEKLVKFNGESHVDV
+TPGEYTQLTGRAGRRGIDVEGHAVVLWRPGLDPSAVAALASRRTYPLRSSFRPTYNMSVN
+LLAQVGAERARGILESSFAQFQADRSVVGLAREVRAKQSSLEKYADAMACDRGDFAEYLS
+LRKELAAAEKSGSRGRRREHLRAVKESLADLAVGDVVELHDGRALGRVVVVAAAGNPQNP
+RVAVVTDKAQLRKVAVEDLVDPVEPVAGAALPQTVQVKTPSQRKDVAAAMREAVRAHRPP
+TGGTRRGTGFRLREEVASPRLEELRRALQAHPCHACPDREDHARWGERWWDMRREVSLLR
+ERIAGRTNTIARTFDRVVELLGRLGYVGDDPDAPSRALTERGQTLRRIYGERDLLTSLVL
+HDPSTRSLTPEEWACVAALLVYQGKGDTQGLPVAMPTARLQALAEAVDRIEGGLREDETA
+ARLEPTPPTDPGLVAPLHRWVRGASLRDSLHGADLAPGDFVRWARQVIDVLGQIAQVPGD
+ARRTRACRKAADLVGRGVVAASLPAAAAGADGVEGEEPDRVDR
+>4_1089
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..050c970fdc9cb3060126a077df73133365e46c2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000990.fa
@@ -0,0 +1,30 @@
+>0_1141
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>1_869
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
+>2_1670
+MRVLTIIPTYNEIESLPLTLGRLRDAVPTSDVLVVDDASPDGTGQWADARAAQDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLDAVRTADLVIGSRRV
+PGGKMVNWPASRKMISWAGSLYPRIMLGLRLTDVTAGYRAYRAETLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRSR
+LGL
+>3_1568
+MRVLTIIPTYNEIESLPLTLGRLRDAVPDSDVLVVDDASPDGTGAWADARAAEDDHVHVL
+HRAEKNGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPASRKLISAAGSLYPRIMLGLKLTDITAGYRAYRADTLRRIDLGAVQSKGYG
+FQVDMTFRVARLGLRIVEVPITFVERELGESKMSGGIVGEAVVNVTKWGLQARWETLTGR
+GPQRG
+>4_1091
+MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL
+HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV
+PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG
+FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR
+LGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57a4dced62d68ced4854b5bddeafc42e694ab204
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000992.fa
@@ -0,0 +1,40 @@
+>0_1143
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>1_871
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR
+RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
+>2_1668
+METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG
+ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE
+ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH
+>3_1566
+MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT
+SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD
+EALQTPPEAEPAPVRREPGMP
+>4_1093
+METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM
+VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN
+VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA
+ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS
+GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR
+RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS
+LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1614ded00b4a1abffb2cdfbcd09f8c81baa1ea34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000995.fa
@@ -0,0 +1,25 @@
+>0_1146
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR
+LT
+>1_874
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL
+YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
+>2_1665
+MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL
+YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH
+DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR
+LA
+>3_1563
+MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD
+DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV
+LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL
+VVARLV
+>4_1096
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eb5b9705e2b1642d74d557edb16e4ceb60f2906
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001000.fa
@@ -0,0 +1,25 @@
+>0_1151
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>1_880
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>2_1659
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>3_1555
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT
+AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA
+ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>4_1105
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..782633ae15458caf218a5156a5b38ca1fb12f1e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001002.fa
@@ -0,0 +1,35 @@
+>0_1153
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>1_882
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>2_1657
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>3_1553
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>4_1107
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2250b0c4964af930577f8eff86ab6ae51ed38001
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001005.fa
@@ -0,0 +1,55 @@
+>0_1157
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWYAYAPLSNTTFSPGVGGDLWVFGLALQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILILMAFPPLAAALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGIVSEIIPVFSRKPIFGYKSIVFA
+TTAIGALSFSVWAHHMYVTGSVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFENPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQLNDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVTGMPRRYADYMVEDSFHAMNAFSSV
+FSFVLGASLIPFFWNVYITARYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ
+>1_885
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFVFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDSFQAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGASLEWTTSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQNTSEAFGEKVAQ
+>2_1653
+MTTYEYATDEVRSQAQPRVVPRSLGKIAVSWLTTTDHKVLGYMYLIVSFMFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFILGASLIPFFWNVYVTARYGKKVTVDDPWGFGASLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTPEAFGEKVAQ
+>3_1550
+MTTYEYATDEVRTQAQPRVAPRSLGKIVVSWLTTTDHKVLGYMYLIVSFVFFCVGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVAFP
+RLNALAFWFFLFGSFIACAGFLTPQGAASFGWFAYAPLSDTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA
+TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV
+FSFLLGASLIPFFWNVYVTTRFGKRVTVDDPWGFGSSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELAAYSPQAEPEVFGEKVASK
+>4_1114
+MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL
+MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP
+RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG
+FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR
+FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA
+TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM
+LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP
+KFTGKMLNERLGKIQFWLLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDTFTAMNAFSSV
+FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE
+RPALDLHHPELFPHSPQHTTEAFGEKVAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dd5334cadb8e876d6365e03beeafd597d1ec8d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001010.fa
@@ -0,0 +1,40 @@
+>0_1162
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPTRPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLAQGYTAFLYEGPF
+WAGRITAGLARSLRG
+>1_890
+MQLPDPKSAVDGILTSRAPRLYPPFFRAVFGGMDAERAHHRGFDAIRLAERTGASAALRA
+AFRPDPMLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADADVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRTTAGLARSLRG
+>2_1648
+MQLPDPKAAVDGVLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLAERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKEGRGTAALADLGFGHIEVGTITAQAQPGNPQ
+PRLFRLVEDRALVNRMGFNNDGAAAVAPRLARTRAVLERRFGAVRPVLGVNIGKTKVVAL
+EDAAEDYRASTRLLTPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRVVTGR
+RVPLTVKIAPDLTDEDVRAVAALAERLGLDGVIATNTTISREGLATPRADVDALGAGGLS
+GAPLKERSTEVLRVLRAALPVGTAVISVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRISAGLACALRG
+>3_1545
+MQLPDPRFRVQSVLRSSAPRIYPPFFRAVFAGMDPERAHHVGFAGIRAAEASGASRALRS
+TMAPDLGLARTVMGLRFPSPFGLAAGFDKTGVGTTALAELGFGHIEVGTITAQAQPGNPA
+PRLFRLPEDRALINRMGFNNDGAAAVAPRLAATRRTLEERFGAVRPVLGVNIGKTKVVPL
+DGAVEDYRASARLLAPHADYLTVNVSSPNTPGLRQLQEISSLEPILAAVREEADRAVPDR
+RVPLTVKIAPDLADEDVRAVAELAGRIGLDGVIATNTTIGRGGLSTPASEVEAMGAGGLS
+GAPLAARSLEVLRTLRAALPAGVALIAVGGVTDGDDVLQRLDAGADLVQGYTAFLYEGPF
+WAGRINAGLDAAQRAR
+>4_1119
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIWLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPDR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLEVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRITAGLARSLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aaac3aac76b124c3498c8dab021d70301c96eac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001012.fa
@@ -0,0 +1,35 @@
+>0_1164
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
+>1_892
+MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA
+>2_1646
+MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT
+SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER
+IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP
+GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV
+AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV
+PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR
+SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT
+TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV
+DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT
+AQPAPSSGAPDSASDADGGA
+>3_1543
+MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL
+DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG
+RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD
+LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP
+DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD
+>4_1121
+MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL
+LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN
+GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG
+EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP
+DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e565c7b93ba65ffb3d4716a1355f4fe3b4df84d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001013.fa
@@ -0,0 +1,55 @@
+>0_1166
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>1_894
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
+>2_1645
+MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI
+TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA
+>3_1541
+MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP
+ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE
+RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT
+YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR
+NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF
+SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA
+DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR
+AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA
+FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV
+EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA
+>4_1123
+MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG
+PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI
+ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI
+TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH
+RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL
+YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME
+VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR
+RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG
+AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY
+VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd48ae7012f41b7ff755d75bbd8745dcb8b946bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001016.fa
@@ -0,0 +1,20 @@
+>0_1169
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
+>1_897
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
+>2_1642
+MAVEILNESGIEVPEDELLRMARHVYASLHVHERTETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGTAEAPAEGMLGDVVLCPEVAAEQAARGGHGRDDELMLLLTHGMLHL
+LGYDHMDDADRLEMFALQDRLVSEVLGRPAPAPTIED
+>3_1538
+MAVEIVNESGVEVPEEALLGMARHVYAALHVHPLAETAVTVVDAQRMAELHVEWMDLEGP
+TDVMSLPMDELTPGTEKSPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHMEEDERAEMFALQDRLVSEVLGRPAPAPTVED
+>4_1126
+MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP
+TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL
+LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..782f3e87795b0548876e23ae55f26b5a7de01152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001020.fa
@@ -0,0 +1,35 @@
+>0_1173
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>1_901
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>2_1638
+MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ
+VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL
+LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA
+RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT
+>3_1534
+MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ
+VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV
+LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA
+RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG
+PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT
+>4_1131
+MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH
+TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ
+VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL
+LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA
+RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG
+PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..743d2e2f7872367ee4dd6b87cfc31362dc38a5b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001021.fa
@@ -0,0 +1,30 @@
+>0_1174
+MDWSSWGPAGHDDLTRRPARTVPDVPAAPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>1_902
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVSGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVFGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
+>2_1637
+MDWSSWGPAGHEEMTRRPGRPARDVPAAPGTVVEDVASGFTGAVIRVERAGGVHTVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPHVASAPRPPARTASGSRRVEGVRARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIAAFDPGPRRRLGILVDHLVPGSKE
+ERIAAEAMRVPGAAGNVLILGHPYVDVWQVIKPAVLGIPTWPVVPKGQDWKTGVLQGLGW
+PHGTKEATGLGWKRLLSHVGSYADLEPSLLGRVEELIDFLTAEPER
+>3_1533
+MDWSSWGPGAHEDLARPAGRTAGEAPATPGTVVEDVASGFVGAVVRVERSGGTHVVVLED
+RRGVRRGFPLGPGFWVDGSPVVLVPPRSAAPAAAARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLPGAIRDFAPGPGRRLGILVDHLVAGSKE
+ERLAAEAMAVPGAAGNVLILGHPYVDVWQVIKPAVLGIDAWPVVPRGQDWKTGVLRGLGW
+PAGTKEATGLGWKRLLSHVRTYADLEPALLGRVEELIDFLTAPGA
+>4_1132
+MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVIGIERSGGVHVVVLED
+RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE
+GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPWRRLGILVDHLVTGSKE
+ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW
+PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f107d5a44c04521aff2d1aedf21e8727e8acf8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001023.fa
@@ -0,0 +1,60 @@
+>0_1177
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG
+VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>1_905
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
+>2_1634
+MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG
+VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM
+STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV
+PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADSAAKK
+>3_1531
+MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP
+REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA
+CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE
+PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD
+GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV
+TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL
+GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK
+VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF
+FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK
+LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR
+MKMVGRVEVPQEAFIAALSSDGAEPAKK
+>4_1135
+MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD
+IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ
+GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG
+VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM
+STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG
+GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL
+HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT
+IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA
+SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV
+PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE
+AFIAALSSDGAGADQAAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28eebf05ed226cd9429c6f416159f515acd595ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001026.fa
@@ -0,0 +1,35 @@
+>0_1180
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>1_908
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>2_1631
+MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH
+SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL
+RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT
+GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH
+AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG
+IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
+>3_1528
+MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET
+HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL
+LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA
+TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR
+HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA
+GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR
+>4_1138
+MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH
+RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL
+RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT
+GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH
+AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG
+IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f85cb4fcb5b57d87fff2190d680be9b9e5149ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001027.fa
@@ -0,0 +1,79 @@
+>0_1181
+MNPAPGPPNDPVDRRARHREVPGPLEARWVPALLGCLTLGILGVGWDAPARSAAALTGLA
+VAAAAILGAARSTGRIRGVATATALAGVAAALMLQHSAGPAAAASGSGWTGAVHAGSPLR
+LELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIVAPEGG
+TWAPDGGPGSRVCVVARPSRSGSTVFLAAASAPQPGPCPGGTQTAGGATGGDPGPPRREA
+LRAAFRQSAEGTVGAAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMILG
+AVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQAF
+GLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLAGAPLDRALHAGLGRMLPDVVARWL
+SASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPGI
+AAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLLE
+RRRTAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRSSGSAPPDWAVAFC
+DVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHAGGLAGV
+VDRASRGAVHYATRDAPAQGREGRGGEADGVDPLADAARLRTGATGTAGPVRWHVLLADA
+RAPEENDASAQVLVTVESGAGPVTTLVTGDMEEDASAAWVAGRRSDAAAPPRVDVLKVAH
+HGARNGGTAVPRAAGARLHVVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTAA
+DGPDPDGAPEIAVHTVRPPSSVRTGP
+>1_909
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP
+>2_1630
+MVSAPAGSRPPEAPGARTDPAARRGDVPGPLDARWVPALLACLTLGIVSDGWEAATRTTV
+ALACLGAAAAAVLLAARAPTPAWIRGTGTAVALAGVAVALMLQHSAVPAAALERTGWADV
+VREQAAVRVELAVTGAAVETAGTFGPRWSAPVRVRAFGHPARAPEAAVAARLSGPGTVPS
+ALGAAPDSEPAPGGRVVGPPAATVLCVVVTPDAGDGTVFLTAAAAPTPGPCPAADAAHGA
+ASVEDEPPPRREALRAAFRAAAAGTAGTAPELIPGLVLGDRSAQGRPLDAAMKASGLSHL
+SAVSGANVALLLGFTAVALRSLRVHRAVVIAAGLGLLAVFVVVVGPEPSVLRAAVMGALG
+AVAVFLGRGRQAFALLAVGGTALLVAVPSLSVEPAFHLSLAATAGIVLAGSWGDRTLHGP
+LRRVLPDAAARWLSASLAVTLAALLACQPVLLAMTGELSAYAVLANLVAAPAVAPVTVLG
+TLAAALVLPAPAVAAALVWLVQWPSAWIGVVAHAAAGLPGALRPWPSGALGVGLGALLTA
+ATLAGFAAVLVLERRRHARVRRVGEGAPLPPERTPALVLLAAVLVAAAVGGVGAVLVPRP
+AGAAPPDWAVAFCDVGQGDMAVFRSGPRAGVVVDVGREPEAARRCLEDLGVDRVEAVLLT
+HLHADHAGGLAGVADRAVPGAVRYATRDAAGVGRSGATAGEAPGVAPPAGGARLVTGERG
+AAGQARWEVLLADARAAEENDASAQLLVTVDAPAGPVTTLVTGDMEEEASGVWAAGRRSD
+AAGPPSVDVLKVAHHGARNGGTAVPRAVRARLHVVSVGAENTYGHPHPATLDALHRLGPV
+ARTDLHGTVALVAEGPDGAAGAGEIGVYTVRPPSAVRTAP
+>3_1527
+MSLGCAALAAVTLTLRLRIRRTGSSRVRTGAATAVVLAGLCGAVLVQHIAVERSGREQVG
+WIETVDTGGPVRLEVTAQGPATAGDSRFGPSWTRPVTVQRFGHPLRPLTPPAEATLTGTG
+SLDAAANGAEVLCVVAEPRPADGALFLAARAAPESDGCGEGSTAASSGPTGRDVLRARFR
+EAAADGVGLAPELVPGLVLGDRTAQSEQTDQAMKDAGLSHLSAVSGANCALLLGTVALVL
+RSLRCPRGVVLGAGLAVLGVFVLVVGPEPSVLRAAVMGALGALAVFLGRGRQAFGLLCAG
+GTLLLVSVPDLAGEIAFHLSLAATAGIVLVAAPVDRWLHGRLGRVLPDLAARGLSSSLAV
+TLAAHLACQPILLVMTGTVSLWAVPANLMAAPAVAPVTVLGTLAAALVVPAPWAAAPLLW
+TVQWPAAWIGVTATAASAAPGAVRPWPEGALGVALGALLTAATLAGFHAVLVLERRPTAP
+VRRVGRSARDARVRVPAGVVLAAVLAASATGAAAAVLVPRPPGTVPEGWAVAVCDVGQGD
+MTVFRSGPGSAVVADAGPDPAAASRCLDDLRIERVDALLLTHLHADHAAGAPGLSGPRAA
+AAVRHGAWSGSGGGGGEEPGLDAPAGSAPLTTGDEGRAGDVAWRVLLADPRAAEQNDSSA
+QLLVTVTTPAGPVTTLVTGDMEQEASAAWAAGTRSDAAPPPRVDLLKVAHHGARNGGLDV
+PRRVRARLQAISVGADNTYGHPAAATVAGLEELGPVLRTDRHGTVALVPGPDARLTPYTV
+RPPT
+>4_1139
+MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL
+AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL
+RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD
+GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE
+ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL
+GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA
+FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW
+LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG
+IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGVGLGVLLVAATLLGFAAVLLL
+ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF
+CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG
+VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD
+ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA
+HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA
+ADGPDPDGAPEITAHTVRPPSSVRTGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87e80eef4cead257e9bb148aac59c23941f095f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001035.fa
@@ -0,0 +1,45 @@
+>0_1189
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRHADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATAANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSGTEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGAIV
+RFIAGSMSVPAPEGVERVVQVESTQDLLEAVLAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDPTSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDQAAAAVVQAIVDDLAGR
+DPAGASGR
+>1_917
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVQAIVDDLAGR
+DPVGASGR
+>2_1622
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGTATWEALSGRPVRTGTF
+EAVDEVNHVRLGRQADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVEPAVGRLTGADSGARRLPEPDEIWELAQAAAADPAARR
+PRATTSRPGPAAAGAAPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGVALARAALA
+AGARVRFIAGSMSVPVPEGVERAVHVESTAELLTAVLEQAADADVLVMAAAVADFRPAEA
+SESKMKKGDDGSSPVIVLERTEDVLATAVRTRAAGGPMAPLIVGFAAETGDAESSVLEYG
+RAKLARKGCEMLVVNEVGRDKVFGRDETAVTILFADGSPAVEAAGSKDEAAAAVVGAVVD
+RLAASAPGSASAR
+>3_1519
+MEVVLGVGGGIAAYKAALLLRLMKEAGHGVTVVPTDNALRFVGAPTWEALSGRPVRTDTF
+TDVPEVSHVRLGREADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWRHPATVANVALLRERGVHVIEPDSGRLTGADSGPGRLPEPARIWAEAQDAAARAGGRA
+GREAAVTAAEPGAASPLAGRTVVISAGGTREALDPVRFLGNRSSGKQGTALAEAVLAAGA
+RVRFIAGPMSVAPPAGTEVTAVESTQELLEAVLSEAADADVLIMAAAVADFRPAQVATSK
+IKKTDDGGAPTIVLERTPDVLATAVQTRDAGGPMAPVIVGFAAETGDEHTTPLEYGRAKL
+ARKGCDLLVVNEVGDGKVFGQDATEVTVLSADGAEPVTRTGSKAEAAAAVVEALERVLAS
+REAGGAPGR
+>4_1147
+MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF
+EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE
+MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR
+PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV
+RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM
+KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA
+RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVRAIVDDLAGR
+DPVGASGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdfe5c465dff06b6789c15a89d3eb94d08692f4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001036.fa
@@ -0,0 +1,21 @@
+>0_1190
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA
+>1_918
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
+>2_1621
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA
+>3_1518
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A
+>4_1148
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7109a27618726df4d7145fcff9eb7d507f43aa29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001037.fa
@@ -0,0 +1,25 @@
+>0_1191
+MTDTFDPGPAPAVPVARTVVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>1_919
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
+>2_1620
+MTDAFDHGPAPAVPVARTAAQERRPGPGVTVLAGPTAVGKGTVSAYVREHYPQAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVAADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRESLPEATFVFLAPPSWEELVSRLVGRGTEGPEEQRRRLDTARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPEHSSPEA
+>3_1517
+MSDLSDLGPAPSVPGERAPSRPPAPGAGVTVLAGPTAVGKGTVSAYIREHYPQAWLSVSA
+TTRAPRPGEEDGVHYFFTTPEEFDELVAGDQMLEWAVVHGRNRYGTRRDRVAEAVAAGRH
+VLLEIDLQGARQVRRTLPEATFVFLAPPSWDELVSRLVGRGTEGPEEQRRRLETARLELA
+AEPEFDAVVVNDAVERAAAELVKLMGIDPHDAPASA
+>4_1149
+MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA
+TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH
+VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA
+AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7467b7b8d0264b75ca34340660909da8285d6dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001042.fa
@@ -0,0 +1,25 @@
+>0_1196
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
+>1_924
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
+>2_1615
+MNALALAAATLASRPVAPQTPGKDYSDVWLPITLGTLAVILVLVGLFALGWRARRRSQAD
+LPAPAAVPAALYEQEPAASASGMHVGTVRGEHRLDRVAVHQLGLRSHAVLEVHDAGEHRG
+LLVLRPDVANLYIPAADLLEAGLSAGIAGKFVEPGGLVAWGWRLGDAELTSAFRPDRAED
+RDRLLAALQTLIDPAPARSAGRAGEGDLR
+>3_1512
+MSAVLPAALPLAATPVPPASPMKDYSDVWLPIVLTTVGVIALLLALIAWGWRGRRRRQAG
+IPAPATVPPEVLEREPAVSAEGMWVGTVSGTDRLDRVAVHDLGLRSSGVLEVHTAGDRPG
+VLVLRPNIAPLFVPAAHLMEAGRSAGIAGKFVEPGGLVAWGWRLGDVDVTSAFRPRRPED
+RDRVLEALQTVIDRAGRPDAGQENAR
+>4_1154
+MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI
+PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL
+LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR
+DRLLAALQTIIDPAPADPAGRAGEGDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f748ec5ad629b5c90c1d8690ef6e5185adadf44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001043.fa
@@ -0,0 +1,35 @@
+>0_1197
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>1_925
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>2_1613
+MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR
+SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
+>3_1510
+MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV
+DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR
+SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG
+AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV
+LEQVANGVSVRMAVLHLVLNQDPALAPQEARP
+>4_1155
+MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE
+AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV
+RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR
+SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG
+AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA
+LEQVANGVSVRMAVLHLVLNHDQEVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3965254b0f36846bc9af53e67e9b42f4cf83396
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001044.fa
@@ -0,0 +1,25 @@
+>0_1198
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
+>1_926
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
+>2_1612
+MGADPAAPRAARTVLSASEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAV
+LARIEPAFDPEAAVGEVDVTLYRDDLRRSAARTPMPTRLPAVPLDGAVVVLVDDVLFSGR
+TVRAALDAISELGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTSERVQVRLVEVDGP
+EGTGEVSEDAVSIADQADRPEQREA
+>3_1509
+MGGIPAAPRAARTVLTAPEIDRALTRIAHEILESNKGPEGLVLMGIPRRGVPLARRLAAV
+LHRIDPAFDPVSAVGEVDVTLYRDDLRRGTARTPAPTRLPDHPLDGAVVVLVDDVLFSGR
+TIRAALDALADLGRPAAVRLAVLVDRGHRELPIRADFVGKNLPTSTAERVQVRLTEVDGP
+DGSGEVPEDAVRIVDAPAETPREA
+>4_1156
+MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL
+LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR
+TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP
+EGTGEVTEDAVSIVDRVATREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30ff63c81e51b2d334974a1128c00077ac4cfb05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001045.fa
@@ -0,0 +1,20 @@
+>0_1199
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>1_927
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>2_1611
+MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
+>3_1508
+MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL
+VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL
+AAALSTDESPEFVNGLLGRLQQVKPTLLA
+>4_1157
+MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR
+LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA
+LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c36033cc8e3c20e9fcca330e4e9ed925d4e94ffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001046.fa
@@ -0,0 +1,25 @@
+>0_1200
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>1_928
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
+>2_1610
+MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV
+EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD
+YLGRVND
+>3_1507
+MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV
+EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP
+LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE
+YLGRVND
+>4_1158
+MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK
+VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN
+TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ
+GTRVKVDTRTGDYLGRVND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8767cf4296ef2af338def3faee4f26ff2584aa1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001049.fa
@@ -0,0 +1,40 @@
+>0_1203
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP
+>1_931
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
+>2_1607
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG
+MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF
+PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE
+AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ
+>3_1504
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL
+GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF
+PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ
+>4_1161
+MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL
+GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG
+MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF
+PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW
+DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE
+AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA
+LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5870ad50269f873dd727272fc9d46311e78067e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001051.fa
@@ -0,0 +1,20 @@
+>0_1206
+MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE
+LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS
+TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR
+>1_934
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
+>2_1604
+MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE
+LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS
+TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA
+>3_1501
+MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD
+AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH
+RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA
+>4_1163
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca10f98a81cfbd4092e6a30340476143f6c4c0d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001053.fa
@@ -0,0 +1,19 @@
+>0_1208
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>1_936
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
+>2_1602
+MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA
+VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI
+PTTTTQKDTHA
+>3_1499
+MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA
+AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA
+>4_1165
+MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR
+QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT
+TTTQKDTPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd16e1337b18f6220f3bffa094e6db5d3d9f6374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001059.fa
@@ -0,0 +1,20 @@
+>0_1214
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>1_942
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
+>2_1596
+MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA
+SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV
+FGAQMDVTLVNDGPFTLVVDTADLTGPRRG
+>3_1492
+MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER
+SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV
+FRADMDVALTNAGPFTLVVDTADLAGPRRG
+>4_1171
+MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER
+SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV
+FGAKMDVSLTNSGPFTLIVDSDELAGPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..775dbb376b1d27fa312f07149d704b9776b4b3dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001063.fa
@@ -0,0 +1,49 @@
+>0_1218
+MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM
+KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ
+RAVKKAQEALDARLKWKQALEASASELR
+>1_946
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
+>2_1591
+MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM
+DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS
+TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV
+KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR
+KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR
+RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER
+AVKKAQEALDARLQWKQALEASASELS
+>3_1486
+MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE
+APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA
+PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA
+QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA
+ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK
+SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG
+KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL
+ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR
+RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS
+ASELR
+>4_1175
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22ceebb0570b5a1d157ff49733e539da67ee381f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001067.fa
@@ -0,0 +1,60 @@
+>0_1222
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE
+RRRQEEDQ
+>1_950
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
+>2_1587
+MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA
+TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD
+PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST
+NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ
+ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR
+RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA
+ERRRQEEDQ
+>3_1482
+MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA
+SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD
+MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR
+DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT
+NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ
+ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV
+YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA
+RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD
+TEEDAL
+>4_1179
+MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS
+TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD
+MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD
+PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST
+NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ
+ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV
+YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV
+YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG
+LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP
+RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR
+RQEEDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99996d40a72323734a0c98c3e2481e163997055e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001068.fa
@@ -0,0 +1,20 @@
+>0_1223
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETTAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>1_951
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
+>2_1586
+MPVATAATLPVIAQQAQGGGGSMLMLIAFAMLAVMLFLSFRKGKKVQQQQAEMRSTLAPG
+VEVMTGAGIFGTVVSVDAENQRVTIETAPGTRMDVHLQGVTNVVEPTAAAAATPADDEAR
+LDRAPGAEYGAQQPVVEPRADDAVDPRDRRGDLA
+>3_1481
+MPLTPLAPVLADDAAGGGNVLVLAMFAALAVMLFLSFRRGKKAQAEAADMRARLTPGQEV
+MTGAGIFGRVVAVDAAAQRVTLETAPGTRMDVHLQGIVKIEEPDVAPAADTAPAVGGAHA
+AETAPAADDTDRA
+>4_1180
+MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG
+VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD
+DAPGTEYRADDADDPRPRRDDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..115952785db9448e13ef68c8e8e0d08fc4acf0c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001074.fa
@@ -0,0 +1,20 @@
+>0_1230
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>1_958
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
+>2_1579
+MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA
+YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER
+VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA
+>3_1474
+MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY
+ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH
+VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA
+>4_1187
+MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP
+FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER
+IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50502ce94ff3dcb3026497caa46bc0567c8d3cae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001080.fa
@@ -0,0 +1,16 @@
+>0_1236
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>1_964
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
+>2_1571
+MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA
+MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG
+VAAPKGLAPRRRYGAERD
+>3_1467
+MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY
+PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED
+>4_1193
+MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML
+LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e986ef3dbc65a952001718114f53250c7a29c46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001087.fa
@@ -0,0 +1,26 @@
+>0_1251
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>1_983
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
+>2_1563
+MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC
+GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV
+RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS
+SPGAGALTDQASQSPRA
+>3_1459
+MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA
+GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV
+RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG
+>4_1208
+MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC
+GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP
+SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV
+RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15c2f3272aac62138340f4d830f1c33cf1a3c3a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001089.fa
@@ -0,0 +1,15 @@
+>0_1253
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>1_985
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
+>2_1561
+MSPAAGERADAGPGDLIERRGVVASVTLPGADDATVFRAALADRLPEPGSVTPAESLQLV
+WHGRRRVPGVMPGQWLAVRGRLTRPDGVLTLHNPAFDLIDAPEAALRARPPREESP
+>3_1457
+MSPRRTPAPAGERPAGERVGVVVAVTFPGADDATVFRAALADDLPAPGRPEPQEVLHLVW
+HGRHRVAGVMPGAWMRVLGHPVAVAGEPTLFNPEFHLIDDEGGPA
+>4_1210
+MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW
+HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b92b985bdef4cd14d16f770cc568b0e015f6f1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001091.fa
@@ -0,0 +1,20 @@
+>0_1255
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS
+>1_987
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS
+>2_1559
+MTDSAELPVPLHALDPDLAPPAYAQPGDAGADLRAAVDVTLAPGERALVPTGVALAIPEG
+FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTDAVELRRGDRIAQLVI
+QPVVRARFAPVDALPGSERGAAGFGSTGGFGTENAPGRTS
+>3_1455
+MNGPREIDVPLRALDPQLPPPEYARPDDAGADLRAAEDVTLAPGERALVPTGVALAIPAG
+FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPVVLRRGDRIAQLVV
+QPVVQARFMAVDRLADSERGEAGFGSTGGFTPAAHDDAPGRTA
+>4_1212
+MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG
+HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL
+QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12f6fbd6bbedf08614c382642d150081e1dc3fbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001095.fa
@@ -0,0 +1,25 @@
+>0_1260
+MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>1_992
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>2_1554
+MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA
+VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA
+>3_1450
+MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE
+LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE
+MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG
+YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA
+>4_1217
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001097.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05fd254fd6a864f3d14f0e31848f7b7795a92ddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001097.fa
@@ -0,0 +1,80 @@
+>0_1262
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR
+LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC
+WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL
+PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR
+EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA
+ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA
+KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI
+EAVGAGASPELLSAPPVADDPVTVSAD
+>1_994
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
+>2_1552
+MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP
+VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV
+DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP
+NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV
+GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK
+LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT
+LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA
+AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL
+REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW
+AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP
+AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE
+VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA
+DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK
+GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE
+AVGAGASPELLSAPPVADDPVTVSAD
+>3_1448
+MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY
+PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI
+VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG
+RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR
+TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR
+LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA
+CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE
+LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV
+GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP
+VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR
+VEAVGAGASPELVAAAPVDDSGVEVSAD
+>4_1219
+MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK
+PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV
+VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY
+PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI
+VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK
+KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ
+TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT
+TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR
+LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA
+CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD
+LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN
+RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL
+AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP
+AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR
+IEAVGAGASPDLVSAPPAEDDAVAVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dca9b6edef04039f3e1bfef383ab803a6fc1b6f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001098.fa
@@ -0,0 +1,107 @@
+>0_1263
+MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>1_995
+MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV
+GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG
+RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL
+VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH
+HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP
+LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG
+RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI
+GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR
+LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH
+DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR
+QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY
+LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL
+VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA
+LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI
+AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE
+GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS
+GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG
+NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR
+ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC
+>2_1551
+MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>3_1447
+MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM
+TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL
+GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML
+GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV
+LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY
+GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW
+PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG
+SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG
+GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL
+LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR
+PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA
+PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA
+DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV
+PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL
+LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA
+LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE
+AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA
+AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV
+FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER
+QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD
+VRVRLGGDAAGHP
+>4_1220
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71cf56c94c236e3ddcf6b2ea2e725d01adf33b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001099.fa
@@ -0,0 +1,35 @@
+>0_1264
+MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV
+WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC
+LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV
+VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM
+AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV
+>1_996
+MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV
+WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT
+LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA
+FIGLKTDGAPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV
+VAARAGREGLAFTSLTLVLVLAWTAIMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM
+AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL
+>2_1550
+MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV
+WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC
+LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV
+VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM
+AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV
+>3_1446
+MTEALPVYWFVIIAVLWLGYLALEGFDLGVGMLMQAWARDERRRRVLLNIIGPVWEGNEV
+WLITAIGAMFAAFPFWYAALLSTLYIPMLLLLFALILRAVSIEYRGKAQTDRVRGIWTWC
+LAVGSFLAAFIVGAMLALTTTGLPLDAHGDRVGGPSAWLNGWAVLGGLAVVGFSIAQAWA
+FIGLKTDGAPRVAAARFLRTWTPVAVLPMLVWALAVLVRGDRPGAWILLLLALAAVLVSV
+LAARAGREGVALAGLTGFAAATWSAVMVAQFPVLTPSAVDRAYDLTAQVSSSGSYTLGVM
+AVVSLVFVPIVLAYSAWSYWVFRHRVKETHIPESHIVEPV
+>4_1221
+MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV
+WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT
+LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA
+FIGLKTDGVPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV
+VAARAGREGLAFTSLTLFLVLAWTALMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM
+AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e09d8d289b1be7383340711908b3f7261cfe0d99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001106.fa
@@ -0,0 +1,50 @@
+>0_1273
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT
+KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD
+GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>1_1003
+MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS
+ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT
+ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA
+EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA
+EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA
+KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR
+IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL
+GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK
+TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>2_1540
+MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA
+KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA
+ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD
+GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY
+LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL
+LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI
+TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK
+YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV
+AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>3_1436
+MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT
+ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP
+KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT
+TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM
+RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM
+LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV
+INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF
+GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV
+YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
+>4_1228
+MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG
+ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS
+AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG
+TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD
+LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG
+RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM
+VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD
+SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI
+GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e19d0b2c6334cfa60fd3a0a964fa0dcbcc575323
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001108.fa
@@ -0,0 +1,35 @@
+>0_1275
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
+>1_1005
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTDDGD
+>2_1538
+MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM
+FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL
+AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR
+ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE
+RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG
+SAPAQEDGPPRPSTDDER
+>3_1434
+MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV
+DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL
+LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL
+ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA
+ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE
+SVQPRPTTPAQDDEGPAPSPDPQV
+>4_1230
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d51b2d81f65b2e5609952ca598abc5e835381618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001110.fa
@@ -0,0 +1,45 @@
+>0_1277
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>1_1007
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>2_1536
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH
+AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI
+YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG
+>3_1432
+MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK
+LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
+>4_1232
+MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH
+AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK
+LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG
+VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE
+TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI
+YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA
+EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL
+IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6b85cbeaaa8faec6b7e0e4950c0f7f74cb043be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001112.fa
@@ -0,0 +1,15 @@
+>0_1279
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>1_1009
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>2_1534
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>3_1430
+MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN
+HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS
+>4_1234
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d5f6cf5fa73f659d40d7d91ba7ae280bd5b8266
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001122.fa
@@ -0,0 +1,15 @@
+>0_1291
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD
+WDSRPVDDAS
+>1_1020
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
+>2_1523
+MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN
+WDNNPFNDAD
+>3_1419
+MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA
+HDDAWDASPLNDAS
+>4_1245
+MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD
+WDSRPVDDAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09f7f03521dd24583f5054c9e4b4956e52269dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001125.fa
@@ -0,0 +1,105 @@
+>0_1295
+MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>1_1024
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG
+AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ
+YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD
+LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD
+VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV
+MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG
+>2_1519
+MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG
+AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL
+SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT
+LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA
+KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG
+LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD
+LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD
+TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY
+APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV
+VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS
+>3_1415
+MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG
+AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML
+AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ
+YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH
+EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT
+LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE
+LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF
+ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV
+MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA
+KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG
+LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM
+MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL
+IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA
+LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE
+CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD
+FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD
+LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF
+ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ
+VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE
+RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG
+>4_1249
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24c911e024f2adf62f1e8eb731bb34d8cf86215e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001129.fa
@@ -0,0 +1,15 @@
+>0_1299
+MQLLLALAYIALTVVLAALTVRIVLDVTQSFVRHWRPTGAALMLASGVYGATDPLLRPVR
+RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA
+>1_1028
+MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR
+RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA
+>2_1515
+MQLILALVYIVLTVVLAALTVRIVLDVTQSFARHWRPTGAALVAASAVYAVTDPLMRPVR
+RAVPPVNLGGIGLDVAFLVVFLGVVLLRVLVLVLAGNL
+>3_1411
+MQLVFALLYFVLTAYMAVLTVRIVLDVTRSFARSWRPSGPVLVAASGVYALTDPPLRALR
+RRIPPLTLGGVGLDVAFLVVFLGVVLLRVLVLTLA
+>4_1253
+MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR
+RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61e9853ea5984018914d8c0317dd818a51e79fc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001130.fa
@@ -0,0 +1,25 @@
+>0_1300
+MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
+>1_1029
+MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGVADSPFDGD
+>2_1514
+MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV
+VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP
+VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR
+ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD
+>3_1410
+MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP
+STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP
+RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT
+PSSVEVVGEEPPAGRDGDAPYDND
+>4_1254
+MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f365da0728a2e25e915e0de35e5aee5d6d62b934
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001134.fa
@@ -0,0 +1,30 @@
+>0_1304
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLGALGWVVFFSPVLA
+VDRVEVTGTRHVSAAEVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVVVREHETRARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRAQEERAEV
+AEVLAALPEAVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGPVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
+>1_1033
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTALGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLAPVYGVPLSRVGAGRVGELAGGLPGVAEVQTVPRLPTGL
+EVVVREHEARARRDGGDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRVQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEAGVAEIDISVPTRPITR
+>2_1510
+MTPGRGGRPPRPAGPAQPPAGSTVVPFPGRSVRRRRAVRWAVAGAVAALLGALAWVLLFS
+PVLAVDEVDVTGTRHVSAEAVQERLAPLHGVPLPRVGSSAVRELVGDLPGVAEVRVVAHP
+PTRVEAAVREHEARARRGGEAGVDLLLDDGTVLAGVPAERVEGESLPEFSEELSAGPRRD
+REEVAAVLAGLPAPVAERVESVDSSRAGQVRLGLRDGVVLVWGDAEDAELKGTVATAFLE
+GDQHGSRAGGVREVDVSVPTRPITR
+>3_1406
+MVAFPGRSARERRRRRAGMLAAVFAALALAAWAVFASPLLAVDRIDVTGTRLVDRAAVEE
+RVAPLRGVPLPRIGSSSAGDLLSGMPGVASARTVAVPPTALEVRIEELAPVARSAGGDRA
+QVLLEDGSVLGSVPVSALPGEGEEGGALPSAPEALLTAGPDVRASAATVLRALPDGVRDR
+VRGVDAGSPEQVRLDLGGGRTLVWGDASEPERKAAVAQALLDGLEDARGVREVDVSVPDR
+PVTR
+>4_1258
+MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTVLGWVVFFSPVLA
+VDRVEVTGTRHVSATDVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL
+EVAVREHEARARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELPQRAQEERAEV
+AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH
+GSAEGGVAEIDVSVPTRPITR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52db2d5a33caa3be486f7dfe41fd94521d2322c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001139.fa
@@ -0,0 +1,56 @@
+>0_1310
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>1_1039
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>2_1505
+MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA
+ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA
+YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA
+SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR
+HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA
+ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ
+FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT
+VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS
+FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL
+MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG
+LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK
+GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP
+>3_1400
+MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA
+ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS
+AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA
+YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA
+SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR
+HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS
+QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA
+ALGDRLAAADVTPSTASPSDTTKETRP
+>4_1264
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b6475f55593e6f56716fc0b4c73435f8e9ce592
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001144.fa
@@ -0,0 +1,20 @@
+>0_1315
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>1_1044
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
+>2_1500
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NAYLAEQEAAFSETDEDVLPGVF
+>3_1395
+MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL
+SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW
+AAYLAEQEAAFSETDEDVLGGIL
+>4_1269
+MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL
+SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW
+NTYLAEQEAAFSETDEDVLPGVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6ff810e68109df083325ef5eaf76a1af776bbde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001148.fa
@@ -0,0 +1,20 @@
+>0_1319
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>1_1048
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>2_1496
+MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN
+LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP
+SLPGRPIDALRDGRKTEVRRRAQALAW
+>3_1391
+MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP
+SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK
+TEVRRRAQALGW
+>4_1273
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001154.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1da89ebfe083204f836a525995e088583ff4aa8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001154.fa
@@ -0,0 +1,50 @@
+>0_1326
+MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD
+SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI
+SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD
+LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV
+STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD
+AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL
+KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV
+KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH
+RLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>1_1055
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
+>2_1488
+MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL
+AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF
+VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG
+GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE
+PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV
+TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA
+VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV
+AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL
+DVPDSGLL
+>3_1383
+MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV
+AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR
+IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV
+PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH
+DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET
+LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN
+AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED
+AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG
+IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL
+>4_1280
+MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL
+AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV
+GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG
+GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP
+VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT
+DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT
+LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA
+EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD
+VPDSGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cee2a71a98396563f4e04e8fc7a8225306dc54e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001156.fa
@@ -0,0 +1,25 @@
+>0_1328
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
+>1_1057
+MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRAAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
+>2_1486
+MTPTAGSGRPPALGAQGTLFDEDVTPGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRGAAGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVIVAPEPGDELAGR
+RRARRSA
+>3_1381
+MTPHAGPGLPLGIDGRQGRLFDVDALAPGGDVGYRGPTACKAAGITYRQLDYWARTDLVV
+PTVRGASGSGTQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVAHLRERGVDDLAQITLM
+SDGASVYECTSPDEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPGEVLGDDHAPEDELS
+ARRRARRPARTAS
+>4_1282
+MTPTAGPGRPPALGTQGTLFDEGATRGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT
+VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD
+GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR
+RRARRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7166d434a6a4beb1cc3ee2c2941cc57c68e5c66b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001157.fa
@@ -0,0 +1,20 @@
+>0_1329
+MTEPRPVPADDAGDVPLSVLGVRVELPEQHHVILLVDPPGRTMIPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
+>1_1058
+MTEPRPVPADDAGNVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRGEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
+>2_1485
+MTEPRPEDAPEAGDVPMSVLGVRVELPEQHHVILLVDPPGRIMVPLWVGAPEAAAAALAL
+EGVSAPRPLTHELLLSTVAALGAEVVRVRLTEVRNDVVHGELELSTGARVDARASDAVVL
+ALRANAPVLASPAVLAEAGMSARSGEEDGQERTVEDFRDFLDSVRPEDFA
+>3_1380
+MAEPPEPAGDVPLTVLGVRVELPEQQHVILLLDPPGEIVLPLWVGSPEAAAAALALEGAP
+SPRPGTHALLLAALAAAGSRLRGVRLTRIEDETVHAALLLDGGAEVDARASDAVVLAVRA
+QVPVLCAAEVIAAAGMAARDAAAGDEDEVDDFRAFLDSVDPEDFA
+>4_1283
+MTEPRPVPADEVGDVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL
+EGVRTPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV
+ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42be6f81da5d62ca130f134d668c79d9b8b222d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001163.fa
@@ -0,0 +1,55 @@
+>0_1355
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLADYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVGEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
+>1_1094
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGSRR
+>2_1462
+MTEHTRDDVATTPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADADAVAAAAVAMELEQSTDPDVEAVRVGGTDVTEAIRGAEVTDTVSTVAVVIPVREE
+LRRRQRETIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGEPGVD
+AGTLHRQGGRAGRPRRHRVHVRPPRRGRGARGLHRARLRADRGGRPGRRRGPGRHPGREG
+RPTMTDNPQHRSGDDEFVPAGEDQVAERLAAMTEEEAEARAASLRAGLADYELEDDDAAL
+LDAWQLGPDEDLDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDA
+EWNGREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSM
+LRRKDRPVIVAANKVDDMVQEADAASLWSLGFGYPYPVSAVHGRGVADLLDAALEAMPEE
+SAHGGLVPRGGPRRIALVGRPNVGKSSLLNRLAGSDRVVVDDLAGTTRDPVDELVELGGR
+LWRFVDTAGIRRRQHMAHGADYYAALRTASALDRAEVAVVLLEAPSVISEQDVRILQMVL
+DSGRALVIAFNKWDQVDEDRRHQLEKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDT
+ALDSWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDP
+GYRRFIVRRLRETFGFEGTPLEIGMRVREKRGLAPLSAAAADDDGVPRARRGSTDPAPAG
+GRRRPTPSRGSSHGFLMFRA
+>3_1374
+MTENTPLTEGEEYQPAGEDHLAERLAAISDEEADARAASLRAGLGDYELEEDDAALLADW
+DGDDEFDLDLPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYEAEWNG
+RVFTVVDTGGWEHDAKGIHKRVADQAELAVDVADAVVFVVDATVGMTATDEAVVTMLRRK
+DRPVIVAANKVDDMVQEADAASLWSLGFGYPWPVSAVHGRGVADLLDAALEELPEESAHG
+GLVPRGGPRRIALVGRPNVGKSSLLNKLAGADRVVVDDYAGTTRDPVDELVELGGRLWRF
+VDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPSVISEQDVRIVQMALESGR
+ALVLAFNKWDQMDEDRRPQLEKEIERDLAHVAWAPRVNISALTGWHKDRLVPALDTALES
+WDRRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQASTRPPTFVLFTTGFLDPGYRR
+FIVRRLRETFGFEGTPIEIGMRIRERRGRKR
+>4_1304
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f292adb74f6822b3e60e65f36be2943512b02166
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001165.fa
@@ -0,0 +1,35 @@
+>0_1358
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>1_1097
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
+>2_1460
+MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR
+GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR
+VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS
+VRALSAQELGHLKALVGL
+>3_1371
+MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG
+KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV
+RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV
+GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL
+AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG
+SVRAMTAQEQGHLKALVDL
+>4_1307
+MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR
+GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR
+VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG
+RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA
+QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT
+VRALNAQELGHLKALVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e9830640eb483ff53c58d661f358b9d4cc4add9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001166.fa
@@ -0,0 +1,60 @@
+>0_1363
+MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLKAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGSLPTLWRDDQR
+YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALGSHPAVA
+ECAVIGVADPLKGQRPSGYVVLKSGVETPEPGSEAEAALLDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR
+>1_1103
+MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLKDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWGDDQR
+YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA
+ECAVIGIADPLKGQRPSGYVVLKSGVETPEAGSEAEAALLDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR
+>2_1458
+MMPPPNPAPPAPTPPPTPAPLHDPEGFWLEAAEAIDWTVPPTRALDDSAAPLYRWFPDGE
+LNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRFTYAELTDAVARLAGALAARGVGKGD
+RVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGIEPK
+RRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADVDGRGGASWEDWGEAVAAAEPAE
+CVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGW
+VVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRAD
+PEGELLQDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANPVGL
+EQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQRYID
+SYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECA
+VIGVADPLKGQRPSGYVVLKSGVPVPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVV
+DALPKTRSGKILRKTMRQMADGEEYAVPSTIEDASVLDALAPVLRPGA
+>3_1365
+MATDTTAAPRSYADVHRRSLEDRESFWLAAAEAIDWTVPPTRALDDSAAPLYRWFPDGVL
+NTAHNCLDRHVAAGRGEELALVHDSAMTGEVTRFTYAELTAEVARLAGALAERGVGKGDR
+VLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELAARIDDATPDVVLTCTGGIEPKR
+RVEYLPAVAEALEIAEHPVRTVLVHHREGFATAREDVADRGGAEWEDWAEAVADAAPAGC
+VDVAATDPLYILYTSGTTGRPKGVVRDHGGHAVALRWTMENIYDVGPGQVMCTASDVGWV
+VGHSYIVYGPLLAGATTVLYEGKPVGTPDAGAFWRLIQDHGVRSFFTAPTALRAVRKADP
+EAALLAEYDVSSLRHFFAAGERLDPETQKWIEGVLGMPVIDHWWQTETGWAIAANPVGLE
+ELPVKTGSSSVPSPGFDVVVVDGLGTPVAPGEEGNIAIRLPLPPGTLPTLWKADQRYVDS
+YLTAFPGHYATGDSGIVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAV
+IGVADTLKGQRPSGYVVLRAGVERPEPGGEAEEALLAELVQTVRREVGPVADFRDVAVVE
+ALPKTRSGKILRKTMRQLADGEQVAVPSTIEDASVLEDLAAVLRPAG
+>4_1312
+MATHDAPTEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP
+DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG
+KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI
+EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE
+PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD
+VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR
+RADPEGELLQAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP
+VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR
+YIDSYLSAFPGHYATGDSGLVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA
+ECAVIGVADQLKGQRPSGYVVLKSGVETPEAGSEAEAALMDELRQAVRREVGPVADFRDV
+VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a26646d80c2da05b6ebee0b5fe45a4508e0c79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001167.fa
@@ -0,0 +1,26 @@
+>0_1364
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
+>1_1104
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
+>2_1457
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPVREALSRLVADGLAEQAPG
+RGTVVADLSLEQADQLFDLRIALESLLARRAAQRATPETAARFTALAARFQEAGEALRAG
+TDPADYYAMTAELDASLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLATSAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRTRADETPTLLSPTEGDRP
+>3_1364
+MPPFTPAGVSVYSGAMRVSDRAYAALRGEILDWTLPPGTVLGEVELADRLGISRTPVREA
+LARLVADGLAAQAPGRGVVVADVSLEEAEQLFELRIALESLLARRAAERADADQAAAMGA
+LADRFLAAVPRLEAGDEPAGYYTLTDELDAGLDAAAGNPYLVSTLRTLRLHLARLRRLAA
+HDPARLASSAAEHADIAAAVAAGAADLAEATTRVHLHHAATHLTRRARAAESTTLLTPTP
+FEGAHQ
+>4_1313
+MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG
+RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEVALRGG
+TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD
+IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..015054d4fdaed1a782617a7062991f41156510bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001168.fa
@@ -0,0 +1,50 @@
+>0_1365
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR
+GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>1_1105
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>2_1456
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR
+GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL
+TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP
+GELDQLNVTADPAFLSQADLDNAPKGLF
+>3_1363
+MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH
+PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV
+ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL
+TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA
+GELDQLNVLANPAFLSEADLAAAPKGLF
+>4_1314
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b5ae9b8ca90fc88b6f8cd8092ab7dacba2cf039
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001169.fa
@@ -0,0 +1,35 @@
+>0_1366
+MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>1_1106
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>2_1455
+MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDENNANL
+>3_1362
+MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDSNNANL
+>4_1315
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53e5a0e01b9329223f2390eed7780b4c12e2a8ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001172.fa
@@ -0,0 +1,25 @@
+>0_1370
+MPEISASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGL
+DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWPA
+>1_1110
+MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSQDPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRALEWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV
+DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA
+>2_1451
+MPEISACAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRMDPEHKGQDPLTRELMVH
+PGAVAVLAVRTQLSTVGPREQVALVRQYRHPVGMELWEVPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTSPGGSTEAIRVFLARQVEVIPEAERHARTDEEAAMPLAWVGL
+DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA
+>3_1359
+MAEVPASAGRSPLRDLSLPRRVKKSKTVFEGRVWDIARESFRMDPDDKGQEPLTRELMVH
+PGAVAVLALRTHLTTAGPVEQVALVRQYRHPVGMELWEVPAGLRDVAGEPLVETARRELR
+EEADLEAAEWHTLADFFTTPGGSTEAIRVFLARQVSAVPEGARHEREGEEASMPLAWVNT
+DEVLDAVLDGRIHNPSTVVAVLALHAHRAQAWRRLRPPDAPFVPDRRGPGADRPA
+>4_1319
+MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH
+PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA
+EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV
+DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66ceb6372acf181cb9224a4682fdcd5ce2b53e1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001185.fa
@@ -0,0 +1,45 @@
+>0_1383
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVKHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>1_1124
+MSTDQSALLKRYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>2_1437
+MSTTQDALLARYADSLTGVFGRPARVLVRGEGVHVWDADGRRYTDLLAGIAVNSLGHAHP
+AVVRAVREQIAGLGHVSNLFTSEPQIRLAEELLAVADAPAGSTVFFANSGTEANEAAFKL
+ARRHGGQDPSGSRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDVDA
+LRAALAPGASGATVAAVVLEPVQGEAGVHGWPVGYLAQVRALTREAGALMILDEVQSGMG
+RTGTWFGFQNPSVTGSDDPVLPDAFTLAKGLGGGVPIGALVCVGPEVSGLLSAGQHGTTF
+GGNPLATAAGLAVLETIRSEGLLEHVRAAGERAAKLLADLPEVAAVRAHGLWIGVDLAAP
+RGPVPDGGLAPAVVAAGLEAGWILNATGPDTLRLAPPLVIAAEDLERFVELLPALVAAAT
+TEGDPS
+>3_1345
+MSTAPGTDPAAPQEELLARYAHALTGVFGAPARALVRGSGTSVWDADGREYTDLVAGIAV
+NSLGHAHPAVVEAVSRQVATLGHVSNLFTSEPQVRLAEALLDRAGLPEGSSVFFCNSGTE
+ANEAALKLARRHGTQDPTGRRTRVLALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEF
+IAGGDAGALAAALAPDAEGRTVAAVVLEPVQGEAGVHGWPAAYLARVRDLTREAGALMIL
+DEVQSGVGRTGTWFAFQNPQVTGSGAPVVPDAFTLAKGLGGGVPIGALVSVGPQVSRLLA
+PGQHGTTFGGNPLATAAGLAVVETLEAEGLLDHVRTVGARVSERLETLAEVTAVRAYGLW
+IGVDLADDAAASPTGGLAPAVVRAGLDAGWILNATGPRTLRLAPPLNVEAADLDRFADAL
+PALVRAARAAAPTPHAPKEETA
+>4_1332
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQIATLGHVSNLFTSEPQIRLAERLLELAGVPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSRLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPVPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001187.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71cb6f373c1b33bcde844ec1450f46d6ff5502b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001187.fa
@@ -0,0 +1,40 @@
+>0_1385
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>1_1126
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>2_1435
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS
+DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER
+LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM
+LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA
+ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP
+NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>3_1343
+MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT
+DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT
+LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM
+LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG
+AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP
+NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH
+AGDAVVELWTNDLTHDYVHENSAYST
+>4_1334
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT
+LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7afeff2fbb20f281afd412103a84ea6943f6534e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001191.fa
@@ -0,0 +1,24 @@
+>0_1390
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>1_1131
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>2_1430
+MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP
+RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA
+LRRA
+>3_1338
+MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP
+ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED
+PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG
+TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS
+>4_1339
+MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH
+GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..243e3d4497f38ec4319268a1da87c9b9c2c7ee5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001194.fa
@@ -0,0 +1,20 @@
+>0_1394
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRASLALGGYIERPVVRGLRRRR
+>1_1135
+MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
+>2_1427
+MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG
+WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST
+WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR
+>3_1331
+MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP
+GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP
+ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA
+>4_1343
+MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG
+GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA
+SRNVFERRAGLALGGYVERPVVRGLRPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d450ee46d0676f52028c7d9d3592f4f15346bca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001195.fa
@@ -0,0 +1,26 @@
+>0_1395
+MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA
+VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL
+QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV
+MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP
+GGTLH
+>1_1136
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS
+ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA
+LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH
+>2_1426
+MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP
+ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA
+HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH
+RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH
+>3_1330
+MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA
+LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL
+PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ
+TPALPAADLARAVAAVARAALVEGPDLDVPGGALH
+>4_1344
+MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP
+ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA
+LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH
+RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001197.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f9dfeb13be0cb9cfb5c44f1fbf34644901ce734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001197.fa
@@ -0,0 +1,20 @@
+>0_1397
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR
+>1_1138
+MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR
+LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI
+PADRPIVAEVLRGAATAFSAGR
+>2_1424
+MVGLALLDDAAAPSRLLAARRSAPAVLRGLWEFPGGKVETGEGPREALAREVREELGVAV
+RLGAEVPSPDPEGWELANGARMRVLWGVLAEEGAEPAALEDHDLLAWVPLSGAGAHHLDW
+IPADRPIVSAVVAGAATAFAAAP
+>3_1328
+MSPATPQTPPVPSAPRPVVGVALVDDAARPTALLAARRSAPASLAGLWEFPGGKVEPEEG
+ADAALHRELVEELGVRVRLGTEVAAPEGPGWELANGARMRVWFGVLREDSGAPAALQDHD
+RLEWTPLTAEALHALDWIPADRPIVDALLAAVEAGRLGL
+>4_1346
+MTSATPARPAPAARPTTSPRDGARPRQVVGLALLDDVAAPTRLLAARRSAPAPLRGLWEF
+PGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEEG
+ATPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e9484fb6da3efa50ed74a9eb32ba6468d867163
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001198.fa
@@ -0,0 +1,15 @@
+>0_1399
+MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLVFNINVNEKFF
+SLGTWIFAIIGGVIVAAVWQAITRRTGTRA
+>1_1140
+MFTIIAWIIIGLIAGAIARLILPGRQGSGWLGALITGLLGAVLGGWISTLLGGEGLGDAF
+SWQTLIWSVIGGVIVAFIWQAITSRRGTRV
+>2_1422
+MGFIAWIVLGLIAGAIARAILPGRQGTGWLGALITGVLGALLGGWIGHLMGFSTNDSFFD
+LATWIFAIIGGVIVAFIWQAITGRRGTRV
+>3_1326
+MGFLAWIILGLIAGAIARLILPGHQGSGWLGALITGVLGALLGGWLGRTLFGASTNDGFF
+DLATWFWAIIGGVIVAFIWQAIAGRMGRGTRV
+>4_1348
+MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLLFDFDVNEKFF
+DLGTWIFAIIGGVIVAAVWQAITRRTGTRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..521ae50356927a9354d2c93382197d381f7834cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001199.fa
@@ -0,0 +1,33 @@
+>0_1400
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ
+WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA
+PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
+>1_1141
+MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ
+WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG
+QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD
+PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA
+RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD
+>2_1421
+MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA
+EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH
+VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV
+ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV
+VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF
+GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG
+>3_1325
+MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER
+TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV
+TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS
+VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL
+GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA
+>4_1349
+MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ
+WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG
+QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD
+PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA
+PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69a3d875ef688c015a78fd1d704ef378dda483e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001200.fa
@@ -0,0 +1,15 @@
+>0_1402
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
+>1_1143
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
+>2_1420
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDKLVSKGSLKQIKR
+MLGI
+>3_1323
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLAGDKVVSKGSIKQIKR
+MLGI
+>4_1351
+MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR
+MLGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cb4aec496e61e43b0276f9353c224afba0632a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001201.fa
@@ -0,0 +1,39 @@
+>0_1403
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA
+TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP
+KPGPRA
+>1_1144
+MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH
+AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV
+GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA
+FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA
+TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA
+>2_1419
+MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP
+TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL
+SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT
+KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL
+KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA
+PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA
+>3_1322
+MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR
+PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE
+ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE
+TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN
+MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN
+SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP
+KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG
+>4_1352
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS
+PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41c2bc52f662ee9f9c9a88a3039100e92a9729b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001202.fa
@@ -0,0 +1,19 @@
+>0_1404
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
+>1_1145
+MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG
+LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN
+>2_1418
+MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>3_1321
+MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL
+DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG
+PVN
+>4_1353
+MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP
+DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK
+GPGEKFTGPVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aede8edb69043510de208dc5217ae5d39ce82dd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001207.fa
@@ -0,0 +1,25 @@
+>0_1409
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>1_1150
+MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI
+AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
+>2_1413
+MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP
+GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR
+RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS
+GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR
+>3_1316
+MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP
+GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR
+PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA
+TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG
+>4_1358
+MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI
+ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV
+ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV
+QLLAPEETLPRIVDAKVKDARVTLVPAHGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..069c6a44c183eddb3a3fb868b0d04952337fc7eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001208.fa
@@ -0,0 +1,15 @@
+>0_1410
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTEADAKAR
+>1_1151
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAQAR
+>2_1412
+MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR
+ARVQEWAEADAKSR
+>3_1315
+MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR
+SRVAERTREDAGHGA
+>4_1359
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAKAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2ca0982907d1e650eb5ba8be914bdaea104f87e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001209.fa
@@ -0,0 +1,25 @@
+>0_1411
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAVAAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
+>1_1152
+MRWNGLFDDLEAHWVDLGWQETVAEAAELTRAEWMALSLVDRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPLDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
+>2_1411
+MRWDGLFDDLEARWADLGWRQSEAEAAELTRAEWMALTLADRLRGERGRPVRLHLAWGEA
+LDGVLHAVGEDWAGLHLSGGRSAVVPLPGVAAVEAGLHRAVPAPTGPATGLGAVLRGIAR
+ERVPVVVTGTRGVTLVEGTVDRVGRDHLDVSRHPRDEARRAAAVRGRLVVPFTALGVVRT
+ASRLA
+>3_1314
+MRWDGLFEDLEARWSALEWDATRAEAAELTRGEWAALTLEERLRGARGETVRLHLVWGEH
+RDVRLGTVGDGWVSVNAAAADSLLVPLTSVVAWEGPLGAASTAPEGVRSRPGLPAALRQL
+ARARAAVRVVAGNGVELGEGTIDRVGRDHVDLARHPRDEARRAGQVRGRLVVPLAALGLV
+ATPGPLG
+>4_1360
+MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV
+VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR
+TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT
+ALRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f9083620343722d162bf75e632cea2fdeaf81cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001214.fa
@@ -0,0 +1,30 @@
+>0_1416
+MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ
+DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP
+DLPGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG
+PSHAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG
+AVVLAAVAPPRDPAEPGPRPGPRVG
+>1_1157
+MRSPPSSPSPAFGALGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQDA
+PALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEPDL
+PGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGGPS
+HAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVGAV
+VLAAVAPPRDPAEPGPRPGPRVG
+>2_1406
+MPHAPAPEPLLESDSGLPAARRAIAALAALGEAFVDLVLPAECAVCAAPGHRLCAPCRLE
+LNAALARPFRAEHGAAALPLGPGGVPLPVVAAGRYADALAAAVLAFKDHHGLHLRAVLGE
+ALCRSAAVARLAPDVPEAAHALLVPVPGGAAGFRRRGYDPLAELVRALPAPWVVSDAVRA
+PRGPGRARRAGPSHAGAGSAQRRRRARRWRPVPGRLPAGAPVLLVDDVLTTGATLGALAE
+AVRRAGGRPVGAVVLAAVAPPADDPGPVTGAGVG
+>3_1308
+MHPLLESVVDLVLPADCAVCGAPGHRLCPDCRCLLGRELSAPHRAEEPALALPLGPDGAP
+LPVWAAGDYRDGLAAALLAFKDHHGFGLRPILGDALARTVAAARLDPGLQEAAHALLVPV
+PGSASGFRRRGYDPLAELVRSLPAPWVRDDVVRAAPAWSAWPPGGGPSHGGAGSRERRSR
+RRGWRVREGALRPGTPVLLVDDVLTTGATLAALHRAVRRAGGRPVGGVVVAAVAPPTGDG
+GAGVGGAGSTLAGAEPGE
+>4_1365
+MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ
+DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP
+DLPGAPHALLVPVPGGAAGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG
+PSHAGAGAGQRRRRARDWRVVAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG
+AVVLAAVAPPRDPAEPGPRPRPRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58be0f417d3c643517b95cf5d901ce2ee34389d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001219.fa
@@ -0,0 +1,40 @@
+>0_1422
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPGRPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
+>1_1163
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPARPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
+>2_1400
+MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVEDFVAEYAAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGGLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADSPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLTPGPIVDADGCAVGEHAGAQAFTV
+GQRKGLAIGRPAPDGRPRFVLEVRPKENTVVVGGRELLDVDRITGIRPTWAGAALPEART
+GEWFDCALQFRAHGEIVDARARQLEDEAGGPRWEIEPARALRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLAAGSDA
+>3_1302
+MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDAQDAWRA
+CEVLGIPFYTWDFSERFQADVVDDFVAEYAAGRTPNPCLRCNEKIKFEALLDRALELGFD
+AVATGHYARVEWGEDGRVQLHRAAEDAKDQSYVLGVLREDQLEHCLFPLADTPTKELVRS
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVGADGEVLGEHAGAQAYTV
+GQRKGLAIGRPAPDGRPRFVLEVRPKDNTVVVGGRELLDVDRITAIRPSWAGAPLPEAAA
+GGWFDCELQFRAHGEIVPARARQAADDDGRPRWEIRPERPLRGVAPGQSAVLYRGTRVLG
+QATIDTARNAAVDAAERA
+>4_1371
+MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA
+CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD
+AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA
+EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGRELGTHAGAQAFTV
+GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART
+GAWFDCALQFRAHGEIVEARARQRADEAGNPGWEIEPARPLRGVAPGQTAVLYRGTRVLG
+QATIDTARNARLSAPADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59e252145abb2503619e70ab3d255b6b7b3ce863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001223.fa
@@ -0,0 +1,35 @@
+>0_1428
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVGRLH
+>1_1169
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDERRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
+>2_1396
+MSAADEHCTAYEVLGVDRDADDAAVRRAYRAAARRTHPDAGGDPAEFRAVSRAWQVLGDA
+DARRRYDLSLPAPGAGRAPASGGAARPGRAAASRPARGAAGRPARTVRYEPPPGEGESDA
+AVLDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLAGR
+WGRPLDVDHAVLCGHRLALVGSVMVPEGAYTWDGSDLRSRGRPVAPPLLGPAMMAWQQVL
+PQVTVGGFVHVMTDRDALHGPVVRHARGADDPGARADLLTVPPAPGREFVRDLLLFLGTG
+EDPDLVDRRVLGTLVERLH
+>3_1296
+MSGTGDRRTAYEVLGVPRDADAERIRRAWRAAARRTHPDAGGDARDFRAVTRAWEQLGDP
+EARRRYDLSLPPEPAGTTGRTASAGRSAAQAWPPAGVRERDRPAPGSVVYDPPPGQGEHD
+SSVLDLVRSSQRLHGAPRPRGILPDEHRVVRQARTLDLLARTLPPVLPAVRILTGLHLGG
+RFGRGLDVDHAVLCGRRLALVGSVQVPDGTYTWDGADLRAGARGRPVAPPLLGPAMQAWQ
+HALPQVTVGGFVLVMTDRDAVHSPVIRQARGADRPEAQADLLTAAPAAGRDLLRELQLFL
+GSGPDPDVVDRRALAVLVRHLH
+>4_1377
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRSRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2a79a502db51743b362d162eccbc1ebbb69ecc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001227.fa
@@ -0,0 +1,45 @@
+>0_1432
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGDAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGSDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGGENAQTVFSDGARVQQVV
+GGSAADAAGLKEGDVITAVGDRAVIDSESLTAVVREYRVGDSVDVTYLRDGAEQKTEVTF
+TEDTQS
+>1_1173
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGTDQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTVFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
+>2_1392
+MRSEDTVAHTPADQTPTDQTPTDQTPAPARPAAEARHPGRRAPRARAGLGLLAAAVLVTG
+LAGCGVAAEPGADASGSAPDSSTSSGSASADPGQDVADTAVGTAAKTALPSVVTISATSG
+QGSGSGSGTILDEEGHILTNTHVVTLGGQASDAELTVRTADGTVYAATVVGTDPLSDLAV
+IKIDAPDLTPIQMGRSADLKVGDDAIAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPRQ
+QESEQGQGPGQGSSSGPERFRFELPGAQQGPQGEVYINVLQTDAAINPGNSGGPLVDGQG
+RLVGVNVAIASAGQGQGEAGNIGVGFAIPVDYAQRVAQDLIEHGEATHAVLGVSVTPEPA
+EVQGGDAQARTVFSDGARVREVVADSPAAQAGLREGDVITAVGERAVIDTESLTAVVREH
+RVGDSAEITYLRDGAEQKAQVEFQEDTSQ
+>3_1292
+MGRAAHRPDCTDGGADQKPAQTRSEATVEHPAPDTVTPEAAPVASSPRPASPRGRRRALG
+GALAATVLAGSLAACGVAGPGAGASASASASGSSSAAAAPAVGSTDQPVADNPVGAAAAK
+ALPSVVTISATSGSSAGSGSGSILDAEGHILTNTHVVTLGGTASDASITVRTSDGKVYAA
+KVVGTDPVSDLAVIKIDAQGLTPITIGSSKDVKVGDDAIAIGAPLGLSNTVTDGIISTLN
+RTIAIQSSAAPEGQTGSSGTERFRFQLPGEQGQSQQQDIYINVLQTDAAINPGNSGGALV
+NGAGELVGVNVAIASAGGSSASGAESGNIGVGFAIPVDYAKRVADDLIADGTASHGLLGV
+TVQPQPAQVQGAAGGSKSTEFSAGALVHTVSSGSPAEKAGLKEGDVITQVGERTVTDTES
+LTAAVREYRDGETTPVRFTRDGREQTADVTLTAMEASR
+>4_1381
+MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA
+SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI
+LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG
+DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGAEQYRFQ
+LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG
+VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTMFSDGARVQQVV
+GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF
+TEDTRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..073eb29ec3437e418397b6c863ac8cc00b7576e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001228.fa
@@ -0,0 +1,66 @@
+>0_1433
+MTVLTRPADVGRLARAVTAAGLGGLGLLVAAPTAQAVAVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEERAYGLDS
+GGDANLQNQVTRTYVGPQLSKIGTDPGSAEWLAVGIAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTTGGGSTAQGASDGGGALTAVLGAGAVAAAVGGGVLVARSRRRTQGGAVER
+GRTEEARRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDI
+DQAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLE
+NQVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETA
+LAKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQ
+DVAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPL
+AGVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSA
+ISLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMGSRYGTRPRAGVGGSFGG
+GLGGALLGGILMNSILNSGHGDSWGGGGFGGFDGGGLGGGDFGDISGGGF
+>1_1174
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFREDID
+RAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGAALAAHKKEFDSLRDLEN
+QVPEALERVDARLPEARSRVQESESAIAALHGQYAESALAEVADNATQARERLEFVETAV
+AKARSAWDAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSNPELAGPVAGMKNAVNAVRRALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>2_1391
+MTAAGLGGVGLVLAAPGAGAGIAPPGVYVVDEAGVLSSADEQRLTQEITDLRRDTGQGLY
+VVFVDSFETNAQGLADDVARQRGLGTNDSVLAIAVEDRSYGLGSGGDASLQNQITRTYVG
+PQLSRIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEYDPEGALPAGSGAGAGT
+GAGSSQGSDEGSGVLTAVLGAGAVAAAVGGGVLVARNRRKKDGGAVERSGRDARPVERDP
+LDEMSLEDLRTRAGSKLVAADDAIRSSEQELGFAMASYGEDAVRTFREDIDQAKEHMRAS
+FQLQHQLDDHIPDTEEDQRSWLKEIIQRSDAVGAALASHQKDFDSLRDLENNVPEALERI
+DARLPEARARVQQAESSISALHGQYAESALAEVADNAAQARERLDFVETAEAKARQAWET
+QDRSTAALAVRAAEESLSQVDTLTEAVGKAEGSLRTIVGNLQTGLAQSEQDLAEAEALVA
+NGSHPELAGPVAGMKTTLAAVRRSLSGGRPDPLDLLHQLEAAHRQLNTPLSGVRDAREQA
+RQASQMLNSAIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRAAIDLSRTDPVT
+ALQQAQRASQLAERASELARQDVEGFGYGGSMYGPGMGGMYGGRQRSGAGASFGGGLGGA
+LLGGILMNSMFNSGGGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
+>3_1291
+MAESVVRPSAPRLSRAAVLGGLGAITTTALLAPGAHAAVDVPPGTFVVDQAEVLSSAQES
+ELTQDITQLQSKAGQNLYVVYVDKFDSTPQATIDSVVQQRGLGNSDSVLAIAVENRNYGF
+DTGMSSTMQSDIRSAYILPALRKAAAGGDWEAPAVAAVQGLDDAANGTLDGRGRSGETYQ
+PDGTLPQAAEQDSSAQTSTSDSGNGASGALVGAGALAAVAGGAYVVSRRRRKSDGGAEPG
+AVATGPQASRDPLDELSVDELRKRAGATLVAADDAIRSSEQEVGFAMASYGEGAVGTFRQ
+DIEKAKEHMRASFQLQHQLDDEIPDTEADQRSWLKEIIARSEQVGATLAAHKKEFDSLRD
+LENSVPEAISALESRVPQAEGAVQAAERELVDLHGRYAESALTEVNDNATQARERLEFVK
+TAEAKARASLEAGDRSTAAVAVRAAEESLSQVGTLTEAVSKAGAALSTHVANLQMGISQS
+EQDLAEAQALLSAGRNPELAGPVGGMQQTLAAVRAELQSGRPDPLALLQRLESAHRQLNT
+PLSGVRDAREQARQAEQMLSAAISQAQAQIDGTADFIGARRGAVGSEARTRLAEADRSLQ
+TAMSLRSTDPVAALDHAQRASQLADRASERAQQDVADFGYGGMGGYGGLGGGYAGAGYRG
+GYGMPRSGAGGGFAGGLGGALLGGILMNSMFGGHHHDSGFGGGDWGGGGFGGFGGGGLDG
+GDFGGFGDADFGGF
+>4_1382
+MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL
+TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS
+GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY
+DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG
+RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDID
+QAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLEN
+QVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETAL
+AKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD
+VAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPLA
+GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI
+SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG
+GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8d6e54123fd5b4949cd2a1bbb6d343c16b5584d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001231.fa
@@ -0,0 +1,94 @@
+>0_1458
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVLAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLMVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGSVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDPEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYSFPTTLHVDRYEVDGQTRDTILAARDVNVDDMQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE
+EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQEQAPAEASPAPSSSPSPTPSG
+>1_1177
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE
+EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQEQAPAEASPAPSSSPSPTPSG
+>2_1388
+MSFGQGGGGPFGGPPRDGGGSAGGSSGPFGAFGPFGGAPQGPGGDGRDGGQGGGPFGPFG
+GGAGGSSAADRPRSGRPGRPSALVLTVIAVAILVGLFVLFTNVYTEVLWFSQLGFTEVFW
+TEVLAKAALFLLGALGMALAVWLAIRTAWRHRPSDASAAGRDSLSQAQRQLEPIRRLVFL
+GVPVVLGLFAGSAAMNGWDTVLLFLNQVPYGQADPEFGLDMMFFMATLPFLSLVAGYLTS
+VVLVAGIAGVLVHYLYGSVRVEEGGGIRVAPAARVHVGVVLALFLLLQAVNFWLNRYRTA
+QSQSGSWAGALYTDVNAVIPTSAILAVTAVIVAGLFVWTVFSGKWRLSLIGTAVLVITAL
+VVGTAYPFVVQEYQVKPSERTLEAEYISRNIELTREAYGLDAVEVTNYEGVTETEAGALA
+GEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPDTLHVDRYEVDGQTRDTILAARDVNV
+DDTQSWVNRHTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDEDYEPRIYFGQ
+NSPSYSVVGAPEGAPAVERDRPQTADSQDDTAYTFSGDGGPSVGGLFNRLAYAVKFGSPE
+LVLSSDVNEASQILYDRDPADRVSKVAPYLTVDTSPYPAIVDGRVQWIVDAYTTSDQFPY
+STAQQLGEVTVDSLSQGPNAALQGRVNYIRNSVKATVDAYDGSVTLYAWDDQDPLLQAWQ
+KVYPSSLRPYSEMSAALMDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPT
+RDGDVKQPPYYMTLQMPGQEEPAFSLTSNYIPQITQGSQQRNVLYGFLSAAGDAGTGEDG
+VKAEDYGTLRLLELPRSTTVPGPGQAQANFDSNATVSRELNLLRQGASEVLNGNMITLPV
+AGGVLYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEG
+QAGDPPQGEDGAAPAPGSVQEELSSALAEAQDALTRGQERLAEGDWAGYGEQQDRLNEAL
+RRATAADDALDGDAPADGEAPAEGQPPAEGSEAPSPAPEG
+>3_1287
+MSFGQEGAGPFGGPPHHDGDGGAHAARRVRAGGGRPSALLLTVIAVAALVALYMLFTQVY
+TEVLWFDQLGFSEVFWTEVLTKAALFVVAGAVMALAVWLSLRTAWRHRPGTAGADGRDSL
+SRARRQLEPMRRLVWAALPAVLGLFAGSAAMNGWKTVQLFLHQVPYGKADPEFGLDLMFY
+LATLPFLTMAVGYLISVVLVAGLAGLAVHYLYGALGVGDDGRVHVSVPARVHLGVLAGLF
+LLLQAATFWLNRYRTLQSQAGNWAGAMYTDVNAAIPTSAILAVTAALVAALFVWAAFTGR
+FRLPLVGAAVLVITALVVGTAYPYVVQQYQVKPSERTLESPYIARNIEMTREAYGLDQVQ
+VANYEGTTDAQAGDLKGEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPGTLHVDRYEV
+DGQTRDTILAARDVNVDPEQSWVNRHTIYTHGYGVVAADASAVGAGGRPQWMLSEIPSRG
+VLGDDSTYEPRIYFGLNSPAYSVVGAPEGAPAVERDRPQTADSTDDTAYTFQGDGGPSVG
+GLFNRLAYAVKFGSPELVLSSDVNEASQILYDRDPVDRVAKVAPYLTVDTAPYPAIVGGR
+VKWIVDAYTTSDQFPYSTAQQLGEATQDSLSEGQAAALQGRVNYIRNSVKATVDAYDGSV
+ELYAWDAEDPLLKSWQGVYPASLKPYSEMSAALLDHVRYPEDMFKVQRELLGRYHVTNPG
+DFYENNDAWSVPSDPTTDKDVKQPPYYMSLRLPGQEETAFSLTSTYIPQITDNGQQRNVL
+YGFLSADGDAGTGRDGERAPGYGTLRLLELPRSTTVPGPGQAQANFDSNAQVSQELNLLR
+QGASEVLNGNMITLPVAGGILYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLDEAL
+NQVFGGDSGATTPDAGEPAQEPRGTAEEELSSALAEAQDALAEGQERLAQGDWAGYGEQQ
+TRLNEALKRATAADDAAKGAQESADPAPEG
+>4_1385
+MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS
+AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL
+FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF
+AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG
+LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG
+ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI
+VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV
+RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR
+HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGHNSPSYSVVG
+APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE
+ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV
+TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP
+YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP
+YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL
+RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP
+VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEVPAPGE
+KPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG
+GDAPAQDQAPAEASPAPSSSPSPTPSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21ff0fda9dbecbb1adb2e47b428128c31f122d11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001232.fa
@@ -0,0 +1,35 @@
+>0_1459
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGASIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG
+>1_1178
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGETPAAARTCG
+>2_1387
+MRAVPPRTTRAYRLPASGWLALGSAGLALLLPTPYILESPGPAVDLLGERDGAEVLRVEG
+GTPDEGEGTLDMTTVMVGGPPISTTSVIDLARSLVDPAVDVVPRELMYPTGMSSEEVGAA
+NTAAMSDSQDTAAAAALHALGRPVPSTLVVHELVPGGPSEGVLRPGDEVIAAAGEPAEDL
+EDLRAAVGAAGPDPVTLTVRRDGAVTELRVPVAAAPEGAPQPWQMGALIETVVDVPLDVE
+LTVPDIGGPSAGLMFALTVLERLTPGAMTGGAPIAGTGTITPDGVVGPIGGIPQKVRGAA
+QAGATTFLAPTANCGELDGRVPEGLQVYAVDTLAQAREIVEAVGRGEPPESARTCG
+>3_1286
+MPYILEGPGPAIDVLGEQDGTPVLTVEGGTADPGEGRLDMTTVLVSGPPGGTTGLGDLVT
+ALADGTVDAQPRELVHPSGVSADTVAQSNAAAMTDSQDVATAAALRALGRDVPAHLAVHA
+TVPGAPAEGILREGDVILAAAGRSVTDMAGIRAAVDAAGPGDLALTLRRDGTERQVSVPV
+TAADPATGRSWQLGVLLEQRFDLPVQVEFALEDIGGPSAGMMFALAVIERLTPGDMTGGA
+RIAGTGTITADGVVGPIGGIPQKMQGAARDGADVFLAPRENCADLAGRVPAGMTVYAVDT
+LATARAVVEAVGRGERPDDVPTCS
+>4_1386
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIESAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTISGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001233.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14ffb9454fa8874a9f8dd872a43486911dd1dad0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001233.fa
@@ -0,0 +1,26 @@
+>0_1461
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>1_1180
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>2_1385
+MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL
+VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS
+QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS
+DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT
+AQDTWVDDEDAMDADAPDDGPTEDERA
+>3_1285
+MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD
+RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV
+TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR
+LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG
+>4_1388
+MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD
+GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL
+SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL
+ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0705da7023ad89b1efb9b76c9665e0c3347bb63d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001235.fa
@@ -0,0 +1,65 @@
+>0_1463
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>1_1182
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA
+>2_1383
+MSTPDEILRGLDPEQRRAATALQGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQGMRMSVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARGREMPAGWDATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPRIAATIRDQYRVFLVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERHPDATVVELVRDYRSSPQVVEAANRLL
+ADRTKAGQRDRTMPRWPDPLELVSQRPNGPDPVFAECTDDEAEAGWVADRIRALIDDGVA
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVPDRVRDVLASLGYSAQPPAATGAARERWESLHALVNLAEQLAGSRGAEFTLTELVA
+ELDERAQHQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRAREHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAPGAAKP
+RRRGATVATCRTCGKPLETGAERKVGRCLDCPATYDEAVLEQLRDWRSRTAAEMKMPAFV
+VFTDATLVAIAEAMPASPKELLAVPGLGRTKLEKHGEALLELLHGTPTA
+>3_1283
+MSTPDEILRGLDPEQRKAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVDGVQARTFHSAALRQLQYFWPQAVGGQMPTLVENKVRLLT
+EVAHRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARDREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPKIAATVREQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRQDLCVVGDSSQTIYSFTGATSRFLTGFRERYPEATMVKLVRDYRSSPQIVGAANTLL
+AERTQAGLRDRSLPFWPEPLALSSQRPSGPDVVFAECQDDEAEAGWVAQRIQGLLDDGVP
+AAEIAVLFRTNGQSEAFETALSAAGIGYQLRGGERFFSRREVREGVLQLRAAAREAQDLV
+GADVVQRVKDVLSSLGYSDTPPSASGAARERWESLHALVNLADQLAGTREDFTLVQLVAE
+LDERAQAQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFADTPAEVDEERRLL
+YVGITRARQHLHLTWTLARSGGGRANRRPSRFLRAIDPTLGGTREHAPAAAMPARRPRRG
+ATVAVCRTCGRPLETGAERKTGRCVDCPALYDEGVLDTLKDWRSRVAKTDKVPAFVVFTD
+ATLEAIAETMPATPAELIKVKGVGKSKLDRFGQDVLDLLHGTSAA
+>4_1390
+MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA
+LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT
+EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY
+EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL
+GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL
+ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP
+ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT
+GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA
+ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL
+LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP
+RRRGAKVAVCRTCGKPLETGAERKVGSCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV
+VFTDATLVAIAEAMPRTPAELLKVPGLGKTKLEKHGPELLELLHGTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ecc7592b83983c2e5e57c201202eaa98a4530c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001238.fa
@@ -0,0 +1,105 @@
+>0_1466
+MAPLTGDPAAPTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG
+KTSTMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAAAGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRAQRAAGGREDPAGAAPDAAPDRDVSPEEDADAAALLEALDSLPGEGTDWVG
+SRGRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAA
+RRHLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHAS
+KGLEWDVVAVPGLQEGTFPSTRADRWTSPGAGALPWPLRGDRASLPQWDGSWAQDQRDWV
+QSAGTKYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKE
+PLPASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAARTLVARWPFDPLDGPEAFVA
+DPEDPEDEERWQPLPHRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDV
+AGTGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGA
+TGMLDIGSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRV
+DAIYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLER
+IGASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>1_1185
+MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTQEQAEVVTAPLTPRLVLAGAGSG
+KTATMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE
+PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG
+VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG
+LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ
+DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR
+LETGPGGAPRRVNADVSHLTIAWRNEESILAVANTVAAPLNAHAAATGGAPVEVRTLRPR
+PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD
+AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE
+RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR
+GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR
+HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG
+LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS
+AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL
+PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP
+EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLVRRRDVAG
+TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG
+MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA
+IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG
+ASFVYVAHGQERSFPDLPGEEELERHITDALARR
+>2_1380
+MAPLTGGPAAPDADRPAGPDAVPADRPGTADAVHAPQDIAARLGLPAPTEEQAEVVTAPL
+APRLVLAGAGSGKTATMADRVVWLVANGVVRPDEVLGVTFTRKAAAELAERINGRVDALL
+RSGLRIPGFDGEPEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLMGGADAHRLMGSV
+VRSHPVVADTLGVAPSRLVSQALHLAGDMAEHLVTPEEVRTHLARVAQQGRDLPLPPRTK
+APTKEIAAFFTGLADRALMADLVARYDEVKREQDVMDFGDLLRHAARIASEVTAAGEQER
+ARFPVVLLDEFQDTSHAQMRIFAGLFGPRGPEDDAAGLGHCVTAVGDPHQSIYGFRGASA
+GQLFAFPHAFPRLETGPDGGRRRVNADVSHLTVAWRNEESILAVANTVAAPLNAHAAASG
+GAPVEVRTLRPRPGAGDGVVRVDRFLTPEEEAHDVVRRLAALAEADGAAPSRAVLCRTRA
+QFGPVLEALEAAGVPYEVLGLSGLLALPEVAEVLAVLHVLADPVRGDQLVRLLTGPRWRI
+GPADLEVLHERARFVARMRARRAAGEDAQDPEGTGGADPEATAAEDVSPEEEADSAALLE
+ALDSLPGEGTEWTGSRGRGFSAEGLARLRAAHAELRRLSARAGEDPADLIAEVVRETGLD
+VEVALRPGLSAAAARRHLNAFQDAARDFGAGTAGADLAAFLAWTESVMEHEDGLGVENAE
+PTPGLVQVLTAHASKGLEWDAVAVPGLQEGTFPSTRADRWTTPGSGALPWPLRGDRGSLP
+QWDGTWAQDQRDWVQSAGTKYSSKAAQEDNPDPYAAAVEAHAEREERRLAYVAVTRARRE
+LWLSTSAYKGTNKDPLPPSAFLEEAAGLAGRVPGVVAGHAPDEDGMPEANPAAGRTLVAW
+WPFDPLDGPEAFLADPEDPEDEGQWRPLPRRARARRDAVEAAAAAVRAAEPSALAAEPEL
+ARQVDWVLLRRRDVAGSGGDVALPDHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARR
+GTAFHAWLEERFGATGMLDIDSAEDAEDLWVDEALDLEPMQAWFRSSRWAERTPAFVEAP
+VETTVGGITLRGRVDAIYRSGGDPRNPVDPEADWELVDWKTGAVPRGRDLELKSLQLAVY
+RLAWSRLHGIPLERIGASFVYVAHGQERSFPDLPGEAELERRLAEALRRR
+>3_1280
+MASLSSPVPLRPAPVDAGPRVDVSRAVHSPQDIAARLGVFPPTDEQVEVIAAPLTPRLVV
+AGAGSGKTATMSDRVVWLVANGFVRPDQVLGVTFTRKAAGELAHRINAKVDALLRSGLPI
+PGFEGEPEDLGRASVSTYHSYAGALVRDYGLRIGVEPEARPLGEADAHRLMSAVAASHPI
+VADGLRVSASTLVAAALRLSGDLAEHLVEPAQVRAHLRERIAVGEALELPPRMKEPSDEI
+VEFFAGLETRVLMADLVERYTQAKAERGVMDFGDLLRHAARVAREIPAAGRAERERFPVV
+LLDEFQDTSHAQMEIFRGLFGPESTDLDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFTF
+PSAFPRLGELPGGAPGRVNADVSHLTVAWRNDEAILAAANAVVAELNAHAADAGTPLELK
+PLRPRPGAGTGEVRVDRHVSAQDEAEALVARLAALGEDPATADLSRAVLCRARTQFGPVL
+DALEAAGVPYEVLGLSGLLSLPEIAEVLSVLHVLADPGRSDHLVRVLAGPRYRIGPADLE
+LLHERARFVSRLRRRAAAHEPLDPATAVEAPDVSADEDADAPALLEALDSLPGESTVWTG
+SHGRPFSAEGLRRLRAANAELRRLSAWAGADPADLIGEVVREIGLDVELALRPGPSAASA
+RRHLDAFQDAARGFAAGDGAPADLPAFLAWTEAVEEHEKGLGIASADPAPGVVQVLTAHA
+SKGLEWDVVAVPGLQTGTFPTARPDRWTSGGTGMLPWALRGDAASLPQWDGSWAENRRDW
+VQSAGTGYSSKTAAATNPAPYGDAVADHAAREERRLAYVAFTRARSALWLSTSHWKGTAK
+KPVDPSPFLVEAAALAGEVPGVVLGEEPAPEELGEANPTAERTLVAWWPADPLEGPEAFE
+ADGEDLDDEAAWTPLPRRTRPRRARVENAARQVAAADPAALAEDTDLARALDWVLLRRRR
+VGAAADGVALPEHLSVSLYGELAADPQAVADQLRRPMPRPPAHAARRGTAFHAWLEQRFD
+ATGMLDIDESDDAADAWVEDALDLAPMQEWFLASRWADRVPAFVETAVETTLAGITLRGR
+IDAVFRTGARPGMPFDPEADWELVDWKTGRVPGGAELRRKALQLAVYRLAWSRLHGIPLE
+RIRASFVYVAAGQERVFDDLPGEEELEAIVTAAVAGPGATSSGEVSPPDAAR
+>4_1393
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7966e7831189a5d21b0d81b3658708f8fe7911a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001239.fa
@@ -0,0 +1,104 @@
+>0_1467
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP
+AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL
+AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>1_1186
+MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG
+TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT
+WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP
+AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE
+AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS
+VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG
+HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV
+LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL
+DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD
+ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER
+WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP
+VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT
+LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE
+RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL
+AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG
+GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI
+GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP
+TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG
+TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ
+VTEWPR
+>2_1379
+MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP
+GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR
+TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA
+AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA
+EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL
+AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ
+GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER
+VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL
+LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS
+DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE
+RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL
+PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL
+TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP
+ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA
+DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG
+TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD
+AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ
+PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE
+QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR
+>3_1279
+MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL
+TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR
+LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV
+IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG
+RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE
+QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL
+DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE
+GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP
+VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI
+RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE
+PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV
+DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA
+WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV
+ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV
+GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN
+PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD
+LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG
+RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP
+AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC
+ALPSVCPLCTEGRQATEWHR
+>4_1394
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7472832c02091484d17b09c4d9adeb73b4cd7be6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001242.fa
@@ -0,0 +1,45 @@
+>0_1470
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>1_1189
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
+>2_1376
+MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL
+VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW
+DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV
+QRVLDALPAAAKAAAAATPQG
+>3_1276
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL
+VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT
+LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV
+ERVLAALPTAAKAAAAATPQG
+>4_1397
+MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL
+VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT
+EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET
+LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW
+DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV
+YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT
+LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV
+TRVLDALPAAAKAAAAATPQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fd29a3dc978596fca231b0a669ed3b287c7d280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001244.fa
@@ -0,0 +1,45 @@
+>0_1472
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG
+LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
+>1_1191
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD
+>2_1374
+MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP
+APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD
+>3_38
+MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI
+IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP
+WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA
+GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG
+MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL
+IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG
+LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF
+GWVVPALVGLVVGLVLEAARGRGRSAAVADA
+>4_1399
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e9566485af4433878187f09adc5f7f3b840292f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001245.fa
@@ -0,0 +1,38 @@
+>0_1473
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
+>1_1193
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA
+AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT
+KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV
+SLVRRRSRRAEG
+>2_1373
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS
+GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR
+GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI
+GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG
+>3_1265
+MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA
+TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR
+GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW
+ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG
+>4_1400
+MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN
+HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK
+RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS
+GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG
+KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT
+STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR
+SRRAEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fd96e33c1e5c3c22cfc54c4acfcc77188ff2b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001246.fa
@@ -0,0 +1,15 @@
+>0_1474
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD
+>1_1194
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD
+>2_1372
+MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASQLLSNTGFNNVAVAILREPRVDL
+MASATGVPQDEKHDAGPAPTEDDATDPDGDRPD
+>3_1264
+MPDSVRMANTLEFLRGVDRLHAFYTENVRMLAHAYDLSDEEASRLLAHTGFANVSVAILR
+EPRVDLLAGLGASVEDEVHTHPVVDDASAPAEEPPASGGADDPEEPPAGSAPADPDDGAR
+>4_1401
+MGNTLGFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI
+MAAATGVPQDERHDAGPAPSEDDAPDPDGDRPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fca66cdb8439d077d5bcce0c4f7a9b8ba0773b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001247.fa
@@ -0,0 +1,30 @@
+>0_1475
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>1_1195
+MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAEVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>2_1371
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAAGPGRSDGSRWLVLTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGGRAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDAAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFLAAGLTPLVGERVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA
+>3_1263
+MDGRPLVLTRQPAQAGTLEADLAAAGRRVAFCPLTDFELPPTPGGLRAVVEAVVGGRCAW
+LLVTSPNAVRALQAAGWTGAVGAGVRVAVTGAGTARVLADAGCAVEPWMPESASAAGILA
+EFPAAPAETGDGARRVLLPQSALATAELEEALTRRGWAVDRVEAYRTVPYPADAARRLLT
+EEPGDAGTVVPVAELAGADVVLTSPSAARALAVHPALDDPELRRTWRLVALGAPTAREAR
+RLGLRLTGQAATPDATGILAALARPVG
+>4_1402
+MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG
+DAVGPVRSDGPRWLVVTSPNTVRALRAVGWGGHVPAGARIAVTGPGTARVLTEAGCDAAP
+WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY
+PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGKRVR
+LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da9e9f1c82da1954f6f5e4096a5ada057c1df7e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001248.fa
@@ -0,0 +1,40 @@
+>0_1476
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLNRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
+>1_1196
+MTPLRIGTRGSALATTQTTHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAVQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
+>2_1370
+MSTLRIGTRGSALATTQTTHVAQALAERAGLEHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAILDGAVDLAVHSLKDLPAAQPDTLEIAAVPERADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLVLVDIRGNVQTRLARVPGLEQHDDGAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPDVMVPAPGQGALAVEVRAEDESFLGAALLEPDAPVGRLR
+AGLELVDDRATHVAVTAERALLRRLEAGCAAPIGAVARVVDGEAGAPRIEMTAMVAAVDG
+SRVLRRTSSVQLDPVPEDLAADPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPQPDDPA
+>3_1262
+MSGPGAPAGDGLRVGTRGSALATTQTTHVAEALTDRSGMPHELVVIRTEGDVTTGSLASL
+GGTGVFASALRSAVLDGRVDLAVHSLKDLPAAQPAGLEIAAVPPRADLRDALCARDGLTL
+ATLPEGARVGTGSPRRVAQLRALRPDLELVDIRGNVQTRLARVAGHEVHDDDAPAAAGAP
+RGDLDAVVLACAGLDRLGLQHVITERIDPEVMLPAPGQGALAVEIREEDGPLLGPSAVDP
+DSHAGRLRAALELVDDRDTHVAVTAERALLLRLEAGCAAPIGAVARVEEGTAVDGSPAPR
+IVMSAMVAAVDGSQVLRRTSSVQLDAVPEDVAGDPAEADEWIEDTLFMAAGALGVHLAEL
+FVAEGADLLPGTVRGVAKPDPEA
+>4_1403
+MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS
+ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR
+VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI
+LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRMH
+AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVSDGEAGAPRIEMTAMVAALDG
+SRVLRRTSSVQLDPVPADVAGDPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT
+VRGVDRGDGAPRPDDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf624bb5517abf9168ab405f3c0fe9691961cece
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001251.fa
@@ -0,0 +1,50 @@
+>0_1479
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>1_1199
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>2_1367
+MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ
+TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG
+DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA
+PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV
+TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA
+TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL
+THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV
+DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG
+TGLAAVVASVDRAFDAPPPAG
+>3_1259
+MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ
+TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG
+DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV
+PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV
+TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV
+AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL
+THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA
+DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG
+TGLAAVVAGVERTVAPAAA
+>4_1406
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..071e15c9128429f5c3e5e680d19fbb76cf4ea18c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001254.fa
@@ -0,0 +1,24 @@
+>0_1482
+MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>1_1202
+MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL
+IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR
+>2_1364
+MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR
+GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS
+ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT
+DDDAL
+>3_1256
+MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL
+ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA
+GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP
+>4_1409
+MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL
+YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL
+IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW
+ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e53cd6e118ac3ee68f8e7304c3e6e9012357b228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001262.fa
@@ -0,0 +1,30 @@
+>0_1491
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR
+>1_1211
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR
+>2_1355
+MSQTSRDARPSRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPEDLRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRLAVQEVATRDFVRGELRGVQEDLRDELREALRAELREE
+IRAELRAELAEGRRERTDPGAEPRPRKQKKHKGRDRGRDERRAGDDGVDPSTTTLAVIAA
+REAAQAAQSAQAGQDAGPEAGRAVDGRDDADGAAR
+>3_1247
+MPQSPRDPRDTRATGLDTPMRARERVMPRLTPNPDAFGEWTEGIARFMGTPQFLLWMTLF
+CLVWVGWNSYAPEPWRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRIALQDMATRDYVRGELRAMNEDLVAALREVVREEVREE
+LRAEEAGPAVAPKPKEKSKKKSSRREPGRPDGTEAHTTTLAIIAAQEAADQGGAAPDAAH
+AADDAGQDAP
+>4_1418
+MTQTARYLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMAWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAQEARE
+AGGSGPVTGPAGGAGPVDGGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f4874f97ed263213bdc36f02eca2586a040d100
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001264.fa
@@ -0,0 +1,23 @@
+>0_1493
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA
+VETEPDPLELLGLAPAPFDVDAT
+>1_1213
+MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV
+ETEPDPLELLGLAPAPFDVDAT
+>2_1353
+MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM
+ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT
+>3_1245
+MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS
+VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR
+SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA
+SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT
+>4_1420
+MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE
+VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP
+RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV
+ETAPDPLELLGLAPAPFDVDAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e131bcb6986c8ff565b3330a72a5fa326076ee03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001265.fa
@@ -0,0 +1,30 @@
+>0_1494
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
+>1_1214
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQASYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
+>2_1352
+MGRGHTLRHLDAYLEDALPSASRRRIARHLDGCPDCRAAVRARARVLDAARTVHQRPAGV
+VASPVLRSRGISGRVVVGLLAFVVLVGGLLAAVWMAGAPRAGVARLAPSPTDAVGLVSGG
+SADGRAAVAQLRGHGWTVPSLLGAGLEPLTVDAAQTPRDVEVVVGWGLQEPTVTVRECRP
+RIAGAAPEGCASAAPLPEDAQERTLTGGDVYRIQPAEADGAWTAELTTAQAAYRVEARLP
+DERADAVLTHLLVSERSRVRELGGPDAVEERLERGIERIVESVPRVRD
+>3_1244
+MGVLARGHCLPVLDSYLEGVLAPRASRRVEAHLSRCPDCRAVAGQRARVLDAARSVDARP
+AAGAVMRPRGVSGRAVVCGLLVLVVLAGLVAAVWMLGGPASTAAPADVDPVRAVSAPVSA
+SADEDDVATRVDELRGQGWALPSLSASGMRPLSVHADRVGEAAEVSVAWGRTSPVVTVRE
+CRGADADERTRCARQGGVGVSGASEARLPVGMDYRIADHADGGWEAWLSTSDAVYRVDAS
+VPRSQAEALLSQLVVVERSGLAPPRRDEDPRDRLERGLDRLLDGRVGGAAVRNPAAGAR
+>4_1421
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAALRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGAAPEGCASTAPLSTGAQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7beb9a1a0f757413bbe1e2a136bad4295385273b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001274.fa
@@ -0,0 +1,35 @@
+>0_1504
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>1_1224
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>2_1342
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN
+>3_1234
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN
+>4_1431
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..453b20192e593d43569149d57f7ae7c8c25924ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001278.fa
@@ -0,0 +1,60 @@
+>0_1510
+MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>1_1230
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>2_1337
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI
+TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS
+VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG
+EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG
+FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF
+IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>3_1229
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL
+PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS
+VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN
+LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG
+EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>4_1437
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1646ba3ff9721e5546b6feb4d1fbc0ce86086f7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001279.fa
@@ -0,0 +1,60 @@
+>0_1511
+MSANDKKGRSMFGKKKENDVTDGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVKLAGREVLTMTPGQLRGIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>1_1231
+MSANDKKGRSMFGKKNQNDVTAGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADITGSVQLAGREVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
+>2_1336
+MTAHGNDKEGRPMSGKKNQHDAAGTEATAVGTGAGEHGSHSADLDARGAAVPGSSGTGGP
+TPGPATSSMGVVARHDDLDGKPVLAFRDVDVKFGTEFGEVHAVKGVTFDVKPGEVVALVG
+ESGSGKSVTSATAMGLLPSNADITGSVQLAGREVLDMTPGQLRGIRGDEVAMVFQEPMTA
+LNPVLTVGDQLTEALELHGIAYGTEADKRAVELLTMVGIPDAAERLKQYPHQFSGGQRQR
+IVIAMAISCSPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMA
+DRVCVMLHGELVEQGTVHQVLQHAQHPYTQKLLSSVPRLGATYEVAEPEPVTATQTTAKY
+AIEAEDLHLEYDYRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEG
+SLRIQGHDLAAMPKSEQRKLRKNIGVVFQDPAASLDPRFPIGDVITEPMVVHKVGDRRSR
+LARAEELLDAVRLPRSVVNRYPHELSGGQRQRVSIARALTLDPQVLIADEPTSALDVSVQ
+AAVLDMFAELQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTKEVLHNPREEY
+TRRLLAAAPVPDPDQQAERRQERRDFLASLGEGVY
+>3_1228
+MSSKAFDPKDSGTTETSAEDLRARAETLPGSSGEAPQGVVTTATGSLKVPGPATTTMGVV
+EHHDDLGGEPVLAFQDVAVRFATEFGSVHAVKGVTFDVKPGEVVALVGESGSGKSVTSST
+AMGLLPPSADITGSVKLGGREVLTMTDSQLRSIRGQDVAMVFQEPMTALNPVLTVGDQLT
+EALQLHGLAFGTEATKRAVELLTMVGIPDAADRLKQYPHQFSGGQRQRIVIAMAISCSPR
+VIIADEPTTALDVTVQAEILELLRSLKDKMNTGILLITHNMGVVADMADRVCVMLHGELV
+ESGTVQQVLQRPQHPYTQRLLAAVPRLGEALETAEPEPVTSTQTAVKYAIEAEDLCIEYD
+HRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKAVLGLLPVASGALRLQGEDLATM
+KAAEQRALRRKIGVVFQDPAASLDPRFPIGDVITEPMVIHGVGDRRSRLARAEELLDAVR
+LPRDVVNRYPHELSGGQRQRVSIARALTLDPEVLIADEPTSALDVSVQAAVLEMFAELQT
+RYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTGRVLHHPQAEYTQRLLAAAPVPD
+PDQQAERRRERRRLLASFGESAY
+>4_1438
+MSANDKKGRSMFGKKNENDVTADGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM
+GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT
+SATAMGLLPGNADVTGSVQLAGRDVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD
+QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC
+SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG
+ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL
+EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL
+ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD
+AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE
+LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP
+VPDPDQQAERRQERREFLASLGEGVY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47d8a385e564240c05e9c1404890206574efcd86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001283.fa
@@ -0,0 +1,30 @@
+>0_1516
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
+>1_1236
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR
+GAALGGVLLGVAAMALSLDLLA
+>2_1329
+MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV
+EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM
+VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA
+FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR
+AATLAGVLLGVAAMAISLDLLG
+>3_1223
+MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA
+RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT
+ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL
+WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT
+ALAGAAAGAAAMLGSLSLLA
+>4_1443
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV
+EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b425f64940d029edd7d781a9979f327ff17819c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001287.fa
@@ -0,0 +1,21 @@
+>0_1520
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>1_1240
+MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGIGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
+>2_1325
+MPRLSAVSEPLTIAPRSDDAPSVPSSSSDAPRGPGGRRALVRRRVFRSPLQRRIVYAVVF
+ELLAILFTTGILAAFGNSGGSSLAVAVVSSTVALLWNIAFNSMFEAVERRAGITGRPWWL
+RALHAVAFEGGLILFLVPAVALILGVGLWQAFLIEAGLLVFFLVYAAVYAYAFDSVFGLP
+DSAAGATR
+>3_1219
+MTPPHDDAPRGPGGRRALVGRRVFRSPLRRRIVFAVVFELLAILFTTLILRAVGNEGAAS
+FAVAVVSSTVALIWNVVYNSLFERLERALGVHGRPWWARVGHTVGFEGGLVLFLVPAVAL
+LLGVTLWEAFLIELGLIVFFLVYNAVYTYLFDAVFGLPDSAGVTAPGTP
+>4_1447
+MSETRRARPGVDPASTPPFDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT
+VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE
+GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44f535904c28db9ed21bfcfe1719be738ac939ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001293.fa
@@ -0,0 +1,35 @@
+>0_1526
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EVSPRR
+>1_1246
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
+>2_1318
+MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL
+SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS
+GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD
+NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN
+FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV
+VDAADAPAPGRR
+>3_1212
+MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE
+EVSPRR
+>4_1453
+MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG
+PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI
+ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH
+LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS
+PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE
+EGSPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc9068764025deedddec1f08a7aaf14cd8e9fafd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001295.fa
@@ -0,0 +1,55 @@
+>0_1535
+MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV
+LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR
+PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV
+AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS
+LLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD
+QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR
+ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL
+MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR
+RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEV
+EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
+>1_1256
+MRAMFVVLGPAPASVGSPGTWWALDGEGDDAVPLGSCAAGSVAGLVAGLPARLGVDPSTV
+RWVLADVGTEYAAWLAAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTE
+PERPARVPAGQESFFDLPDEADPAPDVTVLAAELAAQRAAVEGSAHPQRLRLLAAAESQG
+ALVAAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQALAERIADVLGSPGLSPDS
+QPSLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWH
+WLDQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADSGWTLTVADASQV
+EPRILAAMAADQALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDS
+AALMPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGPTWQESVSDVGTQAAES
+AARRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRMRSAGMRTELVFFVHDEVVLHGPA
+TEAEAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
+>2_1308
+MRDMFVVLGPAPASVGSPGAWWAVDGDDATPLGSCPAGSVAGLVAGLPARLGVDPSTVRW
+VLADVGTEYAAWLAAGVRVDRCWDVALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPE
+RPARVPAGQESFFDLPDGTGSAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGAL
+VAAEIRAAGLPWDRGVHEALLTEQLGPRPAQGERPARLQALAERIADVLGSPGLSPDSQP
+SLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWL
+DQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADPGWALTVADASQVEP
+RILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKVALLGAMYGSTTGDSAA
+LMPHLRRLYPRAIGLLERAASVGEAGGQVATWLGRWSPAPEQAWLDSVADVGTQAAESAA
+RRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRAAGLGTELVFFVHDEVVLHGPAPE
+AEAVRGVVAEAASAAGRLLFGAAPVDFPLTVASLDSYADAK
+>3_1207
+MVIVLGPDPAPGTPPGRWCALVLPDDAAPSPADASPGQGDGGPVARFARDELADVVRALP
+GRLGVDPAVVRWTVADAAEVYPALLAAGVRWDRCRDLSLGQRILRGAAAAGLAYAPTVDL
+PVHEPEAEDPATARRAPGQGAMFELAGPEPAPDAAALARELAAQQAAVAASAHPHRLRLL
+LAAESQGALVAAEMHHAGLPWRADVHEALLAEQLGPRPPEGARPARLQALGERVAAALGS
+PGLNPDSPPALLRALQTAGVTVDSTRKWELTAWADQGGAQRQAREALIAPLLEYKALYRL
+WTAHGWHWLDTWARDGRFRPTYLVGGVVTGRWAAHGGGAMQVPSGVRDAVRADPGHVLTV
+ADASQVEPRILAAMSRDAALAAAGATPDLYREVAEQGRSAGTALDDRSRAKVALLGAMYG
+ATTGDSAALLPHLRRLYPAALAMLEAAAADGEAGRPVHTWLGRTSPAPAERWLERVADRS
+TREAEARARSLRRSAGRFTRNFVVQGTAAEWALCWMGQIRGGLHRAGLSTALVFFVHDEV
+VLHGPAEEAGAVARIVTEAASQAGRLLFGAAPVDFPLTVAQVESYAQAK
+>4_1462
+MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV
+LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR
+PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV
+AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS
+LLRALQTTGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD
+QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR
+ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL
+MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR
+RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEA
+EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22de1708331108da9bbeb4f95eea57bb0b1f4ed2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001298.fa
@@ -0,0 +1,45 @@
+>0_1541
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW
+RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA
+GALADGMRIGADARVRPGMLRYAD
+>1_1263
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA
+AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM
+IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN
+EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGALRYADGAARLTPPRGR
+>2_1276
+MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH
+CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR
+LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG
+FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV
+SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI
+ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE
+EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG
+AIADGIRIDDDGHGAV
+>3_1190
+MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR
+MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH
+GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG
+GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF
+QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN
+EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH
+TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA
+DGMRIGADARVRPGALRYAD
+>4_1468
+MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF
+CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW
+RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA
+AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY
+VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV
+IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN
+EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA
+GALADGMRIGADARVRPGMLRYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a61d32d3f4605ac7f0759911f8f3cf69f3dd44fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001299.fa
@@ -0,0 +1,50 @@
+>0_1543
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>1_1265
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGESLSWHQRFLETGTMRQG
+>2_1273
+MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE
+DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT
+VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH
+DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML
+DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH
+VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
+>3_1183
+MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE
+DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT
+VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH
+DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA
+IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML
+DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRQG
+>4_1470
+MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE
+EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA
+VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH
+DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA
+IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML
+DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN
+GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH
+VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH
+TPHLLGEALSWHQRFLETGTMRHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fb5b573392c3a701ef6bd8e2364bad8277cd294
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001301.fa
@@ -0,0 +1,20 @@
+>0_1545
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>1_1267
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVIPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>2_1269
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGANPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>3_1179
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGSNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
+>4_1472
+METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS
+ALQMVARASRADITDSSVGVRVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC
+PYSNATRGNIDVVLELGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dce2519524635d483276eaff0f2a964e55ad5654
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001303.fa
@@ -0,0 +1,34 @@
+>0_1548
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>1_1270
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
+>2_1267
+MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV
+LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG
+QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG
+GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV
+RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL
+>3_1176
+MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL
+>4_1475
+MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV
+ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF
+SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS
+AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD
+GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA
+GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fb1f7d20d3ba5c39eb690995c401e7341bf1e62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001304.fa
@@ -0,0 +1,26 @@
+>0_1549
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>1_1271
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+ALIAAGADYRKGPDGESFVVTDGTLVTGQNPASSGDAARRLLDLLAR
+>2_1266
+MRLVGTVTLARDSVVYDHKSSVPTNERAPDMSRILMILTSHDQLGDTGRKTGFWLEEFAS
+PYYVFTDAGHEVTLASPRGGQPPIDPTSSKPEMQTEATRRFDQDDEAKAALAHTTPLAQV
+DVDGFDAVFYPGGHGPLWDLVSDADSTRIILDSDAAGRPLGLVCHAPGILHPITAADGTP
+FVRGRQVAGFTNGEEDAAQLTDVVPFLVEDSLIAAGADYRKGPDGESFVVTDGTLVTGQN
+PASSADAARRLLDLLAR
+>3_1175
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+SEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITTADGTPFVRGRQVAGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDQESFVVTDGTLVTGQNPASSADAARRLLDLLAR
+>4_1476
+MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK
+PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII
+LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED
+SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5978097cf32e9bbb3bc315cbed5a3362101ca96b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001305.fa
@@ -0,0 +1,30 @@
+>0_1556
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGAGAVDERTPRIV
+A
+>1_1277
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDERTPRIV
+A
+>2_1263
+MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV
+GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR
+IDA
+>3_1169
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC
+AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTGPGAVDEQTPRIV
+T
+>4_1482
+MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDEQTPRIV
+T
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5646ae0f1807709b62796f48566f4c158b58514b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001311.fa
@@ -0,0 +1,19 @@
+>0_1575
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL
+QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>1_1290
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
+>2_1242
+MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG
+EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG
+>3_1151
+MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG
+RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE
+GEPHIVANGHNPLFGQIS
+>4_1504
+MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL
+EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV
+AAAGIAARVDGDPQVVANGPNPLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..311e07914b792857e41ddab10d39d79ddfbbb79e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001317.fa
@@ -0,0 +1,15 @@
+>0_1581
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD
+>1_1296
+MSEQGMEQTQDPGRPSGVEGFTSADVSDVARMSYEQARAELMETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDVD
+>2_1235
+MSEQQQEQTGAPVEGFTSADTSDVAGMSYEQARAELVETVTRLEAGGGRLEESLALWERG
+EALAARCQAWLDGARARLDEVRGAADSPTA
+>3_1145
+MSEQEQQGTAVGGFTSADTSDVARMSYEQARAELVEVVGQLEAGGAGLEESLALWERGEA
+LADRCQAWLDGARARLDQVRGEAAPDAD
+>4_1510
+MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA
+LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9896490c630e1a3ba69721d8ebec85343e032d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001318.fa
@@ -0,0 +1,34 @@
+>0_1583
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIMRHVIGAMDPLGV
+HVHAFKAPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>1_1298
+MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK
+DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIIRHVIGAMDPLGV
+HVHAFKAPTAEERAHDFLWRIRPHLPRPGLVSAFDRSHYEDVLVHRVRGLSPLAEVEERY
+GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY
+MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR
+RLLAG
+>2_1233
+MAENGTAETVRPDDAEGAETGVFSAPARELFAARRGDAVADPADVDASATPGYTGGKAQG
+KQDLADRADVLADLQELLFAQSTREAPSGEVPSLLLVIQGMDTAGKGGIMRHVIGAMDPQ
+GVHLHAFKAPTAEERAHDFLWRIRPHLPRPGRVSVFDRSHYEDVLVHRVRELSPLAEVEE
+RYGAIREFESRVRAAGTRIVKVMLRISAEEQAERLLARLDDPTKHWKFNEGDLDDRAYWD
+DYMDAYRIAIERTDTEDAPWFVVPADRKWFARLAVQQLLIETLQGLDLDWPEADFDVEAA
+RRRLLAG
+>3_1143
+MADTPENRFTEPVRTLLRARRADGAPVGPADVDPHGKPGFDGGKSEGRAVLAARSERLGQ
+LQELLYAQSTREADGGLPAPSVLLVVQGMDTAGKGGIMRHVVGQMDPQGVDVHAFKRPTP
+EEARHDFLWRVRPHLPMPGTLSVFDRSHYEDVLIQRVRSLAPAEEIERRYTAIREFEAEA
+VAAGIRVVKVMLHISPEEQKARLSERLERADKHWKFNPGDLDERELWDEYQEAYRVALHR
+TDATDAPWFIVPADRKWYARVAVQELMIETLEAMGLTWPEADFDVAAARRRLLAG
+>4_1512
+MADTPATAAGRPARATDAHGVFDAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGK
+KDLAARGRELADLQELLFAQSVRDAPVGEVPSLLVILQGMDTAGKGGIMRHVIGAMDPQG
+VHLHAFKVPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEER
+YGAIREFEAAVRAAGTRIVKVMLRISPEEQAERLLARLDDPTKHWKFSEGDLDDRAYWDQ
+YTDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPEADFDVAAAR
+RRLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed53b787788772f94d3c25e0beb6508d91bcf70f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001323.fa
@@ -0,0 +1,40 @@
+>0_1588
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVAARTFLKVLPPARAARVARRQAAAGAAGVPVPA
+VLATPEHGVLPLASVPGLPWRALLAGPEAAGLDPARVAALLDRLPPVPEEPPGPAGPTAG
+AAGCADTDDGGPAILLEHATWAAVVLDPEAQDEVAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL
+>1_1303
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPDVPAAACPPVPGERGFLEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVGRTFLKVLPPARAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGPEAAALDPARVAALLDRLPPVPEEPPGPAGPPAV
+AAGGADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRIRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRAARRAAADAALARVGL
+>2_1226
+MSIGRASAPLAVRASGLRWLRTRADALHLQRGRRLARVLDVDVMEGRAGDARVRTRTLVL
+ARDPRTGPDAAPPGSARTSERGVLEDGTLWWWAAADPALPGLALTENDAGLAALLGTAPG
+RVRLTWRGYRPRERAVIALDAADAGLAGSRAYLKVLAPAAAEAVAARLSAARAAGVPVPD
+LLAAPERGTLLLGNVPGLPWGALLGDARADALDPARVAEVLDRMPAPPGEAGPAPDAAAA
+LLEHAAWAAVVLDPERQAESAARADRLRAALAAGDPGPPVPVHGDLHPGNLHVDASGGRV
+TGLVDCDGLGLGHRVDDWATLLAHLEAAAADLGPGGGAVRAVAERVRAHARTETDEVALA
+ARAAVVLAALGADPSVPRAARTARRAAADAALARVSR
+>3_1138
+MVLLEGPPGAGVARERVLVLRGPVEPAVAVPGPPGPPVPASGPAPRRRGRGRLPDGTRWW
+LLPHDPALPGLDLALDHERLDAWLPGLGRAGEPAWVAYRPGERAVLRVPLDAVPARPDEP
+GSSLHLKVLPPARLHGMHGRLLAARAAGLPVPPPLAPPDLGVLALGTLPGEPWRARLGAD
+APQPAPAAVAALLDALPDALAAHDDGPSRTPAWSALLAHAVRAGTLLDPGAAEELRERAR
+RLEESLAAADPGPRVPVHGDLHPDNLLLAPGTDRIVGVLDPDSLGPGHRVDDWAVLVGHL
+AVAAADAAVPGPSHDPERARRTAALAAEFTGHACGVVDEEALRARADVTALALAAAPDLP
+AAVRAARRSAR
+>4_1518
+MSIDRAAARQAVRASGERWLRTRADALHLQRGRWLARVLDLDVMTGRAGDARVRSRTLVL
+ARDPRHPAAPGAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALVALLGTAPG
+RARLTWRGYRPRDRAVLAVEATGDDGVVARTFLKVLPPSRAARVARRMAAAGAAGVPVPA
+VRAAPEHGVLPLASVPGLPWRALLAGSEAAALDPARVAALLDRLPPVPEEPPGPAGPTAG
+VAADADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRLRAALAAGDPGPRVPVHGDL
+HPGNLHVDAAGERITGVLDADDLGTGHRVDDWAVLIAHLEAGAADLGAGGAALRAVAARF
+RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61f5db5cde8ec3a63bf68eb5cb2cbb5861264865
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001326.fa
@@ -0,0 +1,25 @@
+>0_1591
+MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL
+GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWASWHP
+GVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP
+RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV
+>1_1306
+MRTPPPVPEPASTGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL
+GPRVAAATADGTAPVVATVLPMATEPDTGVLRTRLLAAGARVLVPVIEPERRLSWAPWHP
+DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP
+RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV
+>2_1223
+MRTPPPAPEPASTGPVAGVDDVVAAKAALRARLRAARRERSPERRAAESAAAVEHLWAWL
+GPRVAQAARDGEAVVATVLPMPTEPDTGPLRERLVAAGARVLVPVIEPQRRLNWTAWHPG
+VATARAAAAPVDEPVGERHGVEALAEAVAVVMPALAVAEDGMRLGQGGGYYDRFLARLPR
+SVPTVALVFEDELLPAGSVPAEPTDRPVDALVTAAGLRHV
+>3_1135
+MPAAAPAPHPDDAAAALASTEAKAALRTRLRAARRGLDPAVRARQAEAAAEHLWTWLGPH
+LEERTADGPPVVATVLPMPTEPDTGPVRERALAAGARVLVPVIEPGRHLSWTAWRPGVAV
+ARAANAPLDEPVGPREPGSVLDGAALVLMPGLAVDLTGARLGQGGGYYDRFLATLPSSVT
+TVAFVHPSEVLEPGVIPLEPTDRPVDGVLTADGLLWCEPASAGPQ
+>4_1521
+MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL
+GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWAPWHP
+DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP
+RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38255d079570bf0886650faaf8a1e97a6cce703f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001327.fa
@@ -0,0 +1,15 @@
+>0_1592
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD
+>1_1307
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG
+TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD
+>2_1222
+MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA
+GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD
+>3_1134
+MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG
+APSSTPAAPSSGAASSTGTSSGSSD
+>4_1522
+MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG
+TGSAGGSTSDSAAGSSTSSTSSSSSAAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc719b275b88e8d7c7f4e760e58322ea778fb2e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001329.fa
@@ -0,0 +1,110 @@
+>0_1594
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR
+>1_1309
+MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN
+SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED
+LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL
+VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN
+ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL
+ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA
+LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV
+LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD
+EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA
+HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG
+ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP
+LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR
+SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR
+>2_1220
+MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN
+SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW
+TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL
+DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH
+LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL
+VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH
+ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA
+MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR
+VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL
+TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA
+LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA
+ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL
+ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA
+LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV
+LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA
+EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP
+MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA
+LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG
+ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP
+LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT
+VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR
+>3_1132
+MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA
+GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT
+WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR
+LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE
+HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES
+LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA
+HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ
+AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA
+RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA
+LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ
+ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL
+AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE
+LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA
+ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV
+ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL
+AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI
+PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW
+AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG
+ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP
+LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS
+RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES
+>4_1524
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60c07b3eb9c94e0d7f0d4c1a7b22a36b6df58c6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001331.fa
@@ -0,0 +1,24 @@
+>0_1596
+MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
+>1_1311
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR
+RY
+>2_1218
+MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV
+MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV
+VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY
+>3_1130
+MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA
+DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL
+SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE
+LAQFPDAARRY
+>4_1526
+MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW
+ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG
+WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR
+RY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b104b5e499f69222279849426facfc8456cb135
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001332.fa
@@ -0,0 +1,35 @@
+>0_1597
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
+>1_1312
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEHRR
+>2_1217
+MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE
+PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS
+AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA
+AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL
+WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE
+NRP
+>3_1129
+MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE
+PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS
+EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA
+AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL
+WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD
+AAHQEPQDGPAGPRKEGQA
+>4_1527
+MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE
+ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS
+ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA
+AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW
+WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD
+GAARPDPRDPGPRGPREEQSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09e2570a8fefd0a70017508612883088c1ef1a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001335.fa
@@ -0,0 +1,46 @@
+>0_1600
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTAEHPTWLGETLAT
+VGSIYISLLKAAVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAVYVGLALVMLVVYPLLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIEMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAELVGTPEPRA
+>1_1315
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTSEPRA
+>2_1214
+MSTTQSSPEPAPRRRLPAWTGNFGWQIVAALVLGLVLGLVARSMGHTPDSPTWLGETLAT
+IGSVYISILKATVIPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVMQPGVGTGQSAPESYQARDVGWLDFLTSMVPANFLGLTVKSTVGEDGAVASSPTFNVL
+QILVIAIVVGIAALKVGEKAAPFLTFSRSVLAVIQKLLWWIIRLAPIGTVGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLAIVMFVVYPVLARLHGLCVKQFFTGVWPAVQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYAAFAVPLGSTTKMDGCAAIYPAIAAVFVAQFYGIEMSLGQY
+ALVVLVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGLALLLAVDPIVDMGRTATNVAGQ
+ALVPALVAKQEGILDQARYDAERVDIMGEDEEEIVEARAQDRDDDQDQMVGAAARPARD
+>3_1126
+MTSHPSSPASGASTPARRRRLPAWTGNFGWQIAAALVLGLLLGLAARAMGHTPDSPTWLG
+ETLALIGSIYVQLLKATVVPLVFFAVVASVANLAQVTNAARLAAKTLLWFAITSFIAVLI
+GLAVGVVMQPGVGTGQSAPEGYQARTVTWLDFLTSMVPVNMLGLTVKTTAGDDGALTSTP
+SFQVLQILVIAIAVGVAALKVGEKAEPFLAFSRSVLAVIQKVLWWIIRLAPLGTVGLLGN
+AVASYGWSTMGTLVKFVVAVYVGLALVMLVVYPLLARVHGLSVKQFFTGVWPAFQMGFVS
+RSSLGTLPVTQRVAERSFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFVAQFYGIDM
+TLGQYALVVLVSVLGSAATAGTTGATVMLTLTLSTTGLPLEGMALLLAVDPIVDMGRTAV
+NVSGQALIPALVAQQEGILDRTRYDAERGDVMADEDETIVEARHDDARGASRADLTEAGS
+AR
+>4_1530
+MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT
+VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG
+VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL
+QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY
+GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG
+TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY
+ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ
+ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTPEPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c994ee98a35f129d666be9c57a763f9e40381e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001336.fa
@@ -0,0 +1,15 @@
+>0_1603
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK
+>1_1318
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>2_1212
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>3_1124
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>4_1533
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64d49b90be36e4e2bd41f78281d3edc6438ee076
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001337.fa
@@ -0,0 +1,30 @@
+>0_1605
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>1_1320
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>2_1210
+MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV
+GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV
+DGPHGPLAVYY
+>3_1122
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYW
+>4_1535
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6e86be262873de2d77a807bb8d775c378ec398a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001348.fa
@@ -0,0 +1,25 @@
+>0_1617
+MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKVL
+>1_1332
+MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>2_1182
+MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>3_1111
+MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ
+AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA
+AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA
+L
+>4_1547
+MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5486251b0b7ac5a0462aea396e1d752925b47335
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001351.fa
@@ -0,0 +1,40 @@
+>0_1620
+MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>1_1335
+MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
+>2_1179
+MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA
+RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD
+AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR
+VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL
+DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT
+LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP
+ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA
+>3_1108
+MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH
+GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV
+SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG
+LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV
+RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL
+VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG
+IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA
+>4_1550
+MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA
+RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD
+AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE
+GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM
+VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG
+LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS
+GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6396ea8bc89fee336a2ac765da82b9e389399218
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001354.fa
@@ -0,0 +1,30 @@
+>0_1623
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAA
+>1_1338
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAT
+>2_1176
+MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA
+LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA
+PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG
+LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG
+AVSAAPAAATPAAPARGEGPA
+>3_1105
+MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG
+LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK
+FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL
+LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD
+LVKRTAGMPVGAVAESAAGVGRAGAGVRP
+>4_1553
+MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP
+VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..738a3509b5ee067464e99536691fe81eb65d3030
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001356.fa
@@ -0,0 +1,60 @@
+>0_1626
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE
+>1_1340
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
+>2_1173
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE
+>3_1103
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE
+>4_1555
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69f8aae2b36678a32b8e1a8c530cc9c969dce2c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001357.fa
@@ -0,0 +1,36 @@
+>0_1628
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
+>1_1342
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV
+>2_1171
+MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE
+HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT
+ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK
+SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD
+FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP
+NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV
+>3_1101
+MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA
+GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI
+HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI
+TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP
+ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF
+MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN
+RQHEVTRVLMRKV
+>4_1557
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38eba7030b2f2de0a0269b37c116acbd4b5ca8a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001361.fa
@@ -0,0 +1,26 @@
+>0_1634
+MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF
+NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS
+VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS
+NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR
+>1_1348
+MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM
+LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF
+YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG
+EVSGGSFPRVR
+>2_1165
+MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL
+EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR
+>3_1096
+MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS
+PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG
+AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER
+VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL
+SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK
+DERIVHLPDPQICASADVLSEIDEADGGSFPRVR
+>4_1563
+MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC
+YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA
+SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH
+RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6be1acdb6222db326ea9780631b6132505426628
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001362.fa
@@ -0,0 +1,20 @@
+>0_1635
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>1_1352
+MSINENDDVELTSYTSESTAAAEAPVASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>2_1164
+MSINEHDDVELTSYTSESTSAGTEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQW
+TINGRTLENYFPNKLHQQEVNDPFTLLELAGAYDVIARIHGGGPSGQAGALRLGISRALN
+EIDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>3_1095
+MSINQNDDVELTSYTSESTAASETAAVSERPALTVPGSAVGRRKEAVARVRLVPGSGQWS
+VNGRTLENYFPNKLHQQEVNDPFTLLELNGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
+>4_1564
+MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT
+INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE
+IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9781c7934e2dbe458a680fdf98110f135e2277ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001363.fa
@@ -0,0 +1,20 @@
+>0_1636
+MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE
+KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS
+KLKVYKGAEHPHTAQQPQTFEIGQVAQ
+>1_1353
+MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE
+KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS
+KLKVYKGAEHPHTAQQPQTFEIGQVAQ
+>2_1163
+MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE
+KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLT
+KLKVYRGAEHPHAAQQPQTFEIGQVAQ
+>3_1094
+MRTYTPKPGDADRQWHIIDATDVVLGRLATHTATLLRGKHKPTFAPHTDMGDYVIIINAE
+KVALTGAKLEKKRAYRHSGYPGGLKSESYAELLEKNPVRAVEKAVKGMLPKNSLAAQQLT
+KLKVYRGAEHPHAAQKPATFEIGQVAQ
+>4_1565
+MRTYSPKPGDADRQWHIIDATDVVLGRLASHTAALLRGKHKPTFAPHMDMGDYVIIVNAE
+KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS
+KLKVYKGAEHPHTAQQPQTFEIGQVAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..469235da88df2068d43ed06e26bb693309ea2edb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001366.fa
@@ -0,0 +1,35 @@
+>0_1639
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPDV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>1_1356
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSFKDSPAGYDPQAHARQMDDDPFSDF
+>2_1160
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLARSLNVEAEGVDLGDEPQT
+AEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGYDPQAHARQMDDDPFSDF
+>3_1091
+MLIAQRPTLTEEVVSDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGSGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADQEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLAKGLNVEAEGIDLGEAPAE
+ADGSADLAQPIEDLELTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKEK
+LYELGLSLKDSPAGFDPQAHASQDDDPFSDF
+>4_1568
+MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL
+HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN
+PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA
+TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV
+VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK
+LQELGLSLKDSPAGYDPQAHARQMDDDPFSDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001373.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87b59dbde7cffdaf237efebb59890665af61940c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001373.fa
@@ -0,0 +1,45 @@
+>0_1646
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>1_1363
+MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW
+ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
+>2_1153
+MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL
+TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE
+NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW
+IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ
+VNAQMEQRHYEGLLR
+>3_1084
+MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF
+VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE
+NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP
+VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW
+VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ
+ISAQMEQRHYEGLLR
+>4_1575
+MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF
+VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL
+TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE
+NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP
+VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW
+ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP
+TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ
+VSAQMEQRHYEGLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efe377577f0f62c06cfb6681f40c6b0f67e0afd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001374.fa
@@ -0,0 +1,20 @@
+>0_1647
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
+>1_1364
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
+>2_1152
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKVDAFSASAVEKIQAAGGSTETL
+>3_1083
+MAENDAIKVHDLRPAPGAKTAKTRVGRGEGSKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSEMFPEGGEVTVETLVSKGLVRKNQPVKVLGTGE
+ITSAVQMKADAFSASAIEKIKAAGGSAETV
+>4_1576
+MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL
+QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE
+ITSAVQVKANAFSSSAVEKIQAAGGSTETL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eea59b4390f94a36554483aadb408fa5109003f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001375.fa
@@ -0,0 +1,15 @@
+>0_1648
+MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN
+TVPHLVSVEEVNNG
+>1_1365
+MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN
+TVPHLVSVEEVNNG
+>2_1151
+MTEPTRKNIQPSDATLVITQTRGVTGTKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN
+TVPHLVSVEEVNNG
+>3_1082
+MLQTTRKNIQPSDATLVITQTRGVTGTKQNQRDTLRSLGLKRIGHQVTRKADAATVGMVN
+TVPHLVSVEEVNHG
+>4_1577
+MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN
+TVPHLVSVEEVNNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f79ff2c5b6f04d0310c6eb10a8c4ba1c6c93e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001377.fa
@@ -0,0 +1,20 @@
+>0_1650
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>1_1367
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>2_1149
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLKL
+>3_1080
+MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
+>4_1579
+MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA
+STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG
+GLQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..601f58cb0ac1174b80d3b31b9993b994e3599f62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001378.fa
@@ -0,0 +1,20 @@
+>0_1651
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>1_1368
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>2_1148
+MSRIGRLPITIPSGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTTGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>3_1079
+MSRIGRLPITVPSGVDVTIDGARISVKGPKGQLEHTLPSPITATLEEGQVIVARPDDERE
+SRSLHGLSRTLINNMVLGVTEGFTKALEVVGTGYRVQAKGQDLEFALGYSHPVPVKCPEG
+ISFTVEGNKVTVAGIDKQKVGETAANIRKLRKPDPYKGKGVRYAGEQIRRKAGKAGK
+>4_1580
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfc2cd7eb503ae3bdb28bf8151d36aa03ac5a02a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001382.fa
@@ -0,0 +1,20 @@
+>0_1655
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>1_1372
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>2_1144
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>3_1075
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
+>4_1584
+MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA
+VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE
+VI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1342d238e7135ebe668c14e9496e84295859f8a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001386.fa
@@ -0,0 +1,30 @@
+>0_1659
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>1_1376
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>2_1140
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE
+RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA
+>3_1071
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE
+RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA
+>4_1588
+MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE
+IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV
+AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH
+TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR
+RRNDRAERAPRQENAGAGAETPAAAPAEGGNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab22158b07934d92e6964aebe8534489a8809d8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001387.fa
@@ -0,0 +1,20 @@
+>0_1660
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>1_1377
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>2_1139
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>3_1070
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGVAFNEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASQDEKGG
+N
+>4_1589
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fff9d279bd3ca8b4181dd69ad3e790f64c74d3dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001388.fa
@@ -0,0 +1,15 @@
+>0_1661
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>1_1378
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>2_1138
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
+>3_1069
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR
+>4_1590
+MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV
+FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaff6a4dd396288d455be3fa9d44c3386e4752fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001389.fa
@@ -0,0 +1,30 @@
+>0_1662
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>1_1379
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>2_1137
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>3_1068
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>4_1591
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d10e20640c12aa3b42d8cc57faaa909d5b4d4b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001392.fa
@@ -0,0 +1,25 @@
+>0_1665
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>1_1382
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGQHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>2_1134
+MTNTQNIKGLLGTKLGMTQVWDENNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFDKAGVTPRRHLVELRTADAAEYSLGQDLTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGVDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>3_1065
+MTNTQNVKGLMGTKLGMTQVWDEDNKLIPVTVVQADANVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYTLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVSASHGAHKNHRKPGSVGGASTPARVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
+>4_1594
+MTNTQNIKGLLGTKLGMTQVWDEDNKLIPVTVVKADPNVVTQLRSEETDGYTAVQIAYGQ
+IDPRRVTKPLAGHFEKAGVTPRRHLVELRTADAAEYSLGQDVTVEVFEAGQKVDVVGTTK
+GKGFAGAMKRHGFAGVGASHGAHKNHRKPGSVGGASTPGRVFKGQRMPGRMGAVRQTTMN
+LTLHGIDVENNLLLIKGAVPGSKGQVVLVRSAVKGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91a4195cf82186da50c057cc92a97b4724783991
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001398.fa
@@ -0,0 +1,20 @@
+>0_1671
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>1_1388
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>2_1128
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>3_1059
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGVRAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
+>4_1600
+MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA
+TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL
+MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a087d09fb955dd8bd55ffc2662888fbd50d7e20b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001399.fa
@@ -0,0 +1,20 @@
+>0_1672
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>1_1389
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>2_1127
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>3_1058
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>4_1601
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44e708019ba458854ee7e5d7c7f5975094197376
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001401.fa
@@ -0,0 +1,105 @@
+>0_1674
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>1_1391
+MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD
+AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA
+PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>2_1125
+MVASSTSNETATVSPRSGASAGRISFAKISEPLDVPDLLALQTESFDRLIGNERWVARVE
+EAQAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFSEPEFADAKMTEEECKDRDATYA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE
+EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQMLLNNLYFTPKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTVKGVRDGEAVDVRVE
+IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAYQIAQANA
+PVAEDGTFEEELVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATAAGVVTEVAADLVTVMNDD
+GTTTHYPIMKFARSNQGNAYNQRVLVSEGDRVEPLSVIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSD
+PVNVATPVFDGAEAYEITGLLGHVNATRDGDRLMGENGKAQLFDGRTGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDEVYRAAEELGIDLSHAEPSSVEEV
+>3_1055
+MVASSTSNETAAVSPRSAASAGRISFAKIHEPLDVPDLLALQTESFDRLIGNERWAARVD
+AAVAADDHSVSVTSGLTDIFEEISPIEDFQGTMSLSFSDPEFADAKMTEEECKDRDATFA
+APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT
+PDKTSDKEIFSARIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKALGWTESRILE
+EFGQYDSIRATLEKDGTADQNEALLDIYRKLRPGEPAAVDAAQNLLNNLYFTAKRYDLAK
+VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTIKGARDGEPVEVRVE
+VDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA
+IKEFFGTSQLSQFMDQNNPLAGLTHKRRLNALGPGGLSRDRAGMEVRDVHPSHYGRMCPI
+ETPEGPNIGLIGSLATFGRINPFGFIETPYRRVVDGRVTDQLDYLTADDELAFQIAQANA
+PVDEDGRFVEELVLCRQRGGGGEPVLSTVDDIDYMDVSPRQMVSAATALIPFLEHDDANR
+ALMGANMQRQAVPLLQSEAPYVGTGMEKYVAVDAGDSVTAAQPGVVTEVAADLVTVMNDD
+GSTTHYPIMKFSRSNQGNAYNQRVRVSEGDRVERLSIIADGPATDNGELALGKNLLVAFM
+PWEGLNYEDAIILSQRMVSDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL
+DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES
+GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM
+PFLADGTPVDVVLNPLGVPGRMNLGQVMEIHLGWAASRGWDIEGEPEWIKDLPDFPRQSG
+PVNVATPVFDGAEAYEITGLLGHVNKTRDGDRLMGTTGKAQLFDGRSGEPFPDPVSVGYM
+YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL
+LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR
+DAEDETYRAAEELGIDLSHAEPSSVEEV
+>4_1603
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1dfbd68da938e926078ccf96b3fb03b0b5c5a7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001404.fa
@@ -0,0 +1,25 @@
+>0_1677
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>1_1394
+MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
+>2_1122
+MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL
+>3_1052
+MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA
+>4_1606
+MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG
+SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM
+GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE
+AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd7313529fc9def2946fdd0deb14178d4d1964ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001407.fa
@@ -0,0 +1,15 @@
+>0_1680
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>1_1397
+MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>2_1119
+MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA
+FMILLVMGLDWVFGTVAGLLFGGGGGL
+>3_1049
+MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI
+LLVMGLDWVFGTLAGLLFGAGPA
+>4_1609
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee3306d2197f92c00932efc632661a8abd81902e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001408.fa
@@ -0,0 +1,41 @@
+>0_1681
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPASGLPELREAIADKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>1_1398
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
+>2_1118
+MIGFGAGEPDFPTPAYIVEAAVAAAKDPKNHRYSPAAGLPELREAIAAKTLRDSGVAIDV
+AQVLVTNGGKQAVYNTFAALLDPQDEVLVPSPYWTTYPEAIRLAGGVPVDVFAGPEAGYK
+VSVEQLEAAVTERTKALLFVSPSNPTGAVYSPEETEAVGRWALDRGLWVITDEIYEHLTY
+DGMPFTSILKAVPELAEQAVILNGVAKTYAMTGWRVGWMAGPLDVIKAATNLQSHATSNV
+SNVSQRAALAAVAGPLDAVDEMKVAFDRRRRAMVEAMNAVPGFHCPTPQGAFYAYVDVRE
+ALGRTYRGGVTPTTSAELATFILDEAEVAVVPGEAFGPSGYLRLSYALGDDDLAEGVERI
+RALLSE
+>3_1048
+MTRAPSNRAGTSAPDGGSVGWPHGRRVRVRRPPEQMRKVPMATPAHRVSARLSAIAPSAT
+LAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVEAAVAAARDPKNHRYSPAAGLPELRE
+AIAAKTLRDSGVELDASQVLVTNGGKQAVYNAFAALLDPQDEVLVPSPFWTTYPEAIRLA
+GGVPVDVFAGPDQGYKVTVDQLEAAHTERTKVLLFVSPSNPTGAVYSPEETRAIGEWALA
+KGLWVVTDEIYEHLTYDGVPFTSILKAVSGLAEQGVILNGVAKTYAMTGWRVGWLAGPLD
+VVKAATNLQSHATSNVANVSQRAALAAVAGPLDAVEEMKTAFDRRRRAMVEALNRVPGFH
+CPTPEGAFYAYVDVREALGRTYTGGVTPATSAELADFILDQAEVAVVPGEAFGPSGYLRL
+SYALGDEDLAEGVERIRALLSA
+>4_1610
+MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA
+ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ
+DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDEAVTDRTKVLLFVSPSN
+PTGAVYSPEETAAIGRWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG
+VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT
+AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALGKTYRGDVTPTTSAELAAFILD
+EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b78ba51dac5b57736f5a7bcbbb9838df0c2fae6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001412.fa
@@ -0,0 +1,35 @@
+>0_1685
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>1_1402
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>2_1113
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL
+ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED
+SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ
+KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR
+>3_1043
+MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL
+ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV
+VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA
+SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ
+HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR
+>4_1614
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001420.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae6db29071f9bb9d4efca07242b9de23f06e5cc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001420.fa
@@ -0,0 +1,15 @@
+>0_1693
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG
+>1_1410
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG
+>2_1105
+MENTAAKSQPEKIVHERLKVTRDPDRERFELRQDGTFIGFLGYAQETVPGPDGEDRTVVR
+LQHTIIDEAHGRKGYARALVTMVLDRLRAEGDSIVAECSYVEDYLRRYPEYQDMVFNG
+>3_1034
+METTANQHPEKIVHERLQVTRDPDRQRFEMRQDGVFIGFLGYDVEELPAADGGEDETVVR
+LQHTIIDEAHGRKGYARALVTIVLDRLRAEGEKISPECSYVQDYLRRYPEYQDMVREV
+>4_1622
+MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR
+LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7fff2cf434fd46311b83250de206f4a74af8bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001424.fa
@@ -0,0 +1,40 @@
+>0_1697
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>1_1414
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>2_1101
+MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA
+PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL
+RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>3_1027
+MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA
+PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL
+RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY
+QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPIRRMLMIATGNL
+>4_1626
+MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA
+PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL
+RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL
+GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bc5f2fc140d1fe925cf989b67ba7ed0849a047c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001426.fa
@@ -0,0 +1,20 @@
+>0_1699
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>1_1416
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
+>2_1099
+MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG
+AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA
+>3_1025
+MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI
+AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG
+AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA
+>4_1628
+MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG
+MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG
+AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73977de81a9ad0d2a828aba2f28180310aedd19f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001428.fa
@@ -0,0 +1,15 @@
+>0_1701
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR
+>1_1418
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR
+>2_1097
+MSSHRPSSQRRPDRGPSTGPQRAGFVSPWENGSALYRALVLTGSALFLVGIVLAVVGATT
+SQLTVSWFALGVLGLGVVVHLSAQMVRFRQAARRQGQRPPGR
+>3_1023
+MPTSARRPEPSARSGGFVSPWEHGSRLYRGMVLTGSALFLIGIVLSVVGATAHVLALSWT
+ALGVLGAGVLVHLSAQLVRLREAGRRESAARSARRKGRGSGR
+>4_1630
+MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV
+SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efa0952fd492a57f727ae62658ed2579abd6d478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001430.fa
@@ -0,0 +1,26 @@
+>0_1703
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>1_1420
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>2_1095
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR
+>3_1021
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR
+>4_1632
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b1799253484e174b979d87ddca097db05375758
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001431.fa
@@ -0,0 +1,40 @@
+>0_1704
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>1_1421
+MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
+>2_1094
+MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA
+HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF
+GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL
+WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED
+>3_1020
+MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG
+NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA
+FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF
+GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL
+WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED
+>4_1633
+MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA
+HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG
+NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA
+FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF
+GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI
+ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL
+WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3de5de703c76a2309be6b00e23710dafef58ac49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001432.fa
@@ -0,0 +1,40 @@
+>0_1705
+MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>1_1422
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
+>2_1093
+MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT
+RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY
+RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE
+VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ
+VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP
+DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT
+HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG
+>3_1019
+MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA
+IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG
+QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE
+TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS
+DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE
+WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA
+ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG
+>4_1634
+MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA
+PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM
+GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV
+WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG
+GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA
+VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF
+QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3660bd8f9beb30b20699692b8dd36f5186011a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001434.fa
@@ -0,0 +1,35 @@
+>0_1707
+MIAPDAERCVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP
+TSLLVSGVRETAGGGTAVTARAWGAGARTAVADVERLLGLHDDGWAAFDALLRPDSGAPA
+LPRHVREARRTRAGLRLPAAGALSRQLLTAVLEQKITHDQARHGWRTLVRLAARIDGDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTVLEVARRAASIDRLGDAVAPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH
+>1_1424
+MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDVASGGPGRP
+TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWDAFDALLRPDSGAPA
+LPPHVREARRMRAGLRLPAAGALSRQLLTAVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVTPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQGFGPKLAPADHRAH
+>2_1091
+MSAPDAVRRVRVPVPVDVPLTLRPLQRGAADPTVRAVPEGVWLTLRVPDQGAPAGSPGRP
+TSLLVSGAREAAGPGTVVTARAWGPGARAAVASVERLLGVDDAGWDAFDALLHRDSSAPA
+LPRHVREARRTRAGLRLPAAGALSGQLITVVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPSGMLPPPSPAAVLRIPSWDWHARAWVQPAQSHTVLEVARRAASIDRLGAAVAPG
+DTAGIAALARRLESLPGIGPWTTAEALQRSHGAADLVAVGDYHLAQFVGQVLTGRRTDDA
+GMLRLLEPWAGHRQRVVRMIGISGARKQAFGPKLAPADHRAY
+>3_1017
+MVPPLSVPPDAVVRLAPGVPVDVAATLRPLQRGAADPTVRAAPTGVWLTRRERVDGATLP
+ATLLVSPQVRGEVTARAWGPGAAAALAGLPALLGLHDTGWDAFDALLAPDPRRPSLPHAL
+REARRTREGLRLPAAGHLSTQLMTVVLEQKVTHDQARHGWRTLVRLAHGIDDATPPGPAP
+AGMLLPPTPRAVLAIPSWDWHARAWVQPAQSRTVLEVARRASAVDRLGAAVAPGDVAGTA
+ALAARLQAIPGVGPWSAAEALQRSHGSADLVSVGDFHLAHLVGQVLAGRRTDDAGMLRLL
+QPWEGHRQRVVRMIGASGASKERFGPRLAPADHRAY
+>4_1636
+MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP
+TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWGAFDALLRADSGAPA
+LPRHVREARRTRTGLRLPAAGALSRQLLTVVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVAPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbd5919082325c721aad60164c9c390601342cdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001444.fa
@@ -0,0 +1,60 @@
+>0_1719
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALEHAGQVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLVPALMESFHAGTRVIALTADRPPELHGTGANQ
+TTDQRDVFGTHVRHAASLGCDAADGVDTEQHLRHVRATVRRALLAAEGVVAETDSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAAPHTPAPAVAPTGASPAAAASA
+YRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSAN
+AIAAYPLLLGAAGGRDADAHPLAARIQRVVLFGRPTLTRTVNALLARPDVATALHAPEPA
+PWFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVTTDAGDRLSP
+QTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVA
+LARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVLNDNGGAIFASLEHGAVAEAPG
+MADPVERLFGTPHGVDLAALAAAYGVPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADR
+PRVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ
+>1_1436
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ
+TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAAAASAY
+RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA
+IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP
+WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDALVTTDAGDRLSPQ
+TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL
+ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM
+ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP
+RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ
+>2_1079
+MTSVDSLSVARAVADALIEAGMRDAVVCPGSRSAPLAYALAERERAGAVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESFHAGTRVIALTADRPTELHGTGANQ
+TTSQEGVFALHVRHAASIGCDAPAGRDADAHLRAVGAVVHRALLAADGVVADGPGHDDGG
+HVPEPGPVTVGEAPAGPVHLNLQFRAPLVPAPDEAAAMGSARQSAPQSPADPASEAAVHS
+AYRAPGALLSGFPELDVARLTQRRTVVLACHGAGPVAAAFALALGLPLLAEPSSNARFSV
+DAIAAYPLLLGSAGGRGPDSHPLAGRIERVVLFGRPTLTRPVTALLAREDVETVLFAPEP
+APWFEPGRRRERPIETLEELADFAGHGEAGWLSAWQRASMRAQAAVEDVLVAEDLRHGLS
+PQSVAQVGAAVTRGPLVLGSSSVIRDVDLTWRPPTAPDAEVYANRGLAGIDGTVSTAAGV
+ALARGMRTVALLGDLTALHDVGGLLVGPTEVEPDLELVVVNDDGGAIFAGLEHGAVAAVP
+GLAAPVERLFATPHGVDVAALAAAYGIPHVAVSDRVGLIHCLADPVRGRRIVEVRCSRAD
+RPRVAAALAEAVRATFPAAADSAPADTDPAPADPAAEEAPQ
+>3_1004
+MSSVDSTTLARTVAAALLEGGMREAVVCPGSRSAPLVYALAEAERRGRIRLHVRVDERSA
+AFLAHGISLATGRPVGVLTTSGTAVGNLLPALMEAFHAGTRLVALTADRPAEMHGTGANQ
+TTRQDGLFALHTRGAASISADLAPGEGAEEHLGRVAATVRRLLVRAEGLVVDPAAARPDL
+AEAPAGPVHLNLPFRAPLVPDAGQLAAMAAPAAPGDDADRPAEPAPWRAPGSDLTARVDL
+DVSRRPERRTVVLACHGAGPVAAAFAMALGLPLLAEPSSNARFTVNAVAAYPLLLGPAGG
+APGSDQGHPLAECIERVVLFGRPTLTRTVTALLDRPDVEAVLYSPEPAPWFEPGRRPERV
+VTDLGELADFAGQGAAGWVPAWQRASHRAQNAVEDALVRADRRHGLSPQSVAHVVPAVTR
+GPLVLGSSSLIRDVDLTWRPPTAPDAGVFANRGLAGIDGTIATAAGVALGTGRRTVALIG
+DLTALHDAGGLLVGDGEPEPDLDVVVVNDAGGAIFAGLEHGQVAGHAGMADVVERFFGTP
+HRVDLAALAAAYGVPHVLVEDRVELVHVLGAPERGRRLVEVRVHRADRPAVAAAIARAVA
+EAVAADPVPACTGAAAPEEES
+>4_1648
+MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA
+GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ
+TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP
+GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAPAASTY
+RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA
+IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP
+WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVSTDAGGRLSPQ
+TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL
+ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM
+ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP
+RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2ce725d332e879c984ea1d3dbd7bddef507b52a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001445.fa
@@ -0,0 +1,31 @@
+>0_1723
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>1_1440
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
+>2_1076
+MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD
+TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP
+RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT
+EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV
+LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA
+>3_1000
+MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL
+LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL
+AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV
+VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE
+RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR
+AEQH
+>4_1652
+MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP
+DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE
+HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW
+HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA
+LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c26965066d555cd0e9c825a149661146084c841f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001449.fa
@@ -0,0 +1,20 @@
+>0_1727
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>1_1444
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>2_1072
+MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR
+VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA
+>3_996
+MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV
+DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR
+HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG
+>4_1656
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb9cc4af94bb21ccdaa5f723492cfca0ce3571ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001452.fa
@@ -0,0 +1,35 @@
+>0_1740
+MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>1_1448
+MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
+>2_1053
+MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI
+AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR
+GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD
+LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV
+NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD
+EAVEGRDAFLQKRDPDWSAFPYHF
+>3_990
+MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE
+GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP
+DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ
+RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL
+AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM
+LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF
+>4_1662
+MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT
+VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ
+RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV
+VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM
+GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY
+MTDEAVEGRDAFLQKRDPDWSAFPYHF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d8278925ff3d86d776312d0486ba122f2e48fff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001453.fa
@@ -0,0 +1,50 @@
+>0_1741
+MLALLDDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITVLAARPWSSSPRDPAP
+VTDGKLRFTAAVATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTGADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMIFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFLL
+>1_1449
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLHFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTAMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLTLGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLITAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDVRVTEGYAQLFALIMVVKIATVPFML
+>2_1052
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLVLFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPAQVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLPTPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGLVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQLGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
+>3_989
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGHRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG
+TEKNIDAAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
+>4_1663
+MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ
+SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG
+VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP
+VTDGKLRFTAAAATSALAVRDIPGISEGLVRVVALRHGGMARIAGSADRIEPGDEVVLDG
+TEKNIDEAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL
+RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY
+LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL
+GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT
+GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57b241c01ea76c5247c531721c5e6df50ba298c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001457.fa
@@ -0,0 +1,20 @@
+>0_1745
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
+>1_1453
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>2_1048
+MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA
+RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER
+GEEPDADDPDAPTP
+>3_985
+MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP
+VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE
+RGEDDATGEPDADA
+>4_1667
+MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA
+RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ
+GDDDADPDGDGPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb1bfcd0f931b4374149b3ec8a56da0b33ff3bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001458.fa
@@ -0,0 +1,30 @@
+>0_1748
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>1_1456
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>2_1046
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>3_982
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL
+>4_1670
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3931b69b914c4175c98c42b3f0fb3efc03af47e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001460.fa
@@ -0,0 +1,15 @@
+>0_1752
+MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>1_1460
+MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRA
+>2_1042
+MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRP
+>3_978
+MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE
+EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA
+>4_1674
+MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV
+PVLFVDGVQRDFWRVDPARLGRLLDAPRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0de1e968fba0a045c6eeb866ae02101e75006603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001466.fa
@@ -0,0 +1,31 @@
+>0_1758
+MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
+>1_1466
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT
+VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP
+>2_1032
+MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA
+DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ
+GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH
+AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA
+>3_971
+MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA
+ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS
+VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM
+YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG
+EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR
+HES
+>4_1680
+MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA
+RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ
+GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH
+AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA
+VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ac69300f7a759879980c4d7aeca308362450b1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001475.fa
@@ -0,0 +1,15 @@
+>0_1767
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD
+>1_1475
+MTHRSHSAQPAVTRPSERDRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVTGALQRD
+>2_1022
+MTQLSHTVHDALATAAERHHLARVADAAADETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVELVSGALQRD
+>3_962
+MTHNSTALTETLVPLVGPQRAAALATWAEDETGAQTAEYGILTLAAVGFAGVLAVVLTSP
+EVRELLVDLVSQALQRG
+>4_1689
+MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP
+DVQSLLVDLVSGALQRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ac7b97c0374393944ce13db292f98efc1984352
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001479.fa
@@ -0,0 +1,30 @@
+>0_1772
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>1_1480
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>2_1016
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA
+>3_957
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA
+>4_1694
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d852d08c1df0e847e7a29e60b0c33a974d5ab2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001486.fa
@@ -0,0 +1,20 @@
+>0_1780
+MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR
+>1_1488
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
+>2_1008
+MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP
+ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG
+VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR
+>3_950
+MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG
+KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN
+GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR
+>4_1702
+MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP
+ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG
+VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..221998b8cb83dfa78df0a1c031a77fe2633c4af8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001492.fa
@@ -0,0 +1,15 @@
+>0_1789
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
+>1_1496
+MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRPR
+>2_999
+MGPRMNSAWLFVGVMFTCALIGFWTLRGLGFARGDLSLPAALGVLAVAAVAAAVITRFVR
+RR
+>3_942
+MTLPPLHHGRDDDADRPAASGPGGRGLGGPAGPGAGLRRTYTFVGVLFACALIGFLSLRL
+LGVERGSMTLPAALGVLAVAAVAAAVITRVVGRR
+>4_1710
+MPPLHHGQPGDDGDPRDPRHRPGAGLGPGLRSVWMFVGVMFTCALIVFWTLRGFGVQRGD
+LSLPAALGVLALAAVAAAVITRYVRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..befe24e4864a1eb68c2b0cf2d4c1a8ae251b1a31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001493.fa
@@ -0,0 +1,25 @@
+>0_1790
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>1_1497
+MSARVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIELLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
+>2_998
+MTVHVMLVDDHPVVRAGVRAVVEAHPDLRVVAEAADGAEALRILEAASGPVDVVLMDLQM
+GEGMDGVSATRAVRERRPDVQVLILTTFDTEADILAAVDAGAAGYLLKDAPSEEIARAVR
+QAAAGQKALAPQVAATLMGRMAGGADVLSAREIELLELIARGATNKAAAKELFISEATVK
+THLVHVFQKLGVDNRTRAVDEARRRRIIR
+>3_941
+MSVRVMLVDDHPVVRAGVRAVLEADPELTVVAEAGDGAAALDVLQARPGEVDAVLMDLQM
+GEGMDGVSATRRLRAAHPGIPVLILTTFDTEADILAALDAGAAGYLLKDAPAEQIADAVH
+RAVAGRPALTPDVAERLLGRTTGATAASALSAREIELLELIARGDTNREAARALFLSEAT
+VKTHLVHIFQKLGVDTRTQAVHEARARRIIR
+>4_1711
+MSVRVMLVDDHPVVRAGVRAVVEAHPDLSVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM
+GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR
+QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK
+THLVHIFQKLGVDNRTRAVDEARRRRIIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4f4205f6460468477195b1c412e09c9ad26ccd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001500.fa
@@ -0,0 +1,40 @@
+>0_1798
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLNFVQGAKGVDGGAVLMRGQYAA
+>1_1505
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVHGAKGVDGGAVLMRGQYAA
+>2_986
+MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG
+KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA
+DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR
+SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL
+LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG
+AGLDFVQGAKGVDGGAVLMRGAYAA
+>3_931
+MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM
+WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT
+DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA
+DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP
+TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL
+PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV
+TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD
+>4_1719
+MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL
+LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG
+RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA
+ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR
+ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL
+VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA
+AGLDFVQGAKGVDGGAVLMRGQYAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fea61737787f0b69fe9743e8c9c53f606aeabaa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001503.fa
@@ -0,0 +1,15 @@
+>0_1801
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR
+>1_1508
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED
+EDDDARAR
+>2_982
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRAPEPELDQKPEYEDPYADLYT
+DDDEDDDARAR
+>3_926
+MGRGRQKAKATKQAREMKYMSLGTDLSALERELTGGRTDAPAVEPEVDYEDPYADLYADD
+DEDDDSRVR
+>4_1722
+MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRSPEPDQEPEYEDPYEDLYAED
+EDDDARAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffc55e26adc1eb8c35f980751e573014e7acddbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001504.fa
@@ -0,0 +1,46 @@
+>0_1802
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKAPMGTTQTADRGLGPGQNRAGGNPN
+SPKKLVRSISSDHLRQDITAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHGHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
+>1_1509
+MGYVAYVTSTPTMRMPMRRTPTLLAAATLAATLTAAPVSLAAPAAPAKAPVATTQTADRG
+LGPGQNRAGGSTNSPKKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVG
+ELEEAGYDVELQEFEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLTAPAGA
+ATGCADADWAGADLTGSVALVSRGDCTFGQKSQVAAASGAEAVIIYNNAEGALNGTLGTE
+PGDVVGTVGVTRELGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVML
+GAHLDGVPAGPGIHDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVD
+TLTAAEREDIILYTNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHAHQPEGSN
+GRSDYAPFVDAGIASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDAD
+ALGTR
+>2_978
+MSMRRRPALLAASVLAASLAVAPAAAAIPGHAAGGPAPAASAADRAGGNPNSPEKLVAAI
+SAANLERDIRAFADIAEEHGNRAAGTPGYDASVDYAVAELEKAGYDVELEEFEITYTETL
+RNEFTQEGPVQRELPHEVLTYSPSATAESAQLAVPTGALGCTTADWGGADLTGRIALVSR
+GECPFAQKSTTAAELGAEAVVIYNNADGPLNGTLGAPSDDYVGTVGITRDLGQELVAQAA
+AGPVTVSLDLEQLVEQRPTVNILAETRTGRDDNVVMVGAHLDGVPAGPGIHDNASGSAVT
+LEVARQMAKVNKTGNTVRFALWGAEEIGLLGAAHHVAELSQSERDAIAMYVNLDMVAPLD
+HQNTLGVLTGDFSLGAESFLQEQLERDGHEHGPAGNGGNSDYAPFVAAGIPATGLLSYRD
+DNYHTAQDDIENVSITSLTHSARAVANLVGTFMHDTSSVNDKCNAGKSGKPKQC
+>2_1480
+MSTSSLSRRSFLALAGAAGAAGAFAMPAWGLDDVRPGAARAPRLTGQDRQIINQIRPARA
+VDHLTLLTEEIGQRYTGTPAEHRAADYIAAQLEGYGYDVELEWFDVPDRRVGLLEAPELD
+GRWSWGVGSAAAAAQDVTVAGRVVLAPSGSVADLTGMVLMRVVTASEDITPLAVAAQARG
+AVAVIATRRDSNPPGQASAFAPALTTARLDIPVVGVSQVQKHALLGVLAAGPLRLTVSTV
+EHRGTRSANVVGTRAGRKGPGKGGRERVMLGAHYDSVIGSRGANDNASGTAACLELARVM
+RNAPTAADLSFGFWGSEEVGLVGSRIHAQAMPADERSRLRGVFNNDMIATSWDPAEKYWL
+LDLRGEANDVNRAVYAAGERLGYRTSMSDLFTMGRSDHQSFSEIGVPSGNFGWLHRDGFI
+LEPEYHSSDDTVKENISVERLMAAMEIQGCAAYALASR
+>4_1723
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKASAATAQTADRGLGPGQNRAGGNPN
+SPEKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHTHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2276a37c1a6c9d13f475febc9f99da291d62d732
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001506.fa
@@ -0,0 +1,40 @@
+>0_1804
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG
+RRDPEDVSSGSPFHADPVSHDGARLEPTPRPDD
+>1_1511
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVVALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSQRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEDFERYEARIRRLARLVAEAVRAGESLTIEATPLLSEEGRLLAVESG
+GRGPEDVSSGSPFHADPVSDDGARLEPTPRPDD
+>2_976
+MSGSTAAPRRLRTYARPRVSLLYVLRRTTHRLLELQVWDVAAAMTFFAALSLLPTVVALV
+SLVSLLGVQEETVDAAAQLATEIWPSLTPDTVREWILTLGSAGTGTAAVVLGILGAVVSA
+SGAVGAFHRAMHRIHDTREGRPFLQFRLVLLVETLALMVGIVLVVILVVLGGDLSLRIGQ
+AVGLPEETVLTWNVVKWPVILVVIALTVTLAYRLGPNVVPPRYRPLSAGAVSVVVLLFAA
+TLALGWITDRFGQFAVVGRINSAIGVLVLAWIACIVLLAGAALDAEMLRGRQLAVGVDAA
+SEIQLATRHTVVLEAAERHEDRSRRLARLVAEAVREDEDLSIDATPLLSQEGRMFAIGSA
+RRTAAEVSSGRPFHAAPVLDDGARLEPTSRPDD
+>3_916
+MPSSPVPDASTGGRAPRTYARPRASLLYVLERTWTRLVGMQVWDVAAAMTFFAVLSLLPT
+LVALVSLVSLLGVEARTVETAARLATEVWPSLDAAEVSAWILNAGRTATGTPGLVLGAAG
+AVVSASGAVGAFHRAMHRIYDTREGRPFLVYRLVVLLETLALIVGAALVMSLMVLGGDLS
+ERLGRLLGVGRGAVAVWNASTWPMILVLLALIVSVAYRRGPNVRPPCHRPFSLGAVGAVA
+LLFAAALALGWIVARFGGLALVGRLNSALGVLGLAWAACIVLVAGAAFDAEMLRARQLAV
+GVESADELQLATRDTWVLRQVERQEARHLRVGRLVAEAVRTEEPVTTPATRLLAEAGSLF
+AVDAAGRSASDLTSGRPFHAVPPADRAGV
+>4_1725
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG
+RRDPEDVSSGSPFHADPVSDDGARLEPTSRPDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf6bdad49ce4fe9441aca67ad9b3d2959dfe4d0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001507.fa
@@ -0,0 +1,27 @@
+>0_1805
+MGALALVGCAGGGGEASSSSADASKSAPTGAGSDLTDEQEERVEALEDVLLTPETAPGGV
+FTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVTG
+LAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVEAAFTKVPGVPDAAHIALG
+NSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEARER
+>1_1512
+MGAHALVGCAGGGGEASSSASADASESGPTGAGSDLTDEQEERVEALEDVLLTPQTAPDG
+VFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVT
+GLAGSQAGAFGMVAVTEDGTDLLEPFGELADTCGTFGDPDGVEAAFTTVPGVPDAVHISL
+GNSGMDTALFTMIVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEKRER
+>2_975
+MEALEDVLLTPQTAPDGVFTDMETQAGGGGEPISTSLSLTGVTPTGACADLIEQINTQQA
+PGLGGALAQYEVDPDAVTGLAGSQAGAFGMVAVTEGGTDLLAPFGELADTCGTFGDPDGV
+EAAFTKVPGVPDAAHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRA
+QVEAFEKRER
+>3_915
+MSRTATSRPRLRALLPLTATAALLASGCAAPGPAASSSATPSSSASSAAAESSSSPTVST
+GPASSSDASSSAAAASSSADASATTSSSSAADLAASSPAAGGASVENPLEPLLLLATAAP
+QEVFSSRTVQSGADQPLTMSLTLTGVTPTGRCQELVDEINATHEPMDVASLATYQVNPAS
+PAVVDQETGAFTMIGTSTAPADLMAPYGELVSACGTLEGEQGQKAEFTAVPGVPDAATVT
+MTTPGQSRKLVMTVGGASEGRDHVYMLMLGLDADVSQQVLADQVAAFQER
+>4_1726
+MLRPAAPARPAVALSLLAVGALALVGCGGGGGEASSSSADASESAPTGAGSDLTDEQEER
+VEALEDVLLTPETAPGGVFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAP
+GLGGALAQYEVDPAAVTGLAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVQ
+AAFTKVPGVPDAVHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQ
+VEAFEARER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6075393ec232e80a6bcbeffc16d9d9655c0036f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001511.fa
@@ -0,0 +1,25 @@
+>0_1809
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>1_1516
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT
+EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL
+VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
+>2_971
+MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT
+EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL
+VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV
+AALREAREELKKLRQKA
+>3_910
+MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT
+EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL
+LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV
+AALREARQELAKLRKKA
+>4_1730
+MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT
+EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL
+VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV
+AALREARDELKKLRKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7abf589b4c538e963b2dcd80d5734738bf9b2dd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001514.fa
@@ -0,0 +1,35 @@
+>0_1812
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>1_1519
+MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
+>2_968
+MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN
+SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA
+AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF
+FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL
+HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV
+DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR
+>3_906
+MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA
+ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM
+AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR
+VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE
+VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA
+LRAGRLVFDLAYARR
+>4_1733
+MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV
+WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD
+WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH
+KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA
+GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW
+APRFEGRPITSFEAKSQRAGRLVFDLAYRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21498d51f64844b7bda05e20bb9dd7fa6e7657d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001516.fa
@@ -0,0 +1,25 @@
+>0_1814
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>1_1521
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>2_966
+MSARDGAARADRGRERGLDRNAPVFVVSVAAEMADMHPQTLRQYDRLGLVVPARQGGRHR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
+>3_904
+MVSGVAGEHPTGAGRLRGTAGRPGRHDPVFVISVAAEMAGMHPQTLRQYDRLGLVVPQRQ
+GGRHRRYSAADVEHLRAVQRLSREGVSLEGIRRILDLQREVERLQDTVVELASQVDRLHS
+ASALARVFSVGLAGDVSARYAAPAAHRAAEAVQGQRRPGEGATRSAARGGLLRALPAGRA
+AAPRGLTRLPAPRD
+>4_1735
+MSARDGAARADRGREPGLDRNAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQGGRQR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e684dcfcdd471505fb53830817e2b772fc5d5461
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001517.fa
@@ -0,0 +1,32 @@
+>0_1815
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW
+>1_1522
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW
+>2_965
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW
+>3_903
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW
+>4_1736
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17665146d989da61b22cd572836490a6089182db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001519.fa
@@ -0,0 +1,60 @@
+>0_1817
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>1_1524
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>2_962
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>3_901
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN
+NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT
+EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA
+DEDIVDAEVVEDEDEKKN
+>4_1738
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bc165880ed7ff6c2c8c17c0cecffb839b5b52cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001520.fa
@@ -0,0 +1,21 @@
+>0_1821
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA
+>1_1528
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP
+GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA
+>2_958
+MSGPGPGRPVLIGVDGRSGAGKTVLADALAARLAPFARVAVLRIESMYPGWDGLAAAVDE
+GGPYPAALRALHADGTAAWRAWDWHRGAPGEPTAIGPADVVVCEGVGALSVAARPLLDLA
+VWLELETPARRSRALARDGETYAPHWERWAAHEEAYLARHGPRAAADLVVRLPSA
+>3_899
+MNASTEPGTARPGGPVSAPRPALIGLDGRSGAGKTTLAAALAARLAPHARVDVLHIEEMY
+PGWDGLAAATADDGPYVRAVAALAAGRPAGWRAWDWHAGAPGEARALDPDALDVVVCEGV
+GALCPGARPLLDLAVWVDAPEDVRRTAALARDGDAYAPHWERWARQEEAYLAAADPAGAA
+DLRLST
+>4_1742
+MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYQGWDGLAAAVGDDGPYP
+AVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL
+ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLVLRLPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00076657d503153719f78b597b7d055b55b041ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001522.fa
@@ -0,0 +1,35 @@
+>0_1823
+MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ
+GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR
+AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL
+DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL
+IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV
+SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG
+>1_1530
+MSPTPFSPSPGEPVLVLLEAGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVAD
+EAGVLRMRKLGAHLGRLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVR
+LTVTRGPEAAPGAVPEPSAWALLSPAPAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLT
+GAKTLSYAVNMAALRHARDHGADDVVFTSADGYLLEGPTSTVLIVRTGEDGVRRLLTPLR
+QKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLVSSVRGVLPVRAVDGVEI
+PVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG
+>2_955
+MLLEVGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVADETGVLRMRKLGAHLG
+RLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVRLTVTRGLEAAPGAVP
+EPSAWALLSPASAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLTGAKTLSYAVNMAALR
+YARAHGADDVVFTSADGYLLEGPTSTVLIVRTGADGTRRLLTPLRQKGILAGTSQAVIFA
+AAGAAGWELGYGPLVPADLEGADGVWLVSSVRGVLPVRAVDGVEIPVDHALTLELQAHLD
+ADGDPGAHVAGDPAPTAG
+>3_894
+MPTSNPAPAAHTPAPGEPVLVLLSPDADPRLADPAAPHLSVTDQGVTRGDGLFETALAVA
+DETGTFAMRKLAAHLGRLASSADALGIAAPDPEPWRAAIEAGLAGFAAANPVAPGDRLSV
+RLTVTRGPEAPAGVEARPTAWALLTPAPRTSDAERAEGVRVLLLERGLDSAAVEGAPWLL
+TGAKTLSYAVNMAALRHAKAHGADDVVFTSADGYLLEGPTSTLLLARTGADGTRRIVTPL
+RQKGILAGTSQSVIFAAAEAAGWRLGYGPLAPADLDGADGLWLVSSVRGVLPIRAVDGQD
+VPVDAELTERLQAWLDADGDPGVHVSGDPVRDED
+>4_1744
+MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ
+GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR
+AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL
+DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL
+IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV
+SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ec2cb73650801623ddd742f00d02594d5002f5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001523.fa
@@ -0,0 +1,15 @@
+>0_1824
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>1_1531
+MNTLVQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPDDAADETLPLVEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
+>2_954
+MNTLAQKALSTGITLVGGIIGSRVVAGGWKLVTGHDAPDDAADETLPIVEALSFAFISAG
+VAAILKVAGQRGAGAALRKVTESTAHRVDNEV
+>3_893
+MDKVIQKVLATGITVVGGIVASRLVAGGWKLVTGHDAPSDATDETVPLVEALAFTFASAG
+IASVLKVAGQRAAAEGVRKVAQKTSSDVDNEV
+>4_1745
+MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG
+VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff1399d2a1c018a755d3aebd321b08294b661be4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001524.fa
@@ -0,0 +1,20 @@
+>0_1825
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
+>1_1532
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI
+VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA
+DPGPRRAGARPRGRR
+>2_953
+MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI
+AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP
+ELDPRSPESRRRRRR
+>3_892
+MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW
+QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD
+AR
+>4_1746
+MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI
+EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA
+DPGPRRAGARPRGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a001059f93a519535e3159f798f10cfd8df17df9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001529.fa
@@ -0,0 +1,95 @@
+>0_1830
+MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAARLDRAVPWVPYLETELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLEAAPALMADAGLRGLLEVAVALVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHGLAMWQVLVIGVGLWTLL
+LGGWRALRQTDIKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMVV
+GIIDHEAGTRDLRQLSGIGRRHPALAAVAVVAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPSTQEAAR
+>1_1537
+MLVILTALFVVALAAPVIFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAAHLDRAVPWVPYLEIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLAAAPGLLADDGGRVLLEVAVGLVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPAFHELATWQVLVLGLGLWTLL
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGVRDAALAGLAMLLAHALFKAPLFMVV
+GIIDHEAGTRDLRELSGIGRRHPALAAVAVAAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRI
+ARMAVAGGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPDAPEAAR
+>2_948
+MLVTLSALFVVALAAPAVFRWTGRQGFYLLAAVPAAGFVWLLTQLPHVFALQEALDAGRP
+IPASAAHLDRSVPWVPYLDIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ
+APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV
+GIIDHEAGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLASLAAHGA
+AHGGVWAWTPLVVMALGSVLTFAYTWRFLWGSFAVKRDEEGAPVPATRFRTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALARRPFEALQERTESPLDAARGYRRLTGYVDETAVWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRAERPLATSFLAADLIWFETPAQLLIVAIIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFALRGAPDLAITQVLVETIILVTLILGLRVLPPDWHDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGANAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGAFGADSALGSRELSVVRSFAVD
+DREGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAGRRRHPRMP
+TPSTPDAPEAAR
+>3_887
+MTVLLTALFAVALLAPVLFRRTGRRGFHLLAAAPAAGFVWVLAQLPQVFVLQDALDRGAP
+VPASAAHLDTTVEWIPYLDIALSFRLDALSAFMSLIVLGVGALVLSYCASYFREHEPRHA
+VFGAELLAFAGAMFGLVTTDDVMVLYTFWEITSVLSFLLIGYSGQRIFARRSAIQALIVT
+TFGGLAMLAGLVMLAVQAGSWRVSGILAAAPELMERAPRGLLEAAVALVLVGALSKSAQV
+PFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPGFASLASWQVLVLGVGLWTLIL
+GGWRALRQTDVKLVIAYGTVSQLGFLMVANGLGTRDAALAGLAMLLAHAVFKAPLFMVVG
+IIDHEAGTRDLRRLSGIGRREPALAAVAIVAAASMAGLPPLFGFVAKESVLESLAGHGEH
+AGTVWGWTPLVGMALGSVLTFAYTWRFLWGAFATKDGRDSPDGEPVPETRFHSRLTAEDL
+LPPGLLALACLVLGLAPGLPEALISAHTAGLAPLDAAEEPAHLALWHGITPILGVSVAIW
+VLGAALAVARRPLQRLQARVAFPVEAAAVYQRITGAVDAAAVWVTGRTQTGSLRRYLFII
+LATATALPALTMLVPAGEEDRVLATAFLEADLVPFTTPAQLGIAALVCVAAVLAVRARRR
+FMAIMLVSVTGYGSAALFALRGAPDLAVTQVLVESIVLITVILGLRVLPPDWHSKTTGRR
+RVPRLLLGVGFALVMMWVAATALGARTAERISLDMPRLAYEHGYGANAVNVTLVDLRAWD
+TWGEITVLAVAATGVASLVFLEHRDKRRRDLDTVVPGSVGNYGAESALGTRELSVVRSFA
+VDDRNDQWLIAGHTMAPERRSIILEVVTRFLFPAMMLLSVYLLLAGHNTPGGGFAGGLLA
+GLALALRYLAGGRYELQEASRIPAGTLLGLGLGIATLTGLAPLLFGGQVLQSYKVEFHDL
+WLFGDSLKIVSATAFDVGVYLVVVGLSIDVLRSLGAEIDRRGDEWQDARRRAARRRASPR
+PARPRPRPVPEGRAPAARAIPAHAARHRSEEDPR
+>4_1751
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..847bfe8ce0dd0ecd17d20d5f489f24cb3bcf218c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001536.fa
@@ -0,0 +1,70 @@
+>0_1842
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
+>1_1549
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR
+>2_936
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR
+>3_877
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP
+>4_1763
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1649c55071825b731bddd517946ec4bf87c22603
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001537.fa
@@ -0,0 +1,45 @@
+>0_1843
+MPTTDPAVRPDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA
+>1_1550
+MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA
+GHASASTAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTV
+PFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTEP
+ELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGD
+DRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTP
+HLDRVVWGVGAEQVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPL
+TGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGL
+IFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA
+>2_935
+MGGGLLGTALGYGAGHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQ
+SARVAVSSPVGTDTVPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDA
+ARLTQGRATIADTEPELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLD
+PAFGDGDLLLQICGDDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNL
+FGQVDGTANPAAQTPHLDRVVWGVGAEQVGITPWIQDGTSLVVRRIEMLLDTWDELDRPG
+KERVIGRTLGTGAPLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGY
+NYDDPRGAIESGAGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCA
+EGGFVGDVLFA
+>3_876
+MPTTDPSRRGVLFGLGAVGGGLLGGAVGYGAGAAQATPAPGGAPSGVDASPSGVMEDTGL
+EGEVGRAGWAEPGGEASRVAVSSPVGTDTVPFHGPRQAGVDTPAQTHAMLVALDLLPETD
+RAGVRALLRLLSDDAARLTQGRATLADTEPELAAAPARLTVTFGFGPELLARVAPERAPA
+WLKPLPAFPTIDALEDRWSGGDLLLQICGDDRISVAHARRMLGKVARPFAEVRWVQEGFR
+AARGTHPTGTTMRNLFGQVDGTANPQGGSPALERIVWGAGQEAADLGIAPWIPDGTSLVV
+RRIDMLMDTWDELDRPAKEKVIGRTLGTGAPLTGELETDAPDLEAIGPTGFPVIPDTAHL
+RRARGPEPEYGMLRRGYNYDDGAGASGTGAGLIFAAFQADVDRQYIPVQERLAASDHLNL
+WTRPVGSAVFAIPPGCAEGGFVGDVLFA
+>4_1764
+MPTTDPAVRPDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d4a40ff0bd9c777f2a89336650242f4fdf20371
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001538.fa
@@ -0,0 +1,25 @@
+>0_1844
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA
+ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS
+GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE
+VTSVVRPFTGANESYHGGQSHESEDHADH
+>1_1551
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGESHESEDHADH
+>2_934
+MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS
+DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG
+FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES
+YDGGEAEESDEHADH
+>3_875
+MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA
+SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE
+MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR
+TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH
+>4_1765
+MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG
+QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM
+VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR
+PFTGANESYHGGDSHESEGHADH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4d912c1b7a87f0ba6a59d50db31f5b9b95202b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001539.fa
@@ -0,0 +1,23 @@
+>0_1845
+MHHQTTPVRRAARAATGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGSTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEAAAGQGDAASAEATAQADAS
+DAAQPADTDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>1_1552
+MHHQTTPVRRAARAAAGLALLPALVVAGAAPAAAHDELIRTAPAVDETVTTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGSAVAGASIAASPEATASQGDAASAAATAQADAS
+HAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
+>2_933
+MAAAPAASDASTPASAGSGAGTGEASEAPAEQGSAEAGESAEAGALPAWVWAVGVAGLLV
+LVVALILMGRRARALGHLDDGR
+>3_874
+MNPTPMHPSTPRRAARAAAALTLLPGLAVAAAAPALAHDELLKAVPADGAALAEAPDAVS
+LTFSGDLISGQGIQSIVRVTDAAGNQWQKGDVQVSGPTLTAPLCPDLAQGEYTAAYRVVY
+SDGHSEEQSLDFSVTDPSAPAAGTAPSGCGVAAAGTASSTAAPASSAEQTGAEQSGAAST
+PAAASSTPAESGASAGVPATVWMLGAAGVAVIAVGLAVMGRKARALGRD
+>4_1766
+MHHQTTPVRRAARAAAGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF
+SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG
+HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEATAGQGDAASAEATAQADAS
+DAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2aa130f857fa042df1499ff3e5f1ffea25ed2a5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001547.fa
@@ -0,0 +1,30 @@
+>0_1859
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLRED
+>1_1566
+MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
+>2_921
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI
+DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ
+LAPRIYPGLEGTVARVAVQTVAAHLRHLREG
+>3_857
+MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL
+ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI
+VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS
+LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE
+LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG
+>4_1780
+MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL
+ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI
+DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS
+LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED
+LAPRIYPGLTGTVARVAVQTVAAHLRHLREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8624c3ab518b2dc306fd76aabe3ef32c839a39b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001549.fa
@@ -0,0 +1,45 @@
+>0_1862
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>1_1569
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>2_918
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA
+>3_854
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA
+>4_1783
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff991054cad187b13c1a9156392980ba76779978
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001552.fa
@@ -0,0 +1,20 @@
+>0_1866
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL
+>1_1573
+MTLTHEPHTATWDTDLSLGNLRSGLSAFPTGVVALAGLADGVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL
+>2_915
+MTLTLDDRTRVWDTDLSHHNLRSGLSAFPTGVVAVAGLAEDRREVMVSSSFGVGISWEPA
+LVAFSAQNTSRTWPRLRQAASLGISLLAADQTHLCRQLASREGDRFAGLDVHVSPNEALL
+IEGAALWLETRLHAEVPAGDHTVVMLEVTGFADHTDEVAPAALHRNLFHGLRAL
+>3_847
+MTLIHAPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLAAREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDDAPPAALHRNLFHGLRAL
+>4_1786
+MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA
+LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL
+IGGSSLWLETRVHAEVPAGDHTVVLLEVTALADHTDAAPPAALHRNLFHGLRAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b8ac25792415a003083e64ced5baf4902537d08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001553.fa
@@ -0,0 +1,15 @@
+>0_1867
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>1_1574
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
+>2_914
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ
+AANVTKI
+>3_846
+MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ
+AADVTKL
+>4_1787
+MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ
+AANVTKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b060f048313b0d71eb8252c7af42aed99a37020c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001555.fa
@@ -0,0 +1,62 @@
+>0_1869
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT
+PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE
+GRVG
+>1_1576
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
+>2_910
+MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG
+YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI
+KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL
+SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR
+MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP
+EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS
+RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG
+RVG
+>3_1561
+MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN
+EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK
+ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL
+SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH
+LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD
+LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG
+LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ
+NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL
+REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH
+>4_1789
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff3bc481f3dab284f1a2ee7f53b514e70b992b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001561.fa
@@ -0,0 +1,26 @@
+>0_1876
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
+>1_1583
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA
+>2_903
+MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV
+GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN
+VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL
+LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG
+PGEGEPDEGAGPGPEGDAR
+>3_838
+MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI
+AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR
+RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR
+TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG
+>4_1796
+MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE
+DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR
+VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA
+EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c152321ab17a60afde86b2dac133d619fb5c13e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001564.fa
@@ -0,0 +1,15 @@
+>0_1881
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
+>1_1588
+MATPHTPDPQDARRAREATDETSGVAFDGDTPPAEGAGVGPHNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLVFILGRVAGLG
+>2_898
+MAAPHTRRPHDSDPHDARRAADEHSGHTDRGGTPPAEGSGVGPTNPQMDVEQPGERSTGR
+IVLFAIIALLVIGILLFVLGRVFDLFG
+>3_834
+MATPHHPDQPADAHRSDHLARATDENSGHAVAGDTPPAEGLGVGPTNPGMEADKSGEGGM
+GRILLGLLIALVVIGVLLFVIGRISSIG
+>4_1801
+MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV
+LGLIIALVVIGVLLFILGRVAGLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae17e8e8055a4a250d82c1e5c1be5dc1ac31029d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001565.fa
@@ -0,0 +1,40 @@
+>0_1882
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>1_1589
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>2_894
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>3_833
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>4_1802
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..990dafe1461dbf784d6af0744d8adda5f7f9bac1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001567.fa
@@ -0,0 +1,40 @@
+>0_1884
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>1_1591
+MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>2_892
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL
+LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>3_831
+MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL
+VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA
+SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA
+AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR
+LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL
+AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL
+EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
+>4_1804
+MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD
+LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC
+ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG
+AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA
+RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER
+LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL
+LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c3a2620680c637a4e02e6fccceb0b4c57bcaafb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001576.fa
@@ -0,0 +1,39 @@
+>0_1911
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT
+TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
+>1_1616
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG
+ALG
+>2_868
+MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR
+MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS
+VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA
+FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW
+EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA
+DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA
+GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG
+>3_810
+MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI
+VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV
+HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA
+APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ
+GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV
+PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ
+>4_1838
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff1d64891c01f360fcdcfca854d2593ace1d8ee4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001579.fa
@@ -0,0 +1,25 @@
+>0_1917
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPTDSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLNVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR
+>1_1622
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR
+>2_861
+MSEATPTTVPATPTPGPGGPGGEARAAILDRIRQALQDGPTPDPVERTYRRTSEAAPGDV
+VEQLVDRLVDYKAGVHREDLTTVADRVADLLGEGARYVVPPGLDPAWLPGDGQGRVRVTE
+PATADAGALGVRELDELDAVVTGSTVSCSETGTIFLTGRPEEGRRAISLVPDHHVCIVPL
+DTVVELFPEALARVEPTAAITMISGPSATSDIELERVEGVHGPRRLDVILLDR
+>3_797
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR
+>4_1844
+MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE
+ETVAAAIAELLGPDARYVVPAGLEPDWLPADSCGAGRERITEPAVGHTGERAAVRGAHDG
+EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV
+ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f73ee062767cd51a45e07b911300c912ea4b914
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001582.fa
@@ -0,0 +1,55 @@
+>0_1920
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>1_1625
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>2_858
+MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA
+AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT
+VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV
+AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL
+TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP
+AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG
+EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW
+SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF
+ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW
+SVALLLMVCTIVFLQSNVLSWMLP
+>3_794
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWLLPAAG
+>4_1847
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6577f5dd18bd9a9b09467eb8a7ffc20c2d378c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001584.fa
@@ -0,0 +1,40 @@
+>0_1923
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
+>1_1628
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>2_854
+MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD
+PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI
+PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG
+PLGLDPRKDARTTADVLASA
+>3_791
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD
+ELGLDPQKDVRVTSEVLAEA
+>4_1850
+MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD
+VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV
+TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE
+AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI
+PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM
+PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD
+ELGLDPRKDVRVTSEVLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eecb1cfd0c2aa839a182df6a6b155f83e20ef63c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001586.fa
@@ -0,0 +1,30 @@
+>0_1927
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>1_1632
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>2_850
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH
+VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
+>3_788
+MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN
+VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW
+AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA
+>4_1854
+MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH
+VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG
+TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR
+VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW
+ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac7fe4bf666d6a9f82d334a7920e0c8375fa9bbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001587.fa
@@ -0,0 +1,32 @@
+>0_1928
+MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR
+ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP
+AEESSWGPAEPTQGTWSPGPEPSAP
+>1_1633
+MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE
+ESSWGPAEPTQGTWSPGQEPSAP
+>2_849
+MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV
+PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE
+TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR
+PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED
+PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE
+PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP
+>3_787
+MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG
+CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS
+TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD
+PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS
+TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA
+GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG
+>4_1855
+MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE
+PSTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb27fa4afe9bb0db3dc0430a86eb3464d0391538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001593.fa
@@ -0,0 +1,30 @@
+>0_1934
+MLDHETHVKIADELHRAGIDRVPVPRLTARYPQMEIEDSYAVQRIWAERQVEAGRRKVGH
+KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP
+GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVDDVDLR
+WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV
+YEGDTVYADYGPLGTITCRFA
+>1_1639
+MLDHETHVKIADELHRAGIDRVTVPRLTARYPEMQIEDSYAVQRIWAERQVEAGRRKVGH
+KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLRDELRGP
+GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR
+WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV
+HEGDTVYADYGPLGTITCRFA
+>2_841
+MLDHETHVKIADELHEAGRTGTPVPLLTARYEGMEIEDSYAVQRIWAQRQVEAGRRVVGH
+KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHEYETARITNPRIEMELAFVLKDELRGP
+HVNLFDVLRATEYVVPALEILDAHVELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR
+WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLVDHGDALAAGEIVLAGSFTRPMHV
+SAGDTVTADYGPLGTVTCHFA
+>3_780
+MLDHATHVKIADELFEAGRAGTPVPLLTARYADMEVEDSYAVQRIWAERRVEAGRRVVGH
+KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHVYETARITNPRIEMELAFVLKAELRGP
+HVNLFDVLRATEYVVPALEILDAHIELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR
+WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLGEHGDALAAGEIVLAGSFTRPMHV
+SAGDTVTADYGPLGTVTCFFA
+>4_1861
+MLDHETHVKIADELHRAGIDRVPVPRLTARYPEMEIEDSYAVQRIWAERQVEAGRRKVGH
+KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP
+GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR
+WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV
+HEGDTVYADYGPLGTITCRFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb705bee1633d71ec0864856963c820a346aa331
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001594.fa
@@ -0,0 +1,56 @@
+>0_1937
+MTTSAPTLSSHFADTFPELALPWQAQVTDGPQLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQPGPHARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEGGDLAPVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>1_1642
+MTTSVPALSSHFADTFPELALPWQAQATDGPRLVLLNAGLAAELGLDAEWLASDDGVRFL
+TGEQSGPDARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDESIARHHPHATDAEHPALALYEAVIAAQAELV
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVPLAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+EWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPGPADGAPFVTYCGT
+>2_840
+MPVRHNTQPLVRDLFTTEAKAARGGRPAAGMFLSSGDCTAAEICAGAGLDYLLIDGEHAP
+LSLENVQAQLRTIAGYGVPVMTRVPFLDWISIKQYLDLGAQTLLVPMIDTPEQAAEAVRA
+LRYPPHGDRGVGSALARSGRWNRIEGYLQHDEEHVSLFVQIETVRGVENAAAIAAVPGVD
+GVFVGPSDLSASMGLIGQQSHADVVAAVRRVIEACNAAGTTVGVNAFATDQAQAYADAGA
+DFVNVGADVALMARGAEALADRWCPTPGTGADEGAGEGAGAGAGARANARPARRTDGGRP
+TRPPAPHAWECGVMDDVAPAHPALAPQPGRPALRHRFADLFPELAVPWQAQETDGPELVL
+LNTGLVTELGLDADWLASDDGVRLLTGEQLGPDARPVAQAYAGHQFGHYSPRLGDGRALL
+LGELVPPRRTRDANDAPQALPTWRELHLKGSGRTPFARGDADGQAVLGPMLREYAVSEAM
+HALGVPTTRALAVVATGRPVRRAGWQPGALLARTAASHLRVGSFQYAAALPERADPVAVL
+RRLVDEAILRHHPHAAEAENPALALYEAVIAAQAELVARWMLVGFVHGVMNTDNMTLSGE
+TIDYGPCAFLDAFDPAASFSSIDTQGRYAFGNQGPVAAWNLARLGEALVPVLDDDAGRAV
+ELAQEALGGFQATHLAAWRGGLRAKLGLSEEVTDADVAALTDRLFPVLAAARTDWTGFWV
+RLAEHVPGGRGRGRAGRGRRRTECPAECRSGRADGRRAGGGADAGPGRGRPGCRGRVAAR
+LAGAGPRRGPDAGGEPRLHPAEPPARRGPHRRRGRGPGAGAPPAGGRHRPVHPAPGPRAV
+RRAGPVGRGPVRDVLRDVRRGRRGLPYSRSPLPAPRPNSHRPTAFVWESGNLPPLSCGET
+GVPVSHTKGDEGRTLLLTRGCGGARPLTPGRATSAARSGRRGPAGPPRSRGR
+>3_777
+MPVPALQHRFADRLPELAVPWQARPAPAPTLAALNAPLAAELGLDPAWLATDAGLAFLTG
+TEPGPGARPVAQAYAGHQFGSYSPLLGDGRALLLGELTAPDGTLHDVHLKGSGLTPFSRE
+GSDGLAALGPMLRELVVSEALHALGIPTTRALAVVATGGPVRRQRVLPGAVLVRVADSHL
+RVGTFQHAAALVHAGRAPEDLLTRLVAESLERHHPGHADDAAPALALLRAVVAAQAELVA
+RWMLMGFVHGVMNTDNMTVSGQSIDFGPCAFLDGFDPDAVFSSIDRGGRYAYGAQPRIAL
+WNLNRFAETLLPLLAPDPEAAVAAAEEALGGFAPAFDAAWQGGLAAKLGLARSADSDALA
+AELLRLLAQDRADWTASWANLSDLPLPADWLARWRALDPDPELARAANPLRVPRNRPLQA
+ALDAAEDGDLADVERILAAVREPFTPRADASDLDVPPAPGAGGEAPFVTFCGT
+>4_1864
+MTTSVPALSSHFADTFPELALPWQAQATDGPQLVLLNAGLAAELGLDAEWLATDDGVRFL
+TGEQPGPGARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA
+RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVGTGHPVRRETVLPGAVLARTAAS
+HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELI
+SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYACGNQGPIA
+AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV
+AALTDRLFPWLAAARADWTLFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA
+DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER
+YAEPWPEDGAPFVTYCGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001597.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab3beba13cd23c1bb9387262a8967ce3e5ce4c62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001597.fa
@@ -0,0 +1,40 @@
+>0_1942
+MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS
+VRAFAGEGVRVSIGEKEANDRFLEVARDFLA
+>1_1663
+MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS
+VRAFADEGVRVSIGEKEANDRFLEVARDFLT
+>2_820
+MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG
+VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE
+AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP
+NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF
+SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD
+ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE
+QEANDRFLEVARDFLK
+>3_758
+MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV
+VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE
+DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP
+NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF
+SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD
+ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER
+EANDRFLEVARAFQR
+>4_1881
+MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS
+VRAFAGEGVRVSIGEQEANDRFLEVARDFLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cc8b26b1ccc0a49a85782064b5ccc247ddd8e12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001599.fa
@@ -0,0 +1,51 @@
+>0_1945
+MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR
+SATWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS
+LEELPGLLWRDGHDGLTTREAERLVRDLVQAVPEAIVSAALAATGFPLLAALARIDVKML
+TRAQKRVLKRPVSTAAKKGTDAASDLTEALRVSPDEAWTVAADALALAGAAPRGAVTPHG
+APQDRPAAPARLDGSAAGLASLIPRGEGDGDLTVTEVVQENGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSESEITAPAVRAALEAAGVPHGVPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTIAAPSGNAVETGRTAVLEFSADGDLAVAADGAPTPVSARRAEVVFH
+PAGHGWDAPGGGFRTGSPLAVKADLDAAHDFEGQVDLIRQFEAAEPAARAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPEGGHRPPGSR
+>1_1666
+MTGGRGASPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR
+SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS
+LEELPALLWRDGHDGLTTREAERLVQDVVQAVPEAIVAAMLAAAGFPLLAALARIDVKML
+TRAQKRVLKRPVSSAAKKGTDAASDLTEALRVSPDEAWTVAADALTLAGAAPRGAVTPHG
+APQDRPTAPALLDGSATGLASLIPREEGDGDLTVTEVVRENGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSESEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTVAAPSGNAVETGRTEVLEFSSDGDLAVAADGAPAPVSARRAEVVFH
+PAGHGWDAPGGGFRPTSPLAAEDDLGAAHAFDAQVDLIRQFETAEPASRAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPERDHLPPGSR
+>2_817
+MTGGRGAGPDGVAFSTHGGPGSLYAETEQMRAVAAGHDRAAGEALRVAGTAESAGAGLVR
+APRVSPTAAVLQARLWEGLERVRALSDRCARMDRDLRAAAVRYEEAERAAAGIVAAEDVG
+LGALPLEAWRRGRDGLTTREAERLGEAAVQAVPEAVASAVLTAAGFPALAALARIDLKKL
+SWWQRKALKRPVSRGASRLVEEASEGTDLLRVSPDEAWTAVGAVARALSIAADREVAVAG
+PPEDRPDAPARLDGSASDLLGLIPRGGVEGELTVTRVERERGGPAWVVGLPGTQGGFAPD
+HASRNPWDASGLADALTADSAATAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGD
+AGFTAAYPVAGVVTVAAPSGNAARTGGAAVLEFSSDADLATAVDGAPVPASRHRAEVVFH
+PGGQGWGPPPAPGEEPGAAPAGGFRTAGPDAVGEDLAATHDFDGHLAMVRQFEAADPAAR
+AEVAGLSATLAGLSAGAVASSRSVRLRRAPAPREAAGSTSPVAPGGPGRR
+>3_755
+MSAPAFRVTGGPGSVYADLGSLEAVAQRQRDNGDLARRAGQWCTVLGLDLVSPARTAPSA
+EVLRARLEDGRAGLERLAERLEDMRRSLEHTAQAYRQVESGNAAMIGLIDPALAGVPEVT
+PESLRDGATASETAGVISEELRAAQEKAYVDAAQRLLLALVGGVPGIPESLAALDFQAKQ
+LPWWHPAKHAWNKGKGEAVDRVTGALPAIVEEGVDSGVLPTATAQDASRELARALVSAGA
+LPRGEGEVRVEPGARDRPAPPLLDGRASTLLSLVPEQDGADGAGAVTVTRVDRPDGPGGT
+ASTWIVGLPGTTTRGGAGDNPFDTLGIVESLADEPGVTRAVQEALEREGVPHGSTVVLAG
+YSQGGMRALDLAADEQFASAYRVEGVLTAGAPANDAAAPAEAAVLQFASEADLIWGLGGG
+HDRPAASRATVMFDAPAQVPLPQPGEVRPFDGLDEFDGALAGHARSEYARLIEGFERAPA
+QDRAEVADLQARLALLTGGAVVSSRVLTLRRTSTEPAVDQRAREVREAAEAAGQRPGPRF
+GPRLP
+>4_1884
+MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAADEAAGASWQVDAAAFGLGR
+SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGITAAEDAS
+LEELPALLWRDGHDGLTTREAERLVQDLVQAVPEAIVAALLTAAGFPLLAALARIDVKML
+TRAQKRVLKRPVSSAAKKGADAASDLTEALRVSPDEAWTVAADALTLAGAAPQGAVTLHG
+APQDRPTAPALLDGSATGLASLIPRAEGDGDLTVTEVVRGNGSRAWVVGLPGTRGGLIPD
+PESTDPWDAGGLLDALGSGSEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR
+EDFTSVYPVAGVMTIGAPSGNAVETGRTAVLEFSSDGDLAVAADGAPTPVSSRRAEVVFH
+PAGHGWDAPGGGFRTASPLAVEDDLGAAHDFDAQVDLIRQFEAAEPASRAEVAGLSAALA
+GLTAGTVASSRAVRLRRTPPERDHLPPGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..166999e6dfb651b69ef96df18db48e3bd376931a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001606.fa
@@ -0,0 +1,30 @@
+>0_1952
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>1_1673
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
+>2_810
+MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG
+RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA
+EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA
+DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA
+EGFKAFQEKRRPEFTGRG
+>3_748
+MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF
+CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV
+YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA
+VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA
+DYAEGFTAFQEKRKPEFTGRP
+>4_1891
+MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF
+CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV
+YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA
+LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA
+DYAEGFQAFQEKRKPEFTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e821f17b8d4ea1f23ec1355816cd462fc80ad02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001609.fa
@@ -0,0 +1,16 @@
+>0_1958
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>1_1678
+MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA
+>2_2481
+MDALDLPALAGARALELPGSELTHPFGPEADVYKVRGRVFMLVLEARGAMLVNLKAVPED
+GAALREAYPAQVTPGYHMSKRHWISLGPPPADPHDDDAPARLDAALVRDLVTESYLLVLE
+RSVPRRDWPVDPATFGRG
+>3_743
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVVKVQGKLFVVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLVVAKLPRTRRPVD
+PDTFGRA
+>4_1896
+MDEPTLLRIARDRALELPGSAASHPFGPDTEVMKVQGKLFAVFIDHDGRRLVNVKARPED
+GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLIVAKLPRTRRPVD
+PETFGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..799796adcee1c12871ec194355599fcb19709a96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001610.fa
@@ -0,0 +1,20 @@
+>0_1959
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRATVHDDGAPAGHAPRCIVVWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPA
+>1_1679
+MSADRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRVTVHDDGAPAGHAPRCIVAWEQEVVLTSPWM
+RAVAHVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTSRP
+>2_784
+MPASARRPFRFTHRWAVPRPAAEVAALLADPLGYPTWWPSVPRARRIDGAGHDGDPRVAV
+LLRGLVPVRLVMARELDDRERGRLVARLDGDLRGTVRVTVHDDDGPAGGTGGCTVAWEQE
+VVLGAGRLRAAARLPGARAAMRLSHAWAMRSARRALGARALPAGR
+>3_742
+MSVDRPFRFTHRWSVPADARSVLALLADPAGYPRWWPAVPRVRHLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPRCIVVWEQEVVLTAPWM
+RAVDRVPGARTAMGLSHAAAMRSARRALGAKAMPTADPAPTTRP
+>4_1897
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRAHRLGPDRAAVRLRGLVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPHCVVTWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTTRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3158484cedeef8c949b762aa98a9113ae3631ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001611.fa
@@ -0,0 +1,20 @@
+>0_1960
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>1_1680
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID
+PADGLLDGLSRPPLSREWNEAQAEL
+>2_780
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI
+AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD
+PADGLLDGVSRPPLSREWNEAQAEL
+>3_741
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWNEAQAEL
+>4_1898
+MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI
+AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD
+PADGLLDGLSRPPLSREWDEAQAEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..275a0d93043ad6700a8b8d7187eb13b089fc38dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001614.fa
@@ -0,0 +1,35 @@
+>0_1963
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKRVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVVEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNAGADWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>1_1683
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>2_777
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DVVGFHVAANVSRNTGVDWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>3_2039
+MTTIQKVTVFGTGVLGSQIIMQAAYHGKDVTAYDVDDKALAQLPARWEWMRGYYQRDLPD
+FDAERFDKAVSSIRTTTDVADAVTDADVVIESIPENLELKKSVWAKIGEAVPERTVLLTN
+TSSLLPSSFADSTGHPERFLALHFANLVWKNNTGEVMATAKTAPEHFDAVLAFAGEIGLV
+PVPVRKEVPGYVLNSLLIPWLDAGAKLYQGGVSDPEDIDNVWKIATGAPKGPFEVYDVVG
+FNVAYNISRVSADPLKKAFAEETLKKGIDAGTTGLGVGEGFYRYDKDGNNLGAVESWKQE
+NRG
+>4_1901
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3af77b3fcbcf2728dc84844fa27acc2f2097ae8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001617.fa
@@ -0,0 +1,45 @@
+>0_1966
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>1_1686
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHASLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
+>2_774
+MLEASIPNPYTPAPLPAPADRGAQDPEETMSRDQIEALQFERLRWSLHHAYENVPAYTEH
+FDAHGVHPSDFKALEDLAKFPYTDKEFLRKNYPFGAFAAQGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTDEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDKG
+>3_735
+MLEASIPNPYSPAPVPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYKEH
+FDNHGVHPSDFTALEDLELFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFRKLGLDPRESSLEVAILGAEPWTEAMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERREHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>4_1904
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b8eedb731f7ddd8c78dc94dfdb12272c3011772
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001619.fa
@@ -0,0 +1,27 @@
+>0_1972
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>1_1690
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>2_769
+MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVRLALLRRDWDSARASV
+>3_1202
+MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS
+FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW
+TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG
+DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG
+SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ
+QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG
+>4_1908
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0be199e924e7c9f50d425c567cd5e2ddf2f2d56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001625.fa
@@ -0,0 +1,25 @@
+>0_1991
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
+>1_1708
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQAGE
+>2_752
+MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL
+GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV
+ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>3_722
+MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL
+GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV
+ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG
+QTGE
+>4_1926
+MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL
+GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV
+ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE
+GIDGQTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6aa2c2d23326fd32123f396f9cd190d8ebbedb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001635.fa
@@ -0,0 +1,20 @@
+>0_2022
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>1_1738
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>2_682
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>3_593
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>4_1962
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d98ef2c1030c274b821385abf50cad9132797d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001636.fa
@@ -0,0 +1,35 @@
+>0_2023
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>1_1739
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>2_681
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>3_592
+MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
+>4_1963
+MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC
+DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR
+ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP
+AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP
+LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF
+VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a343a06ed874f5f4e61460484ea8839f3de60118
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001639.fa
@@ -0,0 +1,45 @@
+>0_2026
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>1_1742
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPATTPAVPETAAVTQEVR
+>2_678
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA
+LAVVSAAGPAVLATTPAVPETTAVTQEVR
+>3_589
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVSAAGPAVPAATPAVPETAAVTQEVR
+>4_1966
+MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT
+VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA
+DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD
+STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK
+ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL
+AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE
+LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA
+LAVVTAAGPAVPAATPAVPETAAVTQEVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..732af4f9c200accbe6d919c934ef13e19712558b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001645.fa
@@ -0,0 +1,15 @@
+>0_2042
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>1_1760
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR
+>2_658
+MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD
+SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR
+>3_574
+MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA
+DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS
+>4_1983
+MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ
+SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc0911ccd38a30f7846a021f36a1080b74dc780c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001646.fa
@@ -0,0 +1,30 @@
+>0_2043
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>1_1761
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLALAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
+>2_657
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPTWLVVLGTVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLADPAVRRRVLRWSCLVAVPFVAVLAGWSIARGQWDALAVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPALYGLVLAGAAFTPALWALLGGFFLWGM
+ASQMFGAVQDVLPDREGGLASVATVLGARPTVWLAAALYAGAGLLMLGTEWPGPLAALLA
+VPYVLNVLRFRAVTDATSGAAHRGWRLFLPLNYVTGFLVTLLLIGWALARGGV
+>3_576
+MIRTLFWASRPVSWVNTAYPFLAAVLLTGGLPWWLVALGGFFFLVPYNLAMYGINDVFDF
+ESDLRNPRKGGVEGSVLADPAVRRRVLAWSALTPAPFAAVLAGRSVLRGEWAAVAVLAVS
+LFAVVAYSWAGLRFKERPFLDAVTSSTHFVSPAVYGLVLAGAEFTPALWSLLGGFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARPTVLAAAALYAAAGLLMLPTDWPGPLAALLA
+APYLLSTLRFRHVTDATSGEAHRGWRTFLWLNYLTGFLVTLLLIWWALVR
+>4_1984
+MIRTLFWASRPVSWVNTAYPFAAAAILTGGLPAWLVVLGVVFFLVPYNLAMYGINDVFDF
+ASDLRNPRKGGVEGSVLGDPAVRRRVLAWSVLLPVPFVAVLAGWSAVRGEWAAVLVLAVS
+LFAVVAYSWAGLRFKERPFLDAATSATHFVSPAVYGLVLAGATPTPALAALLGAFFLWGM
+ASQMFGAVQDVVPDREGGLASVATVLGARRTVLLAAGLYAAAGLLLLATDPPGPLAALLA
+VPYVVNTLRFRRITDATSGAAHRGWQLFLPLNYVTGFLVTLLLIGWALTRGAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..405d15cb9476be642895a389a35885590a45ecfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001648.fa
@@ -0,0 +1,32 @@
+>0_2045
+MAAPTPSPAALYTRTAHTAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
+>1_1763
+MAAPTPSPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
+>2_655
+MPADAPLYTRTARAAAGRVIRRYSTSFSWACRTLPREARRDVEAIYAMVRVADEAVDGVA
+QAAGLDSQRVRAALDDYERACEAAMASGFSTDLVLHAFGDVARRHGITPELTRPFFASMR
+ADLGVSEHGAESLAAYIHGSAEVVGLMCLQVFLSLPGTRARTPAEREAIRAQAARLGAAF
+QKVNFLRDLAADHDGLGRTYLTGAAPDELTEARKAELVAEVRADLAAALPGIRALDPRAG
+RAVALAHGLFAALADRIETTPAAELARRRVRVPDAQKARIAARVLAEQAGLAVARRRRGG
+RR
+>3_572
+MTGTTTPPAPAGPECGTVRARTGETDLELYTATALRVAGEVIGRYSTSFSWACRVLPPDA
+RRDIAAIYAMVRVADEVVDGAAEEAGLPVARVAAGLDAYERACEDAMDTGFSTDLVLHAF
+ADVSRRHGITAELTRPFFVSMRADLTVAEHGEDSLAAYIHGSAEVVGLMCLQVFLSMDGT
+RADGPADRAALRAAASRLGAAFQKVNFLRDLAADHDALGRTYFSGAAPEALTEERKAELL
+ADLDADLDASLPGILALDPRAARAVLLAHGLFAELSRRLAATPAAELARRRVRVPDPVKA
+RIAVRVLAASPVGIGRRGRPLPAGCAEDLAAHQDGDRRP
+>4_1986
+MAAPAPIPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31f66f8a5f8633402727898d60811573f56ba329
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001650.fa
@@ -0,0 +1,25 @@
+>0_2048
+MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>1_1766
+MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDPR
+>2_651
+MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE
+DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP
+QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFEAR
+>3_569
+MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG
+RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY
+RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM
+QWEQGAFGPR
+>4_1989
+MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE
+DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP
+QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA
+DLAAALAAVPRAFSPWLVEQWQQGAFDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14842d68124b079218758331c24c97b6f1d4c7fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001651.fa
@@ -0,0 +1,20 @@
+>0_2049
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDEAVQSTAAHLDDVNGR
+>1_1767
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGAALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDDAVQSTAAHLDDVNGR
+>2_650
+MATKDLTLEEFGTTVSENDTVLVDFWADWCGPCKQFAPVFDAASEKHEDIVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPAPALDQLLEQVKGLDIAEVRAMAEQQAG
+EAEAEPSQDEAVQSTASHLDEVNGR
+>3_568
+MATTDLTLEAFGTTVSENDTVLVDFWAEWCGPCKMFGPVFETASEKHQNVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGQALDQLIDQVTALDIAEVRAMAEQQGA
+QDAEPSEEEAVQSAAAQLDDVNGR
+>4_1990
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHDDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDVAEVRRLAEEQQG
+QQDDAEPGQDDAEPGQDEALQSTAAHLDDVNGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dd7d0ae43f211b9c791d684dd03d52b973f9be6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001657.fa
@@ -0,0 +1,30 @@
+>0_2058
+MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDLYPPGV
+>1_1777
+MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG
+EAATPLPEEGTRVGRPLDPYPPGV
+>2_643
+MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV
+GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC
+HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE
+DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL
+GEEGSDAPPPGEGAPVA
+>3_561
+MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA
+RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR
+SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA
+QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE
+GEEQGGAADPAA
+>4_1997
+MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA
+DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH
+GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD
+VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG
+EAAADAPLPDADTRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d291164b8179fa318a18f35865dd31b964f42aeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001659.fa
@@ -0,0 +1,15 @@
+>0_2060
+MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA
+AVEEAGYTLVEA
+>1_1779
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA
+>2_641
+MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA
+AVEEAGYRLVEG
+>3_559
+MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA
+AVEEAGYTLVEG
+>4_1999
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c993b495a3e32dd2734d857cdcd29847aec3e0e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001660.fa
@@ -0,0 +1,20 @@
+>0_2062
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>1_1781
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>2_638
+MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR
+IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE
+ESGELEQWLEYSRQCLP
+>3_557
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
+>4_2001
+MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR
+IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE
+ESGELEQWLEYSRECLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33b5ee8ca38e74fbbab92e440c83db1ac5efe282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001664.fa
@@ -0,0 +1,35 @@
+>0_2067
+MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>1_1786
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
+>2_634
+MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>3_551
+MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD
+>4_2006
+MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF
+IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD
+GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG
+HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT
+AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE
+FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da144ff093ee700ed13ecff77913d70647dd2523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001671.fa
@@ -0,0 +1,20 @@
+>0_2075
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER
+REQGGTGGDAPRA
+>1_1794
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
+>2_618
+MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER
+REQDGTGGDAPRA
+>3_543
+MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR
+IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA
+ERRAAQGDAGR
+>4_2014
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8690e55697cea8a4b3ad2e01063a0672e921c52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001679.fa
@@ -0,0 +1,35 @@
+>0_2084
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP
+>1_1802
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>2_609
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP
+>3_534
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>4_2022
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bfb3e6ad7e4f26494171fa8041f770be92d0201
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001693.fa
@@ -0,0 +1,80 @@
+>0_2103
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA
+GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ
+PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL
+AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG
+WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>1_1828
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>2_575
+MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL
+PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP
+VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV
+GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD
+AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ
+VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA
+FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV
+VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR
+PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL
+VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE
+DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL
+ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML
+WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV
+AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL
+PARRAARLSPVAGLATV
+>3_499
+MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ
+PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP
+RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA
+PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA
+EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF
+QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG
+ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG
+LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA
+RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD
+LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG
+QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA
+ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE
+RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG
+MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV
+AVAAVAGLLASLAPAGRAARLSPVEGLATV
+>4_2049
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3aaec1fb77181900ffc284f1be184924213a447
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001697.fa
@@ -0,0 +1,30 @@
+>0_2112
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
+>1_1837
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
+>2_561
+MSRIQSTTSPSSMAELKKVLPELSHPDGSPVRVLVVDDEPMIADLLSMGLSLCGWDVVVA
+HDGASAVEQGTARRPDLAILDVMLPDMDGLEVLERLRAHWPEVPAMFLTAKDATEDRVAG
+LASGGDDYVTKPFSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGQVI
+DLTATQYNLLKFLMANVRTVLSKERILQEVWGYDFGGRANIVELYISYLRKKIDADRDPM
+IHTIRGAGYVIRPA
+>3_489
+MTSAEHTVSPASMAELRESLPDLTHQDGSPVRVLVADAEGLEADLLSMGYSLLGWETVVA
+KDTAAAVQEGTARRPDLALLDAGLPDGGGLEVLARLRAHWAEMPAIVLASPAEAEDRIAA
+LLAGADDVVAKPFAVEEILLRSHHLVRRAGLNASTGEELVVGDLVMNTRTHEVTRGGDLI
+ELTATQFNLLKFLMANVRTVLSKDRILQDVWGYDFGGRANIVELYISYLRKRIDAGREPM
+IHTVRGAGYVIRPAEG
+>4_2058
+MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA
+GRPDLAILDVMLPDMDGLDVLERLRAHWSEMPAMFLTAKDATEDRVAGLAAGGDDYVTKP
+FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF
+LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR
+PA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0537700271b38b4fbadb5cce2dfcee656642560
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001703.fa
@@ -0,0 +1,25 @@
+>0_2119
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD
+>1_1844
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYAYAQAKAEADEALRDSGLAWTILGPGTLTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLNEPGTVGRKIDFVDGDVPVAEAVRGD
+>2_554
+MTRTVIIGGHGKVALLAAPLLAEAGHDVTSIIRNPEHAAEVEAAGAAPLVLDVERAGEED
+LVQAFRDADNVVFSAGAGGGDPARTRAVDHDAALATMRAAEAAGVRRYVMVSYLGASLHH
+GVPEDDSFHAYAQAKAEADEALRDSGLAWTILGPAALTLEEPTGRITVDPDLDTPDAPKG
+EVSRGNVARALVAVLADPTTVGRKIDFVDGDTPVAEAIRGA
+>3_482
+MDILIIGGHGKIALLTAPLLADAGHTVTSAIRNPEHADDVRTAGAEPLVLDVEHSSPAEL
+EAAMRGRDVVVWSAGAGGGDPERTYAVDRDAAIASMDAARAAGVRRYVMVSYRGASVHHG
+VPEDSSFFAYAEAKAAADEHLRGSHLDWTILGPGALTLDEPTGRVQVDPQGPSEELPGTS
+RGNVARMIAAAVDSGASIGRQVEFVDGDTPVDDVFRR
+>4_2065
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSLIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LVHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTEEEASGRITVDPDLSGSDASQR
+EASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c15193905771aca713ffb4459413509667aa06f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001704.fa
@@ -0,0 +1,29 @@
+>0_2120
+MPLSTLRVSLPSVRRTRPAPQGVRGRIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+CDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
+>1_1845
+MPLSTLRVSLPSLRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWHVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
+>2_551
+MLRLARPRSRRAPQGLGGRLVRAVAARPVPPVRPRARLAWHVSGALPLIGCLTSFPIGMS
+KDSMVIPGVGYQGGFSAGWHHALNQPAYFTWLSNALVAGTSLTLATRRTAPTSDAFWAVR
+TAGLGSVMVTGIVYNSVLRGREQDTVLYRFNDTLQHIVNPVLAPAVWALFDPRGQITPRR
+AGLASVIPLAWAALTMARGPRIDWYPYPFLDVPRHGARTVGVVLAGILAGFTGLMGLLGG
+LDRRLGGR
+>3_479
+MPAWLARFTRPRPAPRPSRAARAGWWAAGALPLVGCLTSFPIGASKPTMVIPGVGYHGGF
+EAGWQHALNQPAYFTWLSNAMVAGTSLTLAARRDAPTSDAFWALRTAGLGSVMVTGIVYN
+AVLRGMEQDTLLYRFNDAVQHVVNPVLAPLVWAAFDPRGQITYRRAGLAAVVPLMWATAT
+LVRGARIDWYPYPFLDVPRLGWRGVGAAVSVVLAGFSAVLGLLGQVDRRLGTR
+>4_2066
+MPLSTLRVSLPSVRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI
+GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE
+APTSDTFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL
+FDPRGQITPRRAGLASVIPLMWAAVTMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA
+GFTGLMGVLGTVDRRLGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27247530c9dd179e396ac9bc051067fb3bbc878a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001705.fa
@@ -0,0 +1,45 @@
+>0_2121
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASREERLDRAVEIMSLLAGRRLSVDRETYESEMAVSDRNLALAHMLRSYGVL
+QDSAEEIVAGYVAQCAVRVTVKDLAVMGACLATGGIHPMTGERVLPSIVVRRVVSVMTSS
+GMYNAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADRAALSAATGGGAVHEAAAVAARDENDGPIRTVVLNLTRVDWIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>1_1846
+MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRLGIALATPTGRLHSAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLAVDRETYESEMAVSDRNLSLGHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERVLPSIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALAAATGGGAVYEAAAVAAQDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
+>2_550
+MRHPFVDYLEGLLGSLEHVTEGDVARYIPILAEADPSLSAVAVATTSGRVHTAGDADAEF
+SIQSVSKPFTYAGALEDRGVELVDEYVALNPSGEAFNELSLEADSHRPDNAMINAGAIAV
+HQLLVGPGATPAERTERAVSLMSTLAGRRLRVDERTFESEMATADRNLALGHMLRSHGIL
+QDRAEDVVAGYIAQCSVMVTVRDLAVMGATLASGGLHPLTGERVLSSLVCRQVLSVMSSS
+GMYDAAGQWMAHVGIPAKSGVSGAVLGALPGQVGIGTYSPRLDPFGNSVRGVEMCRIMSE
+DLDLHIMEADVIGSTVVRSVRREGDTVHLHLQGVIRFGGGESVLAAMTELGTGADPDPVE
+WAHCFYPFSEEPDTAAGRAAAQDEGRTAAEALEQEAPVRAVVVHLERVDRVAPVGRRLIE
+DGLKRLRADGVQVRVEDPDGVLTGG
+>3_478
+MKHPVPDYLQHLVDSLREDRRGALADYIPVLAQADPERLGIALATVTGRLHSAGDDETEF
+TIQSVSKPFAYAAALQDRGLDAVDARVGLNPSGEAFNELSLEAESKRPDNAMINAGALAV
+HQLLVGPYAGRQERLDRLVGFMSTLAGRRLEIDRETFESEMATSDRNLSLAHMLRSHGII
+QDRAEDVVAGYIAQCSVRVTVRDLALMGACLASGGVHPLTGERVLPSLVCRQVLSVMSSS
+GMYDAAGQWLVNVGIPAKSGVSGAVLGALPGQVGLAVFSPRLDEVGNSVRGVEACRRMSE
+DMDLHLMEGDSLGGTVVRFARREGDTVLLHLQGVIRFGGGEAVVTAMTDLGTGAAGGGRA
+AWSEHDYPEWEDAPHGDVAAEAGDRRPVDAADPEAARAAATGDGSVHEAAACAVAEDGLP
+IRTVVLNLERVDRVTAVGRRLIDEGVDRLRADGVAVEVVDPDGLLG
+>4_2067
+MRHPIPDYLASLITDLGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF
+TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV
+HQLLVGPEASRKERLDRAVEIMSLLAGRRLSVDWETYESEMAVSDRNLSLAHMLRSYGVL
+QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERMLPYIVARRVVSVMTSS
+GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE
+DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG
+WDAAVYPRWQEAAADSAALSAATSGGAVHEAAAVAARDENDGPIRTVVLNLTRVDRIDDV
+GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abc893cf3cf6b5b25a2fe649da64c75ead28e834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001706.fa
@@ -0,0 +1,26 @@
+>0_2122
+MTSPDPAPPRPRVHVLTLRPDGAREDTARRVGIVLAEAFATDPYTLGLVPEDRREARLER
+KFTAAVRHGLRTGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA
+VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGAVPSARGRGAASALVRHGQRRASGLP
+VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA
+>1_1847
+MTSPDPAAPRPRVHVLTLRPDGAREDTARRVGAVLAEAFATDPYTLGLVPEDRRGPRLER
+KFTAAVRQGLRAGADGAPLGAVDVAVDAADGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA
+VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRASGLP
+VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA
+>2_549
+MTSPDRAAPPAPPTPAFGPAPEAPAADNAAPARRRLQVVSLRPEGLSEDAVGRVAELLAE
+AFAEDEFTLGLLPADRRAERLARMFALDVHDALRPARAAGGEAGPRGAVDVALDPEDGTL
+LAAAVWDGPDAPRGTTVPGALAALPARLRVHGRRTWDAARTDAACERARPAAAHWHLTQL
+GTAPAARGRGAASALVRLRQRRAARAGVGIHLEASSAEAVPFYARLGFRETGTVRAHGTR
+DLTAMWWEAQA
+>3_475
+MSDAARRPRPLVTSLRPAAAADHPDAAAVAGMAGALAEAFAEDPYTTSFLPPDRREERLR
+DYFDLLVRESLDAAARGHGAVDAAVDPRTGEVLGVALWERPGAPRPPAGLLGALRPAVPT
+AARRWRAFGRHALDHVRTVAACQAVRPSEEHWYLLELGTVPSARGRGAGRALLERRRREA
+RAAGVGIYLESSSAESTRFYEHVGFRPHGTATVHGADDLTTMWWKD
+>4_2068
+MTSPDPAAPRPRVHVLTLRPGGAREDTARRVGAVLAEAFATDPYTLGLVPEDRREARLER
+KFTAAVRHGLRAGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA
+VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRAAGLP
+VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8dc2c010a19f1aaa7290b41deb4453860700f3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001710.fa
@@ -0,0 +1,41 @@
+>0_2129
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKARGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAQGTTHVGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYLRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>1_1854
+MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWPDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMRHWHEEVEPILGPT
+DMLIYPFGADVTGPGKYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP
+>2_536
+MAPSRRQILLTGSALLGSGLLAACSSEGGSAPASSSPAGTPAPAPSSSSAAPAGPGPAGE
+PVAWPNTALVPHLFFHSLVVDPKRAFDGDHKEAGYLDFMVTMDEFAAILPQLYAKGYVLV
+SPHELYEVGEDDVVRPKTLMVPENRTPLVFSLDDCSYYLYMEGDGFADRLIVDEDGRVRN
+EYTDADGTTHVGSYDMVPMLDDFLEEHPDFSLNGARGVLAMTGYEGVFGYRTSAREFGDS
+PTFDADVAAATEVADAMKATGWEFASHTWGHRTVPKLELDELQRDLELWHGEVEPILGPT
+DMMIYPFGADVARTGKYEADNERYQYMRSLGYRSFFLVDGTAKAWGQLEPGYYRGSRINV
+DGISLEAAISGKRPVLDEFFDSRSVLDPARPASIRGTQQSPAAPPGGQSGSASPSATG
+>3_466
+MEYSRRHVIFGGSALLGAGLLAACAPAQDGAAPSAGGGSSSEAASSSAAPSPSSTRPVIP
+SAPEPAGKPVAWKDVAKVPHLFFHSLVVDPEKAFHVHGESDGYLNYMVTQAEFERILPQL
+WALGYVLVSPHELYEVGRDDVVRARTLMVPENRTPLIISLDDCSYYEYMEGDGFATRLLV
+DDSGRVRTEYTDQEGKTTIGANDLVPILDDFVRDHPDFTLNGAKGVLALTGYNGVLGYRS
+SPTMYPEGPELDEAVATAKEVVAAMKETGWEFASHSWSHRSMAQMSLADLKEDCERWIED
+VQPIVGPTDMLIYPFGADIAGIEKYSGPEYEHLRSLGFRSFFLVDGSSKAWGQLEPGYYR
+GSRINVDGISLAGAKDGSRPVLDEFMDVDSVLDPARPESIHAPSYVPPEERAAASSGAPS
+ASPSS
+>4_2075
+MPPPVPQPTRRQLLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE
+PVAWSDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV
+SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN
+EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS
+PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT
+DMLIYPFGADVTGPGTYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV
+DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRSPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52154919abcc5cda021abbe2049cb6aff5fa68a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001711.fa
@@ -0,0 +1,24 @@
+>0_2133
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPSSLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAATPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNTRANRFYERLGFATIGARQFVVGGERVEDDWV
+RLLTVE
+>1_1857
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVA
+>2_528
+MIQAHIDEHLNERVVAAWIADPARIVLVGGTAPDEVLGYAMLETAATPEAPVVEHLGETP
+AGHLSKVYVLAESRGTGLAETLVRDGVARLEALGFRHVWLGTNAQNARANAFYERLGFEK
+IGARTFVVGGTRVEDDWVRLLSLG
+>3_465
+MPTSPTPRPVPAVIRPATPADVPALVRVAAETFPDACPPTTSQEAKDEHIASSLNAEVIG
+GWVAGPGHAVHLAEAPAGRDDAGRLLGYVMAELAPEEEPAVTAVLGEGAAVGCLSKLYVV
+REARGTGAAAALMAAGLDALRVRGLTHAWLGTSEENHRANAFYERVGFRTVGSRTFLVGG
+RPERDNVRLITP
+>4_2078
+MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA
+DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL
+AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV
+RLLTVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00a04933c3931357aa774233e105cca3e6d960a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001714.fa
@@ -0,0 +1,25 @@
+>0_2136
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>1_1860
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>2_529
+MATRPRREDVRAAILDHAAQVFGREGYARSSLTRIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTQAMDGVADALDDPDLPREDLVARVAEALADVVLEPTGSWPLLLHEFQSVG
+LREPAVGRAYRVLTVRRRDFLAGLLREHRVLADVPDAQVTHTAAMLLMLVHTLTVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
+>3_463
+MGGLRGVRRFDTVGIQYHRYRKGKMASRPRHQDVRADLLQYATEAFERDGYGRASLAGIA
+ADAGYTKGAVYSGFGSKAALFAEVCGAQFEALTRRTLDVVGRELAVEGGGRADLVARLAA
+VLTSLTFDGDARWPLLLHEFQAVGLRDESVASEYRALTARRVRFLAEALGEHPRLAGLSA
+ERLERTSSLTLVLVHTLAVEHRLSPEAMDRRGGELSFTALLDSALPD
+>4_2081
+MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA
+CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG
+LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA
+PEDLTVDDVRDTLAAAVRSLLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..088a7c2109579d33622d891f51d9ccde77985814
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001715.fa
@@ -0,0 +1,30 @@
+>0_2137
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV
+GGTVALVRGVAGTLG
+>1_1861
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV
+GGTLALVRGVAGTLG
+>2_527
+MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL
+SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV
+HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA
+SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS
+RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA
+>3_464
+MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG
+GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA
+PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG
+FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW
+WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL
+>4_2082
+MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA
+VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL
+QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL
+TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV
+GGTVALVRGVAGTLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42d3a2a95383e990f8109efa4250a552c1b1d25d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001716.fa
@@ -0,0 +1,30 @@
+>0_2139
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>1_1863
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>2_524
+MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS
+RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN
+LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP
+VDPEPYLRERGVELGSSWERPRRR
+>3_1750
+MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ
+TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN
+DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT
+LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA
+TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG
+QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ
+PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH
+VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL
+QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS
+>4_2084
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55732527fb7d6ef5f180dabf18a0a971dea2c437
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001717.fa
@@ -0,0 +1,20 @@
+>0_2140
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
+>1_1864
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
+>2_478
+MPSRLHLRPLTVADAEEMSAVLADPALYAHTGGEPPSEELLTQQFRIQTRGESADGSERW
+QNLIVVLEETGEAVGYVQATTPKDGGPTEVAWVIGVPWQGRGLGGEAAAQLVEHLAGQGV
+RELIADIAPGHAASEAVARHIGLEPSDVVVDGEVRWTGTVADRER
+>3_1273
+MTPPIHLRPLRPDDADEMVAVLADPALYTFTGGEPPTRGALSGQYAVQARGHSEDRSETW
+LNHLVVLDDTGEAVGYVQATIPVAGGAAEIAWVIGVPWQGRGHATAAARLLLDELARRGV
+SEVVADIHPGHAASAAVARRLGLRPTGHIVDGEQRWEGPVAVVDGAASAPGG
+>4_2085
+MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW
+ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV
+RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dd676cb18002723f576141d9d7af4491c133bf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001727.fa
@@ -0,0 +1,28 @@
+>0_2183
+MTEHTSEHTPENPHVVRRGSGVPLIEVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>1_1896
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAESGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
+>2_484
+MSRGGCLSGGLQSKCGEFRLQFPDRHSPRTACRPHRASAPHLRTAPHVRTFLATLDPDDA
+EPFLEMSPRLVPETWERFRDHALPGIRAVDEDAVERPSARYVLDPVPEEAGPRVEAPALI
+LTGRSWGSGPPRRRGRRGTEAPVREARSAHPLATRPAGFPSATCRGALAPWPT
+>3_2037
+MSQPAPHLVRRGSGAPLVLVHGMGVDHRLLLPLDAALEAAGGWERVYVDLPGFGGTPALP
+APGGLPELADWLDGVVGEIAGEDRFALLGNSLGGLLVREVLARRPGQVAGLAMIAPVVDP
+DPERRDVPERVVLEQDEALLAELDGDDAAPFVEMAVIQTRPVWEGFREHVLPGVLAVDED
+AVDRLEDRYALDGPLPEERFGEFDRPTLIVTGRQDDKVGWRDQLALAEHFPRLTLAMLDR
+TGHNAHLDQEAAVGAMVRNWAEDAAREL
+>4_2116
+MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF
+GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL
+LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG
+VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT
+YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8018ad0560575c3bfda3190b6c33df22a4341d18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001735.fa
@@ -0,0 +1,50 @@
+>0_2209
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIASAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGVMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTTDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG
+>1_1913
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERALRLWKKAVERSRDWVDEDVESAQG
+>2_443
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVHNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGAG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEKPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAASVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVTETTALGAAYAAGLAVGFWSSQDELVANWEEDKRWEPTMDE
+EEAERALRLWKKAVERSRDWVDEDVESAQG
+>3_477
+MSAPRYVMAIDQGTTSTRAILFDHAGDAVATGQLEHAQHFPRAGWVEHDPLEIWRNTREA
+IGQALSRADATRDDVAAIGVTNQRETAVVWDRTTGRPVHPAIVWQDTRTQHLCERLGGDA
+GPDRWRERTGLPLATYFAGPKVAWILEHVDGAREAAERGDLLFGTTDSWTVWNLTGGVLG
+GQHVTDVTNASRTLLMDLETLEWDAEIAAEMGIPGGMLPRIVSSSAEVGHAAPTSLLGGV
+PIAGILGDQQAALFGQACFEAGQAKNTYGTGNFLLVNTGARPVRSRHGLLTTVAHRIGDE
+PPAYALEGSVAVTGSLVQWLRDNLGLIRDAAEVEELAAGAPDNGGVFVVPAFSGLFAPHW
+DPTARGTIVGLTRYADRRHLARAVLEATAFQSREVLDAVLADVAEAEEGAGVVGGLTELK
+VDGGMVANDLLMQFQADVLGVPVVRPEVTETTALGAAYAAGLAVGFWASTAELAAHWSED
+RRWEPAMDPERAARLLRLWARAVARSRGWIDDDVEALAAETRTAPDATPAGRTP
+>4_2142
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..092f4e2a8236249c3d5663e84d91346100167b38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001736.fa
@@ -0,0 +1,45 @@
+>0_2221
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF
+>1_1923
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>2_436
+MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF
+>3_389
+MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI
+VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF
+>4_2161
+MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH
+EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI
+VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH
+AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA
+IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF
+FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL
+AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA
+GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8ba29a06dc0723722a136fe3a4bf5779d56d767
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001738.fa
@@ -0,0 +1,21 @@
+>0_2225
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>1_1927
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
+>2_433
+MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG
+RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA
+>3_387
+MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA
+MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR
+AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS
+YLGGQPPRGVRRRNRGHA
+>4_2165
+MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG
+IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG
+RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59661a5584906e26126f3f3347f08b1ec3e9d50f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001739.fa
@@ -0,0 +1,41 @@
+>0_2226
+MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>1_1928
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>2_432
+MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI
+HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL
+TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS
+WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
+>3_386
+MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA
+EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL
+GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP
+QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI
+SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV
+HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK
+AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP
+AATP
+>4_2166
+MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI
+HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR
+GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF
+HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL
+TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST
+WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG
+DALVHIGGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03eeb874b19ca22dfb0efc7a1224ab873d3a1868
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001740.fa
@@ -0,0 +1,20 @@
+>0_2228
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVQLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
+>1_1931
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
+>2_431
+MAKLILTQEVTGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAEKLQSATVKLERTAGAEGRLFGAVQAADVAEAIEAAGLGSVDKRAVTLPA
+HIKSVGNHQAQVRLHEDVVAVVDLQVVAAKAKK
+>3_384
+MAKLILTQEVPGLGIDGDVVEVKNGYARNYLLPRGFATVWTQGGEKQVESLKAARAARAT
+ANLEEAQALAAKLQSATVRIDRKAGAEGRLFGAVQAADVAEAIEAAGLGSVSKRSVTLPN
+HIKTVGNHEAQVRLHDEVTATVALQVVAAKGSKK
+>4_2169
+MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV
+ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA
+HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88d696fea095f31ab72f497877215e9d1b3a51ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001744.fa
@@ -0,0 +1,50 @@
+>0_2232
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV
+>1_1936
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
+>2_425
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV
+>3_379
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV
+>4_2174
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaa5527e1b7a7b18a359a9e49c5fb60e0cbd3c1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001752.fa
@@ -0,0 +1,35 @@
+>0_2245
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID
+CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPSVKG
+>1_1949
+MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPTALKS
+>2_412
+MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM
+FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA
+AAEIAGRGAPAAKG
+>3_366
+MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK
+TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD
+APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP
+PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD
+ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA
+EIARRGAPQAR
+>4_2187
+MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV
+GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV
+QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID
+CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM
+FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA
+AAEIAGRGAPAVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2af13d9ea10562ae2fb8d8c85d28022fbbebfe9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001755.fa
@@ -0,0 +1,35 @@
+>0_2248
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSTIFGARMSDTFLNSFGDPGSAPVII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGAVLNGEVVRQSGQRVQPQRKNRRRK
+>1_1952
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSGPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK
+>2_409
+MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGASERGESMDALSADQIRSFEGSMIFGARMSDTFLNSFGDPGSAPLII
+TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEQELNERRAAKGLPPVGQKVTDSKAEPSSAH
+TQAAGGGTATLNGEPVRDSGQRVQPQRKNRRRK
+>3_363
+MFDAILAPFRWIMSWLLGAFHTVLDTIGLPADSGWTWALAILLLVILIRTLLIPLFVKQI
+NAQRAMQTMQPELQKLQAKYKGKKDQLSRQAMALEQQALMREHKANPFAACLPLLIQMPF
+FFALYQVLVGARGAAERGESMDALSAETIRSFESSQIFGARMSDTLMGSIGQPGGAAVVV
+VAIVLILLMTGSMFFMQKMLMTKNMTQTALEGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRHNPTPGSLAEQELNERRAAKGLPPVGKKVASSEAKPGSAH
+TEAAQGAVVNGEVLREGGQRVQPQRKNRRKK
+>4_2190
+MFEAILSPFRWLMSWLLGAFHSILEFAGLPVDSGWTWALSILLLVVLIRTLLIPLFVKQI
+KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF
+FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSTPVIV
+TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV
+LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH
+TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9434e8c9ea03130b0f0773a658bcc1f15bd629db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001758.fa
@@ -0,0 +1,12 @@
+>0_2251
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+
+>1_1955
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+>2_406
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILAARRGKGRAELSA
+>3_360
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSTRRGKGRAELSA
+>4_2193
+MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04cd5bef021d3113673ec1ea79cc42499534e326
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001761.fa
@@ -0,0 +1,39 @@
+>1_313
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>1_352
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>1_1071
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPLTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGTAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRCKRP
+>1_1917
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>1_1965
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d372f1169c75a021260ffffa90fc898f305172c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001763.fa
@@ -0,0 +1,47 @@
+>1_1810
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
+>2_596
+MLLERIYDEDLAQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHVSGEGGEDWTYGFEGNLLHDGDVITLGNITVTAQHTPGHTPEH
+LSYLITDGAFAQAPGYYLTGDFVFSGDLGRPDLLDEAAGFQDTRFAGAKQLFRSLKEKFV
+GLPDHVQVFPGHGSGSACGKALGALPSTTVGYERTYAWWAEYVANDDEQGFVDELLDGQP
+DAHAYFARMKKQNKLGPAVLGELTPLAELTGEQAVARVAAGDVLADTRSVDEIHAGTVPG
+ALALPAKDKAATHIGWAYDPEQDDAAIILLADDQGDAEAIRSHMIRVGVDAADAFVTSLD
+GFELQPAAVISPEELQRRIDAGDVVPATADAAPGEGGLALLDVRNRTEHAEGTVPASGGA
+EAAQLNSGKVLFHQGELPKDATLVTFCQSGLRNVVAAQSLRRAGFDVVELEGSYLGWLGR
+TRA
+>2_2601
+MLLERIYDEDLAQAGYFIGCQAKGEAVVIDARRDIADYLALAAKHGMRIVAVTETHIHAD
+YLSGTRELAAAVGAEVYVSGEGGADWQYGFDARRLYDRDTITIGNITIQARHTPGHTPEH
+LVFLVTDGAFASEPGYLISGDFVFAGDLGRPDLLDEAAGGVDTRFEGARQLFTSLREVFL
+TLPDHVQVHPGHGSGSACGKALGALPSTTVGYERANAWWSRHLAADDEQGFIEELLDGQP
+DAHAYFARMKKQNREGPAVLGERGPVPELAVAEVARRLEADETTFVDTRPPAQAHQGTVA
+GSLNIPDGSKTATYAAWAYDPEADSRPLVLLAEDQTAAQAIADRLLRVGIDQTAGYVTTI
+DGLPRFVPPLIEPAELAGFDAALLLDVRQRGEYAAGHIPGATQLSAARVLWHKDELPRSG
+TIVTYCQSGMRNTVAASALRRAGHAVVELDGSYNAWRAWQETTSETALA
+>3_521
+MLLERIYDEDLSQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHLSGEGGEDWTYGFEGHLLHDGDTIQLGNITVQAMHTPGHTPEH
+LSYLVTDGAFAAAPGYYLTGDFVFSGDLGRPDLLDEAAGLQDTRFAGATQLFQSLKEKFV
+NLPGHVQVFPGHGSGSACGKALGALPSTTVGYESTYAWWAEYVENDDEQGFVGELLDGQP
+DAHAYFARMKRQNKQGPAVLGELTPLAELTGEQAVARVSAGDVLADTRPVDQIHAGTVPG
+ALALPAKDKTATHIGWAYDPESDDAAIILLADAQDDAEQIRAHLIRVGVDAADAFVTSLD
+AFDLRPTAVISPEELERRIQDGGVVPATADAAPAEDGLALLDVRNRTEHADGTVPASDDA
+EAAQLSAGKVLFHQDQLPKEATIVTFCQSGLRNVVAAQALRRAGFDVVELDGSHLGWLGR
+SQA
+>4_2030
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001767.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1a65989f842fa895ea3b50c7b410661dedf1d31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001767.fa
@@ -0,0 +1,24 @@
+>2_140
+MEVPFTFDAELREGRLDLAEITGGGGAQVLGFDMLPESFTTMKLTTADEPYAPVGPMKPE
+GSPEGVLVQEPRHGDLVPVVASWDPSVVDRFIYVADAGFTGKDTPAPDGEHTVPETVETG
+SATAWWLAAAGALGAGALLRLRPARRGA
+>2_1827
+MTITASTTAPTAPSRRVRLAASTPDAHAAEDVDVRVRPEGGDAWTTVAHRSGADPVGAVS
+SRDIQEAIGTPERGRAARQRLGQCRRHGRAGDLA
+>3_1715
+MDHVASHPRIRPASMRLITAAGTVGLAAAVLAAPASATPHLGEQAVWGCVYDTAGVYTFT
+DQETGATASSASVPFVLQDAAADPEAHTAEDVTVAVRPAGSDAADAVQIPFAGGDPVGAF
+ETRDIVAALGPDVRQAVVEVRVDGVTEAATVLEVETGTNAADQACFAYEYGTEVMGPQVE
+RIDVPLHQPADLGRPADGSFAFGVSSTPAAVEVTVEGETHSLPVAGVWQEGSFFGVDEPV
+AALKEVDGGYGYKEWMSEALARFDGTDYALVYGEDADGVTRSRLALLHPYVDRAVEDAAA
+PAEGGHTVPSKVQTGDEAAWWLAGVAALGAGALVAARRRLGLAA
+>3_1722
+MVYLQGGPSSGTPGGGVTVLAEEPQHGRLVVVPGEQGALPYAESHVLAQLGAGEDPAPTA
+PDAEHAVPGKVQTGDEAAWWAVGLGALGAGALVAARRRFGLGEAR
+>3_1728
+MSARRVVIALRGARTRPAPITEDTLKKTTPRLAAAAAGVALITGLGAAPASAATWTSAHG
+VPSGLFDTSLTSEGLLGFSLVDNFTADQVKVVVTAADGTQTPVPFEFYGESDGGVVLLED
+VRAAAGGADQPYTLTVDAAGQEAFGLTYTPGAGYEDVDAEDFVAFEDWATVSTRSVPVDV
+DGWLYEPLAVDEAGNAASGVAAVVTVQPQHGTVTVGSGAYLYTPAEGFEGLDTFTVVLTS
+DGIKRTVEYSAYVQDIEGEQGTAPSVDAPVAPAEPVEEPAPTEEPAPTDPSDEPTPSTTA
+PSTPAETGEETAPTTPADGHEVPGKVQTGGEPAWWLAGAAALGAGALVVARRRLGLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f5de58cb5b83f3d045a276e0e9f7dc140cc9d76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001768.fa
@@ -0,0 +1,26 @@
+>2_372
+MARCTVERLMRAAGLRGISRAKGPRTTVPGRGPDERQDLVQRDFTAAAPNQLWVADITYC
+RTFSGWVYAAFIIDVFSRRVLGWQLSKSLRTDLALDTLEMAFWTRQRAGQDVAGLRHHSD
+KGVQYVAVRYTQRLAQAGAVASVGSTGDSYDNALAEAFNSLFKAELIRNKGPFKSIEDLE
+IAVAEYIDWFNHRRVHGEIRLVPPVEFEDVYHHENPVPAPAGTALTSL
+>3_316
+MHTCCRLLGVSRQGYYRYQKRPTSATELRRRWLTGLIREIHIASRGTYGYRRIHAELTMG
+MNIPCSSRLVWVLMTRAGIGGLPGPARIKRLKGVATADDLVNRKFHRLELNELWVTDITE
+HPTREGKVYCAAVLDACSRKIIGWAIDSKQDSTLVVNALDMAIRARQPDPGGIVHADHGV
+QFTSWVFTQKIRSAGLLPSFGTVGDGLDNAMMESFWSSMQIELLNRKKWKTRIELANAIF
+EYIEVFYNRHRRHSSLEYATPNDYDLARTPQALATTGS
+>3_639
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGVYGARKVHAQLRREGLQVARCTVERLMRAAGLRGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGLQYVAVRYTQRLAQAGAVASVGSTGDSYD
+NALAEAFNSLFKAELIRNKGPFKSIEDLEIAVAEYIDWFNHRRVHGEIRLVPPVEFEDV
+>3_1185
+MQIGAWAQGGEIELANAIFEYLEVLYNRRRRHSCLECATPYDYDPAGTPRALTTTGS
+>3_1792
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDVQVL
+VEIRRVHEANYGLYGARKVHAQLRREGLQVARCTVERLMRAAGLGGISRAKGPRTTVPGR
+GPDERQDLVQRDFTAAAPNQLWVADITYCRTFSGWVYAAFIIDVFSRRVLGWQLSKSLRT
+DLALDALEMAFWTRQRAGQDVAGLRHHSDKGVQYVAVRTPSGWPRPAQSPRSARRGILTI
+SVLAEAFNSLFKAELIRNKGPFTSIEDLAIAVAEYVDWFNHRRVHGEIRLVPPVEFEDVY
+HHENPAPAPAGTALTSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04ca91c072e2fb8fddd1c69c8a25a7b8a0d82c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001769.fa
@@ -0,0 +1,35 @@
+>2_500
+MKAWQFSGTGKPLELNEVPEPTPGPGEVVVDVKAAGICHSDVSAIDDAGWMPLFPELPHT
+MGHENAGVISAVGEGMDHWKVGDRVGLAPMNSKGEAIGYHTWEGGFGPKLRATDDNLVKL
+PDEVPFDLGAMATDAGLTAYHAVVAKGGVKKGMKVGIIGLGGLGYIGAKVAALMGAEVYG
+AEVNPKTRELKDEIGLTAVAESILEFKDVGLELVVDYAGFGTTTAEGITALKKDGVFVQV
+GMGKLEAPLNTYELITKTISVLGSNSGTKEDLAGIYELMQRGELNPPINRITQADIPDAI
+ETLRAGGVIGRYIAMYDDAK
+>2_793
+MHQAYAVYEGDTAIHEIEVETPEATGRSVLLKVLRSGVCHTDTHLREGGYDLGSRGTMSL
+TDRGVPYPLVMGHEVVGEVTAVGDEVQDVRVGQRMLVYPWIGCGECRMCREGRDNACAAG
+KNLGVARHGGYAETLWVPDAKYLVDIGDLDPSWTATLACSGITAYSAVDQVLPLDEEESV
+VVIGAGGLGLTAIALLSARGHRTVVAVDRSEKNLELARQMGASATVVSDDDVAAALKEAL
+GGGAAAVIDFVNNGATATLGFDSLAKAGQMVQVGLFGGEVTLPNALLSLKMIRISGSFVG
+TLQQMKDLVQIARTTDLPKIPIIERQLSAEQVAASLDDLTAGTVSGRVVLTA
+>2_926
+MTTMKAVRFTAYKTFPELKEIERPTPGPGEVLLKVAGAGACHSDVAVYDEFEAGMNPLVD
+PEYTLGHETSGWVEELGEGVTGFEVGSAQLVYGPVGCGHCPACSRGQDTYCQNVAEMDYA
+GIGLGRDGGMAEYVTVPARNLVPLGDADPVPASALADAGLTPYHAIKLALPRLNRAGTYA
+LVVGLGGLGLMAVQILKDLTGATVIATDMKPEAMAEAEKYGAVTVPSGEDQVARIREITG
+GRGVDAAFDFVGIAATARAALDSAAVQSRVTIVGIGNGSTIDWSFLSTPYEAELVTTYWG
+TVEELHELAGLYRDGKVEPLYTTYAMDGALQAYRDLQDGKISGRAVVVPHGQA
+>2_2335
+MKALYESGPHAGFEFTERPEPECGAHDVKIRVFTTGICGTDLHIEAYDAAAQAMIQAPMI
+PGHEFYGEVVEVGDLVEHVEVGHRVSGEGHVVCGMCRNCRAGRRQMCINTVSVGVQRDGA
+FAEYVVIPEANVWVHKGEHVTPELGAIFDPLGNAVHTALSFPLVGEDVLITGAGPIGLMA
+IPIARHAGARYIAITDVSAERLELARSMGADAAIDVSATRIREAQRELGLAEGFDVGLEM
+SGRASALQEMVANMNHGGKIALLGLPAEEIAIDWQTVVTHMLTIKGIYGREMFETWYAMA
+AMLQTNATLRERVESVVTDVIAAADWKRGFDAARAGATGKIVLDWRNL
+>3_867
+MVTMRAVRFEAYQQFPALKDVEKPVPGPGEALLKVAGAGACHSDVAVYSEFQPGMNPLID
+PEYTLGHETSGWVEELGDGVVGLEKGEAMLVYGPTGCGRCRACSRGQDTYCENVAAMAAA
+AVGLGRDGGMAEYVSVPARNLVPLGDADPIPASALADAGLTPYHAVKLALPTLGRPGACA
+LVVGLGGLGLMAVQIIKALTGATVIATDMKEDAMAQAEAYGAVTVPGGEGQVERIRELTG
+GRGVDAAFDFVGVAATARLALDCAAVQSRVTIVGLGNGSTIDWSFLSTPYEAELVSTYWG
+TLEELHEVARLYRDGRIEPLHTTYSLDDALQAYRDLQDGKVAGRAVVVPHGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ba1677838686f15428d52fd35d1559bb77d0e4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001770.fa
@@ -0,0 +1,12 @@
+>0_9
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW
+>1_1978
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNEVRVEHGGRDVVVTVPDRVGLEVELE
+VEDGGDAELEITLSW
+>2_368
+MSDEIFEHETTETMTREQAAARLRELADQLSRQNEVRIEHAGRDVVVTVPDQVELEVELE
+IEEGGESELEISLSW
+>4_9
+MGKDLFEHEQQQTLSREQAAARLRDLADQLSRQNKVRIEHGGRDVVVTVPDRVGLEVELE
+VEDDGDAELEITLSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9489d5497bf23de7eac5983ef0ad7a6fa1a17dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001773.fa
@@ -0,0 +1,36 @@
+>0_47
+MSTTLQPARTDGVASEAPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEVTQLELPAELAELLSSQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTGLEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMRGVIESTAGIRGTDA
+>1_2011
+MSTTLQPAQADVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+KHVETIVAAVEELAPLFPHDAAYLAALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAALEAGDYGNRLFLSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLADAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
+>2_337
+MSTSLHPPQAVIGEPEVLEDVRADVVSHPAWLRLKAAATALQGLQAKDGSVPDPADHPAA
+GGHVETITAAVAELAPLFPHDAAYLAALPRDFARWRDGGFGVPDFLDSLVAFQPQEHRVD
+GIRHLVVFPMYTQNGSSSRHVEALLVEAIWPEFIAQLEAGDYGNRLFLSLRLLDFTPGYE
+TNSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVAAAAEITRLDLPEDAAELVADQD
+LAEQTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDLTAFRETVRIEREL
+SARAAAGEELTAVQAQTLRHAKLVQYAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHR
+RHVVQWRDVKLTIDWDRLAEAVVELGDAIDRLYWESIDRPKTVHWLKAYELVASVVAPHP
+ASVWAQGLPREVLAGPPKEMTDLVLDDEFPLSMFFEALGKKLRGVIESTAGIRAADA
+>4_42
+MSTTLQPARTDVVVPETPADARTVETHPAWLRLKAAATALQPLQVKDGSIPDPADHAAAR
+EHVETIVAAVEELAPLFPHDAAYLTALPRDFARWADGGFAEPDFLDSLVAFQPQEHRVDG
+VRHLVVFPMYTQNGSPDRHVEALVVETIWPEFIAELEAGDYGNRLFVSLRLIDFTPGYDT
+NSAVLFPETVAMREIPTFTWGAIFQDREAARFRRVVTAAAEITQLELPAELAELLSCQEL
+AEGTFVMWDLIHDRTHMRGDLPFDPFMIKQRMPFFLYTLEEMRCDMTAFRECVAIERRLT
+ARAAAGEQLTALEEQTRRHAGLVQHAVLFDRVFRFALTGSRVRNYDGLGGQLLFAWLHRK
+DVIQWRDVELSVDWDRLANAVVELGDAIDTLYWESIDRPKTVHWLQAYELVASVVTPHPA
+SVWAQGLPREVLAGPPKGYTDLVLDDEFPLSMFFEALEKKMCGVIESTAGIRGTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09e8e54951a873a182a93d6fc114aa6a3951f79e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001774.fa
@@ -0,0 +1,16 @@
+>0_48
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYILFVRVGSPRELEALVT
+EIRQTASVATRTTVVLQTFYEHRPMLELPAED
+>1_2012
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPAED
+>2_336
+MDDPVDARLAAEVSRDPRATLAQLSERVGLSASAVQARLRKLESTGVITGYQAILDPEAV
+GKPLAAFIEITPLDPRQPDDAPELLEPIAAIEACHSVAGDAAYMLFVRVGSPRELEALVS
+EIRHTASVNTRTTVVLQTFYEHRPMLPLPDAGE
+>4_43
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40cc9b1700ee562889d05d00c42d6fe288553ffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001776.fa
@@ -0,0 +1,29 @@
+>0_69
+MRHPAPLPAALLHGPFTAAQARAAGIDRNRLRRSDVERLARGLYRRREATPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDGVHVSRPRD
+RGRLALPGVISHRTALPPADVERVRIGGLAWHVTAPPRLWVDLAALLDDDELVILGDHLV
+RRAKLSGGPGAAERARAALAQAAEASPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALT
+AAGLPEPALQLEARDPEFSLHHPATADLGYRQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGYRNITVSSSDARRGFTRVIVEVRRHLGDAGDLSRKESEWGVNGTSERPLT
+>1_2033
+MRRPTPLPASLLDGPFTAAQARAAGIDHNRLRRSDVERLARGLYRRREAAPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDEVHVSRPRD
+RGRLALPGVTSHRTALPPADVERVRIGGLAWYVTAPPRLWVDLAALLDDDELVILGDHLV
+RRAELSGGPDAAERTRAALTQAAETSPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALT
+AAGLPEPALQLEVWDPEFSLHHPATADLGYPQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGYRNITVSSSDARRGFTRVIVEVRRHLGDAGGLSRKESEWGGDPASERHHA
+>3_247
+MERWPPHTDIMSRPPRDLPAVLRRGPFTTASALALGVPASRLRRSDVRRLRRGVLVWTGA
+TDGGSTVDPALPPRPAAASGADTPWVLASRLTPSEQETLAGVLAAAPDATASHLTAARLT
+GLWLPTRLAADRTLHVTRPPGTANSAPAGVRMHRRRPTSEGAQLVRGSGPPLDGPIPVTG
+PARTWRDLASLLDLAELVVLGDRLVCSSGPERADPLCSRAALVQAAARPGQRHAVLARDA
+AALVRDGAHSPPETRLRLALLDAGLPEPELQLEVWDPAFSRSRPATADLGWRRHGVVLQY
+EGAGHDDPVQVRGDTLRDAAFQRRGVVVIRAAAADLAEGFRGTTALAEAALRRRGWTPGR
+E
+>4_63
+MRHPAPLPAALLHGPFTAAQARAAGIDLNRLRRSDVERLARGLYRRREVTPAAVERPAAG
+SSPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAREIWLPERLDAGDDVHVSRPRD
+RGQLSLPGVTSHRTALPPADVERVRIGGLAWYVTAPPRLWVDLSALLDDDELVILGDHLV
+RRAQLSGGPDAAERTRAALAQAAEASPSAHNRRRRLRTAATLVRVGAHSPKETRLRLALR
+AAGLPEPALQLEVWDPEFSLHHPATADLGYRQARVALHYDGGHHGADRQIDRDVQRNAAF
+ERRGCRNITVSSSDARRGFTRVIVEVRRHLGDAGDLSRKESEWGVNGTSERPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a647934149f27abbb1d0c5a24834900b45f9d0d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001778.fa
@@ -0,0 +1,54 @@
+>0_81
+MTSTPDTPDNTPATPFHDLDAFTALPRVAGLTLSPDGARLVTTVATRDAKGTGYATALWE
+VDPAGERPAHRLTRSREGEAGAQFAADGTLFFTSARPDPADAEAEKRSALWALPARGGEA
+RVVLSRPGGVAAVTCASAADRVVVTADRLLGATTEAEHATLAQTRKDAGVDAILHTGYPI
+RFWDHDLGPARPELFVLEPGPDPQGEPATDADAAEPGPAASGLAPEADDVAHHLRHVSGF
+PRSHAFGIGAQVAPDGSFLLTTAATAEARGNVREGTVVRVDLATGEHHVLHDVPGEDVAV
+GPVSHDGTRAVVVRTPDSTPHSAVHPRLYVMDTATGQTTPLAHGWDRWADVVAWLPDDSA
+VIALADSEGRRPVFRIEVATGAVAQVTREDEAWTDVVLSPDGATAYGVRSSYLFPPEVAR
+IDLATGETTRLPNPVERPAIPGTLEDVETVAEDGTRVRGWLVLPEGEAPAGGHPLLLWIH
+GGPLGSWNAWSWRWTPWIMAARGYAVLLPDPALSTGYGQDFIERGWGRWGQAPYTDLMAL
+TDAVVAREDVDGDRTAAMGGSFGGYMANWVAGHTDRFRCVVTHASLWALDGFGPTTDAAF
+YWAREMDEQMQQENSPHRFVGEIVSPMLVIHGDKDYRVPIGEGLRLWSDLLAKSGRPAAA
+DGTTDHRFLYFPHENHWILAPQHAKVWYEVVLGFLGEHVLGDGAPSAPETLGLTRPSSTA
+G
+>1_2045
+MTSTPDTPAAPATPFHDLDAFTALPRVAGLTLSPDGARLVTTVATRDAKGTGYATALWEV
+DPAGERPAHRLTRSREGEAGAQFAADGTLFFTSARPDPADAEAEKRSALWALPARGGEAR
+VVLSRPGGVTAVTCASAADRVVVTADRLLGATTEAEHAALAQTRKDAGVDAILHTGYPIR
+FWDHDLGPARPELFVLEPGPDPQGEPATDADAAEPGPAASGLAPEADDVAHHLRHVSGFP
+RSHAFGIGAQVAPDGSFLLTTAATAEARGNVREGTVVRVDLATGEHRVLHDVPGEDVAVG
+PVSHDGTRAVVVRTPDSTPHSAVHPRLYVMDTATGQTTPLAHGWDRWADVVAWLPDDSAV
+IALADSEGRRPVFRIEVATGAVAQVTREDEAWTDIVLSPDGATAYGVRSSYLFPPEVARI
+DLATGETTRLPNPVERPAIPGTLEDVETVAEDGTHVRGWLVLPEGEAPAGGHPLLLWIHG
+GPLGSWNAWSWRWTPWIMAARGYAVLLPDPALSTGYGQDFIERGWGRWGQAPYTDLMALT
+DAVVAREDVDGDRTAAMGGSFGGYMANWVAGHTDRFRCVVTHASLWALDGFGPTTDAAFY
+WAREMDEQMQQENSPHRFVGEIVSPMLVIHGDKDYRVPIGEGLRLWSDLLAKSGRPAAAD
+GTTDHRFLYFPHENHWILAPQHAKVWYEVVLGFLGEHVLGDSAPTAPETLGLTRPSSTAG
+>2_291
+MTSTADTPAPTPATPFHDLDAFTALPRVSGLTLSPDGTRLVTTVATRDAKGTGYASALWE
+VDPAGQRPAHRLTRSREGEAGAQFAADGTLYFTSARPDPADAEAEKRSALWALPARGGEA
+RVLLSRPGGVASVACASAADRVVVTADRLLGASTEAEHAALAKARKDAGVDAILHTGYPV
+RFWDHDLGPARPELFVLEEGVDPQGEPASDADAADPESTPQSGHDDGAAGSASTAASAST
+PASSSATTAASGLAPEADDVPHHLRHVSGFPRSHAFGIGAQVSPDGSFLLTTAATAEARG
+NVREGTIVRVDLATGEHRVLHDVPGEDAHVGPVSHDGSRAVVVRTPDSTPHAAVHPRLYV
+MDTATGETTPLAHDWDRWADVVAWLPDDSAVIALADSDGRRPVFRIDVATGEVAQVTAED
+EAWSDVVLAPDGATAYGVRSSYLFPPEVARIDLATGDVVRLPNPVERPVVPGTLEDVETT
+AEDGTRVRGWLVLPEGQAPAGGHPLLLWIHGGPLGSWNAWSWRWTPWIMAARGYAVLLPD
+PALSTGYGQEFIERGWGRWGQAPYTDLMALTDAVVAREDVDAERTAAMGGSFGGYMANWV
+AGHTDRFKAVVTHASLWALDGFGPTTDAAFYWAREMDEEMQEANSPHRFVGDIVSPVLVI
+HGDKDYRVPIGEGLRLWSELLAKSGRPAAADGTTDHRFLYFPHENHWILAPQHARVWYEV
+VLGFLGEHVLGEGAPSAPATLGLTRPSSTEG
+>4_76
+MTSTPDTPAAPATPFHDLDAFTALPRVAGLTLSPDGARLVTTVATRDAKGTGYATALWEV
+DPAGERPAHRLTRSREGEAGAQFAADGTLFFTSARPDPADAEAEKRSALWALPPRGGEAR
+VVLSRPGGVSAVTCASAADRVVVTADRLLGATTEAEHAALAQTRKDAGVDAILHTGYPIR
+FWDHDLGPARPELFVLEAGPDPQGEPATDADAAEPGPAASGLDPEADDASHHLRHVSGFP
+RSHAFGIGAQVAPDGSFLLTTAATAEARGNVREGTVVRVDLATGEHRVLHDVPGEDVTVG
+PVSHDGTRAVVVRTPDSTPHSAVHPRLHVMDTATGQTTPLAHGWDRWADVVAWLPDDSAV
+IALADSEGRRPVFRIEVATGAVAQVTREDEAWTDVVLSPDGATAYGVRSSYLFPPEVARI
+DLATGEATRLPNPVERPAIPGTLEDVETVAEDGTRVRGWLVLPEGEAPAGGHPLLLWIHG
+GPLGSWNAWSWRWTPWVMAARGYAVLLPDPALSTGYGQDFIERGWGRWGQAPYTDLMALT
+DAVVAREDVDGDRTAAMGGSFGGYMANWVAGHTDRFRCVVTHASLWALDGFGPTTDAAFY
+WAREMDEQMQQENSPHRFVGEIVSPMLVIHGDKDYRVPIGEGLRLWSDLLAKSGRPAAAD
+GTTDHRFLYFPHENHWILAPQHAKVWYEVVLGFLGEHVLGDGTPSAPETLGLTRPSPTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9fb6e6c10a60320194fea8d0ed7499e312b41c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001783.fa
@@ -0,0 +1,34 @@
+>0_145
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVPAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
+>1_2110
+MGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAYIFVFVVAAA
+ASLITWGLGLVVGALLAKEVAAQARERGLVLHFPMLVAAGFSGFVVWHMGYSGSGPLTAA
+TPGSFLTESLGGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDRIVELEIDAR
+DQDAVSAPEIETPADRLDASRVPTLLVGAMLVIYLVMHFVGGGTLTLDIVNWSFLALILL
+LVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTSTGLVAVLSDAFVAISNPVTFGL
+LAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQWTNMIQPFWA
+IPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
+>2_220
+MPAPPPPAASPPHADGRATSDGNAFSRAMRPVNTVMERFIPSSLMFSILLTAIVAVLALI
+LTPTAPVDVLMGWGNGLSGLLAFMTQMALILLLGHILANTGPVRALLTALARVPRSAVQA
+YSFVFVVAALASLVTWGLGLVVGGLLAREVAAQGRERGLRLHFPLLVAAGFSGFVVWHMG
+YSASGPLTAATPGSFLEDSLGGRTVPISDTVFTWWNLTAAAVAIVAVTLVLYLIAPRGDD
+RIHELDVDARERAVVTEPELETPADRLDASRIPTLLVGLALAAFLVVHFVQGGTLTLDIV
+NWSFLALIFLLVRSAQELIQLTAHAASNVGEILLQFPLYAGILGMMTASGLIQIFSDALV
+AVANPTTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLSAGAELGVDPAITIMAVSYGDQ
+WTNMIQPFWALPLLAIAGLRMRDILGYTTVVLLVTGVVFAGTMLLVSL
+>4_153
+MSATSTRPPTPRPPGRAAREGTFFSRAMRPLNTTMERFIPSSLVFTIVLTFAVAALCLLL
+TPAGPADVVVGWGDGLSGLLAFITQMALVLMLGHILANTGPVRRLLARLASIPRTPLAAY
+IFVFVVAAAASLITWGLGLVVGALLAKEVAAQARECGLVLHFPMLVAAGFSGFVVWHMGY
+SGSGPLTVATPGSFLTESLDGRTVPVSETTFSWWNITAAVVTVLVVALALFLVAPRAGDR
+IVELEIDARDQDAVSAPEIETPADRLDASRVPTLLVGAMLVVYLVMHFVGGGTLTLDIVN
+WSFLALILLLVRSPHELIGLTQSAASNVGEILLQFPLYAGILGMMTTTGLVAVLSDAFVA
+ISNPVTFGLLAFLAAGLVNFFVPSGGGQFAVQGPIMLQAGDALGVDPAITIMAVSYGDQW
+TNMIQPFWAIPLLAIAGLKMRDILGYTTVVLLASGLVFGGTLLLVSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46bba0af2a93d802bbbe73864f607755a5775211
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001785.fa
@@ -0,0 +1,32 @@
+>0_169
+MTATQDAPAVDPRPAAALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDDAGPCGSGAAVAAEDVRPDTGAEGAVKPELRRRGAGTAEPANA
+>1_2113
+MTATQDAAAVDPRPAAALDPEALVDRVEAGHRLTAEEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDGAGSCGSGAAVASEAGAAEDARPDTGAEGTVKPELRRRGAGTAEPANA
+>2_215
+MTAAQDAAVVAPALDPEELVDRIEAGHRLTAAEAVAVLDAPDAETFRLVAAASRLRERHF
+GRTVKVNYLVSLKTGLCPEDCTYCSQRLGTEAQILKYTWLKPDEAVRQAGLGIAGGASRV
+CMVASGTGPTDRDVDRVTEMIGRLKDEHPQVEVCACLGKLKDGQAERLKAAGVDAYNHNL
+NTAESHYESICTSHTYADRVDTVERATAAGLSSCSGLIAGMGETHAQLAEAVLALRELDS
+DSIPVNFLMPFDGTPLAGHVQLTPLECLRILAVVRLACPDKELRIAGGREMHLRSLQAVG
+LQVANSIFLGDYLTSEGQDAEADLSMIADAGFTVLGAAAAPADDDGAPDGGCCGGGGCGE
+GGVEDASTRGGTSPSPSPAPRRRGAGTAEPANA
+>4_161
+MTATQDAAAVDPRPADALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERAQQAAADDGAPAGCCG
+GGCVGTHDNSKNGAAATPSKPVLRRRGAGTGAAANA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001786.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..900735cdae8afb845d97759787190aefc1d68676
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001786.fa
@@ -0,0 +1,24 @@
+>0_191
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG
+>1_2138
+MARPQTVLTVVAAHRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRRMDAAARTMDVDFVVHGASDDGAAPGRDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAVGVALI
+EVTDARDEVPLTAPAGVEVRWLHRGDPFTPETTRFAAAVEDAAWREGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPAGQIFEDGTTGG
+>2_184
+MTRPATPGRPARPQTVLTVVRTERLTPHMVRVSLGGDEFAAFHARWAEKGATDQYIKLLF
+ADPALGLTPPYDLDALRERLAPEQMPVRRTYSVRAVDVAAGTVDVDFVVHGDDGLAGPWA
+ASVQPGEQVCFGGPGGNYRPDPAADWHLFAGDEAALPAIAAGLEDLATTAPDAVGTALIE
+VEGPEDEQPVTAPAGVEVRWLHRGAEFTPQSTRWAAALREEPWREGRVHAFVHGEREQVK
+AARAYLADERGVDRRDLSVSAYWAFGRAEETFQAEKQTPLGQIFPDGTTGG
+>4_194
+MARPQTVLTVVAARRLTPHLVRLTLGGEQFDAVHARWAEKGATDQYVKLLFADPALGLEP
+PYDLDALRERLAPEQLPVRRTYTVRHMDAAARTMDVDFVVHGASDGGAAPGHDGGLAGAW
+AASEPVGQQVAFLGPGGAYRPDPTADWHLLAGDEAALPAIAAALEDLAATDAAAAGVALI
+EVTDAGDEVPLTAPAGVEVRWLHRGGPFTPETTRFAAAVEGAAWRDGRVHAFVHGEREQV
+KRVRAYLTDVRGVDRRQLSVSAYWAYGRAEDVFQAEKQTPVGQIFEDGATGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75853cd6b614c275d386d19a2a96fc72863e55cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001788.fa
@@ -0,0 +1,36 @@
+>0_193
+MDRTAPTPPANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLRSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDTVVATVGHLSAGTAANIIPDSATLALTLRTFSADARA
+RLRAAVERMVHGIAAAHGMSAQVRADCAFPVTANDADAVAFARGVVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGVDPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPVPAS
+>1_2139
+MDRTAPTPPANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLLSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANIIPDSATLALTLRTFSADARA
+RLLSAVERLVHGIAAAHGMSAQVRTDCAFPVTANDPDAVAFVRGVVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGMDPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPGPAS
+>2_195
+MTPETADALAPRVPDGLAQDVIALRRDLHAHPELDLHLPRTQAAVLDRLAPLQERAGQDA
+RTGGPALEVSTGRELSSVVLVLRGAKPLPAGTRRPVVLLRGDMDGLPVTELTGLDWAPPT
+PGTMHACGHDLHTAGLYGALAWLVERRDELAADVIGMFQPGEETDGGAARMIDEGLLEAA
+GPHPDAAYAIHVYSGKYPHGALVSRTGAIQAGCDDLIVTVRGRGGHGSVPHLAQDPVPVA
+AEMVLALQSLVARQFDAFDPVVATVGHLSAGSAANIIPDTATLAITLRTFSADARERLVP
+AVRRMVDGIAAAHGMSAEVRADCAFPVTVNDGEKVDFARGVVEDLYGAEAWQELPEPEPG
+SEDFSEVLVRVPGAYLLLGAVPPGVDPETAEGNHSPRAVFDDAVLPRAVEVLAELALRTP
+PVPEG
+>4_195
+MDRTAPTPPANALAPDLPEDIAREAIAFRRRLHGHPELDLHLPRTQAAVLERLEALRAEA
+GEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLEY
+APSVPGTMHACGHDLHTAGLHGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEGL
+LEAAGRPVDAAYAIHVSSGTYPRGVLISRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQDP
+VPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANVIPDSATLALTLRTFSADARA
+RLRAAVERMVHGIAAAHGMSAQVRTDCAFPVTANDADAVAFVRRTVEDLYGADAYRELPE
+PEPGSEDFSEVLQRVPGAYVLLGAVPEGVAPDEAPVNHSPQAVFDDAVVPRAAQVLAELA
+LRTAPVSAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..168293eeaaa1160d000020e332307e05a2ebb483
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001791.fa
@@ -0,0 +1,20 @@
+>0_219
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>1_2183
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>3_101
+MTTTYMHTDAEDTIHSTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFEEDAEGKAGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAAF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
+>4_220
+MTTTHMHTDAEDTIHPTQPAPDAGPLSQAEIDRLFADRHTTQLFSDEPVDLALIERAYAD
+LRWAPTAMNNQPLRLDVVDSPEARARLAPLMIEFNREKTERAPLTLIASYDLDWHRHMGH
+LAPFREGFAEDAEGKPGMREGMGRTNALIQVGYLLVALRAHGLEVGPMAGFDAAAVDAEF
+HADRAWKSLLVINVGHAAADDEKAQQPRQGRLDFDQAAQVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1abc08665e0bc7ad325a46b8f96361c6475468d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001793.fa
@@ -0,0 +1,40 @@
+>0_238
+MSEKTAPTETAPVIPHFVHGERREGASGRHSDVYHPATGRVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSMRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVVMPDADLEMTADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>1_2201
+MSQKTAPTETAPVIPHFVHGERREGASGRHGDVYHPATGGVAGRVPLASAEEIDAALASA
+EEGFAAWSRLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERIKGLTVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGAELVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>3_82
+MSQQSQTQQTIPHFVHGARTGTDAARTSDVFDPSTGQVQARVALASPEEVTAAVDSAAEA
+FRTWSAMNPQRRGRVLLTWVDLINANADELAETLSREHGKTFEDAKGDIQRGVEVVEFAA
+GAPHLLKGEFSTSAGTGIDVHSLRQPLGVVAGITPFNFPAMIPLWKAGIALAAGNTFVLK
+PSERDPSVPVRLAELALEAGLPAGALNVVHGDKAAVDALIDDPRVKAVGFVGSTPIAQSI
+YEHAARRGKRAQCFGGAKNHAVIMPDADLEMAADALIGAAFGSAGERCMAISVAVPVGEE
+TADRLVALLRERMASLTVGPSLDPSSDFGPVVSAQAKERIESLIQAGVDEGAELVVDGRG
+VVVEGHEGGFYVGATLFDRVRKGMRIHAEEVFGPVLCVVRAKDYEEALSLPSDHEYGNGV
+AIFTRDGDTARDFSTRVECGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLKFYT
+KTKTVTTRWPSGPRQGGAAASEGASFVMPAGS
+>4_238
+MSQKTAPTETAPVIPHFVHGEQREGASGRHSDVYHPATGSVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTVPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc0b6890098083075c44cfccb44a9e312034885b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001795.fa
@@ -0,0 +1,16 @@
+>0_244
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHKEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>1_2207
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>2_107
+MYTRSRNDVEKVEWGGGTSERLLTAKDEMGFAVAHTIVRAGSSSKLQYRHHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>4_244
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4a0cc94a00c8e8e8c8047f6165cea098da1417
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001796.fa
@@ -0,0 +1,17 @@
+>0_263
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>1_2229
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>2_75
+MDALGWTTLAISLLALVAAGWSAFESWRLGRVERQRDQRQEDRERQEQARQVAAWMCVVA
+EREHNLAATVRRRWFLAIENSSQVPVYDGHATITSKYPVPALEAAMFPPGRTYFELGKNE
+WGYGVQSDELAIVPRPLTNAERFRVTSLAFTDAAGTRWTRDEQGRLAEGPAAADTGAMST
+GT
+>4_261
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a519af94b97f373578cf6cc9bbecd83d779bc11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001803.fa
@@ -0,0 +1,28 @@
+>0_314
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA
+>1_39
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLDD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFAKRLSLRTRGTAATPGPAAA
+APATAGMPLTGEPGGAAPAASVPEEAPRA
+>2_3
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMVAA
+FVAGTLAGLVTGLLHTKGKIDGLLAGILTMIALYSINLRIMDKANIPLLGQDTLFSWLGD
+MGLARNWGSVLVLFLGVFVLKMILDWFLHTDLGLSLQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATFAVIVG
+AVLYRLIIQAALNAGLSPNDMKLISAALVVLALLLPRFGLAKRLSLRSKSTAAPAQAETP
+ATATPAASAATAEEQTRA
+>4_321
+MLTAVELGLIYAVVALGVYLTFRILDFPDLTVDGSFTTGAATAAVLITGGTPVPLAMLAA
+FVAGALAGLVTGLLHTKGRIDGLLAGILTMIALYSINLRIMGKANIPLLGQDTLFTWLGD
+LGLARNWGSILVLFLGVFVVKLILDWFLHTDLGLALQATGDNEEMIRSYGVSTDRMKILG
+LMISNGLVALGGSLLAMYQGFADISMGIGLILVGLASVIVGQAVFGQRTVFWATLAVIVG
+AVLYRLIIQFALNAGLSPNDMKLISAALVVVALLLPRFGFARRLSLRTRGTAATPAPAAA
+APATAGMPLTGEPGGATPAASVSEEAPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001805.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b36fefd88da29dac9e2b45afc906d67139fcf816
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001805.fa
@@ -0,0 +1,51 @@
+>0_327
+MTEPRPADAPAPGLHPIGSDPVDPAAAERAAVEAARAVPYAVWAPHAESVELVLVDTEPG
+ALRYAEDRWPVAAVVAMDPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRSVAWPDEGWAGPPGVESDPTVLQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLTDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDGADSDEVRRF
+VLDNVRFWLEEMRVDGLRLDAVHALRDTRAVHLLEEMAALADGIAARAGRPVPLLAESDL
+NDPRLVLPRQAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR
+>1_52
+MTEPRPADAPAPGLHPIGSDPVDPAADERAAVEAARAVPYAVWAPHAESVELVLVDTEPG
+ALRYAEDRWPVAAVVAMDPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRSVAWPDEGWAGPPGVESDPTVLQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLTDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDGADSDEVRRF
+VLDNVRFWLEEMRVDGLRLDAVHALRDTRAVHLLEEMAALADGIAARAGRPVPLLAESDL
+NDPRLVLPRQAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR
+>2_2565
+MTRTRPDSDTAGLRPLGEDRVDPAAAERAAVDAARATPYAVWAPDAETVELVLVTAEPGA
+LHDAEDRWPAAAVVAMDPAAGGWWTPVEDPLAALGLDTAAEDADPGYGYRVDGSDPVPDP
+RSRRQPDTVHGPSRRDVAGQAFAWPDEDRAGQADPAEPQGGGLRGAVLYEMHVGTFTAEG
+TLDSAIERLPHLADLGVTHVELLPVNSFSGPRNWGYDGVAWSAVDESYGGPAAYRRFVAA
+AHAAGLGVVQDVVHNHLGPSGNYLPVFGPYLGPGGTGWGDGLNLDAAHSDEVRRLVLDNV
+RFWLEDMRVDGLRLDAVHALRDGRAVHLLEEMAALADEVAARTGRPVPLMAESDLNDPRL
+VLPREAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHDGTRST
+FRGRDHGRPVPDHVPNHAWVASIQNHDQVGNRAAGDRTSAVLSEGSLAAEAALLLAGPHV
+PMLFMGEEFAAATPWPFFTSFREEELGEAVRQGRRREFAAHGWDPAQVPDPQDPATRDSA
+VLDWSETEGDGRGARVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAPRRHVRLTRAGEE
+ADVVLLAALGEEPLPVPADLAGAELLAGHGDDGPLAPGRAPAAVPAPGFLLLRR
+>4_334
+MTEPRPADAPAPGLHPIGSDPVDPAAAERAAVDAARAIPYAVWAPHAESVDLVLVDTEPG
+ALHDAEDRWPVAAVVAMAPAAGGWWTPTEDPLAALGLDAAQPPADPGYGYRVDGADPVPD
+PRSRRQPDTVHGPSRRDVAGRVFAWPDEGWAGPPGVESDPAAPQGGGLRGAVLYELHVGT
+FTAEGTLDAAIARLPHLRDLGVTHVELLPVNSFSGPRNWGYDGVAWFAVDESYGGPAAYR
+RFVAAAHAAGLGVVQDVVHNHLGPSGNYLQVFGPYLGQGGTGWGDGLNLDGADSDEVRRL
+VLDNVRFWLEEMRVDGLRLDAVHALRDARAVHLLEEMAALADGIAARAGRPVPLVAESDL
+NDPRLVLPREAGGLGLAAAWNDDVHHALHVAATGETHGYYADFAPLEAVAKVMERTYFHD
+GTRSTFRGRDHGRAVPDAVPNHAWVASIQNHDQVGNRAGGDRTAAALSEGALAAEAALLL
+TGPHVPMLFMGEEFAASTPWPFFTSFREPELGDAVRQGRRREFAAHGWDPADVPDPQDPA
+TRDAAVLDWAEAAGGTDGQGRGVRVLAAYRTLIGLRRTLPQLTDPRRDRVRAEVDAARRH
+VRLTRAGEDADVVLLVALGAEPLPVPADLTRAELLAGHGDHGPLGPGTVPAAVPAPGFLL
+LRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a3b36509f0a42b94fa7dbe3a6b48abb16b250d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001811.fa
@@ -0,0 +1,28 @@
+>0_441
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLQDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>1_168
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAAGILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAAAPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>3_2313
+MSEPSIPAPTTASVPDSTGLRLLAVHAHPDDESSKGAATMAAYAAAGAEVLVVTCTGGEA
+GSVLNPSYAHPVRAERDIAGVRHAEMAAAARALGVRHRWLGFLDSGLPEGDPLPALPDHC
+FAEVPLETAAAPLVAVVRRFRPHVILSYDEAGGYPHPDHIRAHEVTRVAWERAGDADAYP
+GTGPAWEPLKLYYDRAFHPAKYQALHEGFLAAGEESPFTDRLEMHARMEAMREVLRRREE
+GEEVPDPEHLPPFVPPVHEVTTQIPVQDFLDERDAALRAHATQVDPEGMFFAAPNELQRS
+TWPWEDYALIESRVRTVPPETDLFAGVR
+>4_441
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGVRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1036f5841ad15396aa224bedfb9c58e9ee5ffcc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001813.fa
@@ -0,0 +1,31 @@
+>0_487
+MAPAEKRVPGPRFRELDGLRGIAALAVVFSHYTGAHNSHYPQDPAAFHDAAWGAAGVQLF
+FIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVVLLLLHPVPGFPFTWSQAF
+LNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRVVLWGSLAWSVISW
+AVVLFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQTGQHRGWVAAAAV
+SAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLAPVQWYGKISYSLYILHAIPG
+YILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGLTRVRSVVDARTGH
+PRSLEPAR
+>1_216
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGVAALAVVFSHYTGAHNSHYPQDPAAF
+HDAAWGAAGVQLFFIISGFVIFMSARRANRPSDFAISRAARLYPPYWISLVFAVGLLLLH
+PVPGFPFTWGQALLNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSIAWSVISWGVVSFTAPHVGWDPQRDPMWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSTFVMRGMPLALEVLVVVLLAVTVMLRERTSVLLLPPIQWYGK
+ISYSLYILHAIPGYILIHALWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVDARTGGPRSPGKALG
+>3_2270
+MTAASSNEPGAATVPPIEKRHPGPRFRELDGLRGIAALAVVLYHFTGHFAARFPAAPRAF
+HDFWWGEYGVQLFFLLSGFVILMTAWRAKRPSDFAISRVARLYPPYWISLAVAVSLLLWR
+PMPGFPIDPATVVANVTMVQRWFLFPNVVEVYWTLAVEMQFYVIVFVLLLVTRCRLRGRV
+LLWAAAAWTAVSWVVILAAFRVTSDNPQADPTWVKLLTNATVAEYGPLFVTGMLFYLVRE
+TGRHPGWAIASAASTALGATLLRGSEHGVMVAAVCALAWLVWRVGEQWLGKHARTGLVSL
+RDHVSPRAVASKREAAR
+>4_486
+MTAASPNEPGAASVAPAEKRVPGPRFRELDGLRGIAALAVVFSHYAAQHNSHFPEDPPPF
+HGFEWGAAGVQLFFIISGFVIFMSARRASRPSDFAISRAARLYPPYWISLVFAVVLLLLH
+PVPGFPFTWGQALVNLTMVQRWVGVDNVVDVYWTLAVEMQFYVIILILLYLTRCRLSDRV
+VLWGSLAWSVISWGVVSFTAPHVGSDPQRDPLWVKLLNNATVAEYAPLFVLGMALYIARQ
+TGRHRGWVAAAAVSAVGSSFVMRGMPLAFEVLVVVLLAVTVMLRERTSVLLLAPIQWYGK
+ISYSLYILHAIPGYILIHTLWPYVGRNMAMLVALAVVSVLAWALQKYGEEHLGRAAKRGL
+TRVRSVVEARTGHPRSLEPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001814.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b48b5932bc62a52f0f2249ae9ee61a1bd30d874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001814.fa
@@ -0,0 +1,22 @@
+>0_500
+MVSAAPSFAASLRKDPGINGWVLNTTTNHGGCRYSLEVNSAPTRGGATPDGAPWGLYLYD
+VSKDASYSGAKLVYWVRGTHTATQNPITWQAATGHSTKWSGPVRGAAQTKADGFKYTPYT
+WTYTGTINPADVKSDGRLYLETFHVKATNFSMSENGQCLPLDYWTYREIVVDPDGPTGPQ
+QPMTLSFERRNGPSGPYVPGAQGRMAVTPDAEATANLQQLSS
+>2_2373
+MSAHSASTTASGLGRRAVATGLAWSVPAVAMVSAAPSFAVSLRKDPGINGWVLNTTTRDR
+DGCLRSLEVNSAPSNPGTTPDGAPFGLYLYDVSPQGVYTNAKLVYWVRGNHVAQNKITWG
+TGAQHSAKWKGPETGAPQTKADGAVYTPYTWTYTGTIDPRNVKKDGRLYLENFHVYTNVF
+SQREPRGCVPLDYWTYREIVVDPDGPAGPEKSQTLHFERRNGDSGPYAPRAQGRSAATPD
+AEATAELQQLSS
+>3_2255
+MNARSAHTTASGPSRRAVATGLAWSVPAVAMVSAAPSFAISLRKDPGINGWVQVTPSGRA
+GCASGYSLDVTSAPAGGGRTPDGAPWGLYLYDFSSEGVYTNAKLVYWVRGDHVKQNPITW
+KAATGHSSKWEGPVTGSPQRKADGFTYTPYTWTYTGTINPANVKSDGRLYLENFHVTSST
+FSQLEGGRCVPLDYWAYREIVADPDGPNGPQSPRTLHFERRAGMSGAYVSGGQARMAASP
+DAEGTSQL
+>4_500
+MVSAAPSFAASLRKDPGINGWVLNTTTNHGGCRYSLEVNSAPTRGGATPDGAPWGLYLYD
+VSKDASYSGAKLVYWVRGTHTATQNPITWQAATGHSTKWSGPVRGAAQTKADGFKYTPYT
+WTYTGTINPANVRSDGRLYLETFHVQATNFSMSENGQCLPLDYWTYREIVVDPDGPTGPQ
+QPMTLSFERRNGPSGPYVPGAQGRMAVTPDAEATANLQQLSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a5af6ea4c380067e88f5ae41f8520c9470ded7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001817.fa
@@ -0,0 +1,32 @@
+>0_552
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>1_293
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>2_2305
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRVAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGPVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
+>4_553
+MTAMPSPAASTRASRPAGPRPGVGHAVSVADLGASYGEGPVLEGVQFDLEPGELLAVLGP
+SGCGKTTLLRCLAGFERIESGRISLAGSVVALPRVHVPAHRRHVAVVPQDGALFPHLSVA
+ENVGFGLRRRRPGRMARIQECLELVDLAGHGERMPHELSGGQQQRVALARAMAPRPPLIL
+LDEPFGALDASLRSGLRRDVRQALKEDGATAVLVTHDQSEALSMADRAAVMRAGRLRQLG
+TPDEVYAHPADAWVAAFVGEASLLPLLDVTGPERDGGRRIGRTALGAVPLHGARAATAVP
+GDLVVVRPEHVRGTLDPTVDVDGVEAARVWTPATVVDVDYRGHDSVATVQLADGTRAQAR
+VEGALPPLDAACGVRLAGPCAVVAPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf72776d3a893a3691dc771e5c226902e8542f7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001819.fa
@@ -0,0 +1,32 @@
+>0_554
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>1_295
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>2_2303
+MPQSRALSRGVRLSAMSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLVELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEPPAGFPELSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
+>4_555
+MPQSRALSRGVRLSAVSATLLLALTACAGGTGGSGSDSASGAASGSASAAESDKKVTLYS
+GRSEDLVQPILDEFTDETGIEVEVRYDKTPAMAAQLIEEGEGSPADVFLSQDAGALGAVA
+KEGLFTPLAQETLDRVPETYRDDEGDWVGLTGRVRVLAYNEEKVPEADLPTSVDELTDPK
+WKGRVGVAPTNASFQTFVTALRLQKGEDEARTWLEDFAANDPQRREKNGEILADVDAGTL
+DTGLVNHYYLFELAREKGVAPEELGASLHFFPDGDLGSLVNVSGMGLVGEQEDGDAAALV
+EYLLSEDGQSYFAEETGEYPLVEGVEQPAGFPGLSEVKAPDVDLNDLDDLQTTIQMIQEA
+GLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04f424a4407293c4a525c15431b0909f516fcaa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001820.fa
@@ -0,0 +1,23 @@
+>0_557
+MVPLMVVTLFTVVASQIRGAGERLPALAAVVPLFAAFAAVMVALGVVAARWTHLDVPAGR
+ALVFSGATRNSLVMLPLALALPASLDPAPLVVVTQTLVELGVMVSLVRLVPRLLPLHGQS
+AGAGARRTVT
+>1_299
+MPSSPPRRALVAALLVGVLLVLLAPCVDYVIAFTALAGGAAERLLAAAPLLMLVQLVVLP
+VLLRVVAGEAAVAAVDVGPFVRALVLLILAPLALAALLQWGTARGRGGVRRTAAGVVRGC
+TAAMVPLMVVTLFTVVASQIRGVGERLPALAAVVPLFAAFAAVMVALGVVAARWARLDVP
+AGRALVFSGVTRNSLVVLPLALALPASLDPAPLVVVTQTLVELGAMVSLVRLVPRLLPLH
+GQSAGAGAGRTVT
+>2_2300
+MESAQSRRAAAVAWMERHQAALYAAGIAAGAVVGWVVPGAGRLAVLVEPVLGLLLLATFL
+AVPFAALGAALRDVRFLAALLVLNFAVVPAVVFGLSRFVAHDDALLVGVLLVLLAPCVDY
+VIAFTGLAGGAAERLLAAAPLLMLLQLLLLPVLLRVCAGPAAVAAVDVGPFVRALVLLIL
+LPLALGALVQGVARRGAPGPRRAARAVEAATGAAMVPLMAATLFLVVASQVRAVGERLPA
+LAGAVPVFVGFVAVMVPLGLAVAALARVDARSGRALVFSGATRNSLVVLPLALALPPSLD
+PAPLVVVTQTLVELVAMAVLVRLVPRLLPERAAPAEEAALAVRPEPDVTGS
+>4_558
+MPGADAWAVLVEPVLALLLLATFLAVPFAALGAGLRDGRFLGALLVLNFVVVPAVVFGLS
+RFVAHDDALLVGVLLVLLAPCVDYVIAFTALAGGAAVAAVDVGPFVRALVMLILVPLALA
+ALLQWGAVRGRGGVRDTAAGVVRGFTVAMVPLMVVTLFTVVASQIRGVGERLPALAAVVP
+LFVAFAVVMVALGVVAARWARLDVPAGRALVSSGATRNSLVVLPLALALPASLDPAPLVV
+VTQTLVELGAMVSLVRLVPRLLPLHGQSAGAGAGRTVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4f214f08a81d6f1cef261b63f928786a29bcf67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001821.fa
@@ -0,0 +1,12 @@
+>0_599
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLRLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAVAAA
+>0_613
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>2_734
+MESFFALLQKNVLDRRDWDTRDELRAGIITWIERSYHRRRRQVRLGRLTPVEYELIMDHT
+PADPA
+>4_568
+METLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNVLNRRRWQSFDQLWLAIVSWIERTY
+HRRRRQARLGKLTPVEFEMVQSVQAAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30df3ea6018796ca94f1d70b136165047e60fe5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001823.fa
@@ -0,0 +1,40 @@
+>0_603
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADTVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTTTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>2_384
+MTSSLTTRRTFLGASVGALALAGLTACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEGTSVHWHGL
+ALRNDADGVQGLTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMDHGSMSQDSSSGMP
+MKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDTAYR
+VGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGHAYG
+IIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYDWGI
+NGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVIIKP
+RQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>3_2149
+MTSSLTTRRTFLGASVGALALAGLAACADPAISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRQTIVFDFEADNPGQWLTHCHNAYHAEAGMMGVFSYIH
+>4_578
+MTSSLTTRRTFLGASVGALALAGLAACADPVISPQPSGRILPTDPLVAEYEKRRAASGTT
+VTHRLSAAPLETSLQGRGLTTWGYNDGLNGPLLRAQTGDLLKVSVANDLPEDTSVHWHGL
+ALRNDADGVQGVTQDPIAAGGRYTYGFRLSHPGTYWYHSHFDTQRERALYGALIVEDPNE
+PLSYDQEWVVILDDWLDGITGTPQDVVEELSAGMDMSGDMEGMAGMAGMDHGSMSQDSSS
+GMPMKHMLMGAESDYLGGDAGDVKIPVHLFNGRPPSDPDTFSSTPGNRIRLRLINAAGDT
+AYRVGIPGQELTITHTDGFPVQPRQADAVVLGMGERLDVLITLGDQAVPVLALPEGKTGH
+AYGIIAAGPKTTLSGRLPQTLGGTVLDGSRLKAHESVLLPPKDPTRTHEVRLTGSMMEYD
+WGINGRRFDPANPFEGAFELRLDERVRVTMTNDTDMWHPMHLHGHTFQLADHGARKDTVI
+IKPRHTIVFDFEADNPGQWLTHCHNAYHAVAGMMGVFSYIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e3b7e2feaaf6518a6ed2d365c9ece77e6b72b38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001827.fa
@@ -0,0 +1,24 @@
+>0_614
+MTLMQIPTDHGTIGLNVEESGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLYGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFEGS
+GKRTHKAIDGSRVELVKDAPHGFNTSHSEEFNRILLEFLAE
+>1_360
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAAVSPHYRVITYDRRGF
+GVSEKPTGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGADRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
+>3_2134
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPMTLDSWKDQVAALSPHYRVITYDRRGF
+GASEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARHMSRFGADRIHSVVF
+AGAVPPYLLKTEDNPDGPLTEKQAAEMRAGLEKDREAFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRKEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPTLVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
+>4_583
+MTLMQIPTDHGTIGLNVEEAGHGRPVVLIHGWPLTLDSWKDQVAALSPHYRVITYDRRGF
+GVSEKPAGGYDYDTMTADLHGLLTELDLRDVTLVGFSMGGGEVARYMSRFGSDRIHSVVF
+AGAVPPYLLKTDDNPDGPLTEKQAAEMRAGLEKDRESFFDDFTTTFFSTPKLAGLTSSLK
+VTEEQRQEAIRMALQSDQTAALACMDAFGATDFRRDLPAVTVPALVLHGDADQIVPFKGS
+GKRTHKAIDGSRVELVKDAPHGFSISHSEEFNRILLEFLAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001829.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..582539c2f95811ecab22c6f91aeddcb53e3e3636
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001829.fa
@@ -0,0 +1,20 @@
+>0_621
+MSVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>1_367
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>2_2266
+MRLIDVGLREGHEYRVRDTWLTVPNVITLVRLALVPVFVWLTVTDQFLAAFLTLAFLSST
+DWVDGYIARRFDMISTVGRWLDPVADRLSLVTVALTFVLTGIAPAWLVLSILIPDVVLTL
+VCLRLFGGSPDLKVTVLGKVRTALLLAGTPLLLLARVPGVDQDLWGGLALVLVGAGCVLH
+VLAAVDYLVRAVRKARELRAAGVDPRDRRARPAQGA
+>4_591
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDVVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4481baaf4d34cafcdd14bec9c53414edf431ae60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001831.fa
@@ -0,0 +1,32 @@
+>0_639
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFTDARVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYATQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEIGEGTTEVQLMLIARELGL
+>1_385
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>2_2247
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEFGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTQEQKEAWLPDL
+VAGRHLAGFGLTEPGAGSDAGGTQTTAVLEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGADGKPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGTRGRGFANFLEILDEGRIAIAALATGAAQGCVDESIAYAKQRTSFGQRIGEFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>4_609
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001834.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a3cb217042e520316e30d600dcde7a8c7f7ff98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001834.fa
@@ -0,0 +1,12 @@
+>0_652
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
+>1_398
+MTSRTVVRTCIGCRSRADQQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLLL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
+>3_2095
+MSPRTVVRTCVGCRSQADQQELMRVALEPGTTPPTVVWDPLRRRPGRGAWVHPGPECLQL
+ALRRRAFHRAFRGQVDPDGLEAGTRASAARPTDEGGSEI
+>4_622
+MTSRTVVRTCIGCRSRADRQELVRVALDSSTEPPSVVWDPERRRPGRGAWLHPGEDCLHL
+ALRRRAFGRAFRSAVDADALGRTAEAPADRPTDEGGSEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5777c96b74a332282775260a880c3b35e9a3792
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001835.fa
@@ -0,0 +1,36 @@
+>0_672
+METASPPTQPEHAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDDGPSP
+TDEPPEPDTAALRGIAPLVDVDADVTTTTRMGGGSRRTSTVYVKGWTGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+GETMSRE
+>1_418
+METASPPTQPERAPQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGRGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIAPLGDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMSRE
+>2_2206
+MSSASPPFRSASDPSAQDPSASDPRVAADGREEDPHAPADGRPPRVVGLVAGPGYPWVLV
+RRIARDFEQRLQERMPAPHGWRVETRQESLPVGADGGMVLEEPVRALADEHGWDTVIAVV
+DLPRFEDGRGVVADVVPQLRLGVVCVPALGLITPARRLRETVLRVVDHLDTVPEVDPPDG
+ELDVQSSDRSAEVEEDGAADTEELRALTPLGGTEAGVSTTTGMGGGRREASTVYVKGRTG
+TLRLLAGMVKANRPLRMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPWRLAAVTVLS
+IVLLVAWLIATNGLWTRGTRHRHSSRLDNLSTVITVGLACTLVYAVLFATLFLVAVMIIP
+VDYLGGELERASDLSDYANLVWLAASMGTMAGAVGSSLDDSERIRNATYSLREWHRRRGW
+DEAREAADEPAAASRE
+>4_642
+METASPPTPPEHAQQDGDDAPGPRVIGLVADPGTPWALVRRIAGDVEDRLDERLPQPGGW
+RVETRQESLPVGATGGMVLEEPVRSLADGQGWDTVVAVVDLPRFDDRRGVVADVVPQLRV
+GVVCVPALGVITPARRLRETVLRIVEHIDTAPHVDPPDGELDVQSSDESGEVEEDGGPSP
+ADEPPEPDTDALRGIASLVDVDADVTTTTRMGGGSRRTSTVYVKGWAGTLRLLAGMVMAN
+RPLLMPRDMTFTIASASAAGAYGVFFGSIWVLSSVMSPVRLAAVSVLSVVLLVAWLVTTN
+GLWTHGATHRHSSRLDNLSTVLTVGLACTVVYVLLFVTLLLVALMIIPVEYLEEELDQPG
+GVGDYVRLVWLAASMGTMAGAVGSSLDDSDRIRNATYSLRERHRRSERHEGDGAAEGPTA
+EETMCRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a477fc22e66769bc9d64949572064f53ad645db5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001838.fa
@@ -0,0 +1,21 @@
+>0_816
+MNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTPAALLAAMSLDEST
+QIHEQAGQLWEVLPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTRALTVAGG
+AVFFFGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLHLRPAPGH
+LQVTADGVPDAGADDVVLGAGPGPAARLDDCD
+>1_547
+MSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVALPRRTR
+ALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVAPWAHLH
+LRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
+>2_2043
+MVSMKRSTEQSDVPAPLADPGSGAGSVTASGAVRPAEADPAAGQPVQGRWARRVALTLIG
+VSVALAAWSFAIPFLFGLGVRELPWWRQFFDLNHETNLTAWWSSGLLLLGAIGFAVVGLV
+RRSLRADRPLALLAWLTPSALLAAMSLDEFTQIHERLGEVWDALPFTPENPLHAFQGLIL
+GVPIALAVIALLALTAMMLPRRTRALTVTGIVVFFVGAIGLEAVPLVFNIARASWAYHAV
+THLEELTEMIGSSLLIVAPWVHLHLRRAPGSLLVTTDGLPAAAEHDDAAPAGR
+>4_775
+MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFVFGL
+GPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGADRRRSLLAWLTP
+AALLAAMSLDESTQLHEQAGRLWEALPFAGENPLPAFQWLILGAPAAIVVLGLLALCTVA
+LPRRTRALTVAGGAVFFVGAIVLEAVPLVFGIGRSTLAYHVATHAEELTEMIGASVLVVA
+PWAHLHLRPAPGHLQVTADGVPDADADDVVLGAGPRPAARLDDCD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aede465863cb023d4aff3178ee21738a2f94111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001840.fa
@@ -0,0 +1,52 @@
+>0_912
+MSTPAVTRPGRPRARFALSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAMYAGTVATAGLLQVQARGVGADTTLARIIHRVEAAQEAR
+ARTQQFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPIVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDHPGVAQAVARQVGVDDVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>1_640
+MSTLAVTRPGRTRARFTLSRRWRRPVVAGLLIAVSLVLAPEQLAHGTGHLVAAGLMLAAA
+VVAGLPIARDAIAALRVKTVGIDLLVATAAIGASLLGNFWEAAAVTFLFALGHALEDATL
+SQTRSALADLVSTAPETAVVVDADGTQRTVPAHEVAPGATVLVKAGARVPVDGVVLTGVG
+AVDEASITGESIPAEKTDGDAVYAGTVATAGLLQVEARGVGADTTLARIIHRVEAAQEAR
+ARTQRFMDRFSRWYTPAIMVLAFATGLITRDVPLALTLLVIGCPGALVISIPVAIVAGIG
+RGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVAFEPGAEDEVLRWAARL
+EAASDHPLAAPVVAAGRDRGLLDGPLATDVDVVLGRGLTGEVDGRVVAVGNVAMLRERGV
+DPAATDRVETVAAELAEAGRTPAAVVVDGIPLGVLAIADTLRPEAAGMIRALHGIGVREV
+VMLTGDQPGVAQAVARQVGVDHVRAGLLPQDKLEAIEALQAEGRVVAMVGDGVNDAPALA
+TADIGVAMGAAGSGVAIETADIALMGDRLERLPQALDLARRTVRVMRQNIAISLVTVVAL
+LAGVFAGGVTMAVGMLVHEASVLLVIVNAMRLLRRPGQPRSTTSNSSRSAPVATGAGRPP
+CSAA
+>1_1070
+MVTLAVAAVLLVAGLVVEWTIHSEPVALALFWGAILIGGVYPLRSAIRAVRHKRLTITVL
+LVVAAIGAIALGVIEEAAMLVVIFSLGEAMEAYATDKARGSISALMELAPPTANRLNDDG
+ATKTVAVEELHPGDVVLVRPGERLPTDGAVIDGASWVDASPVTGESVPVEATAGTEVFGG
+SLNGNGVLRIEVTKEYYDTVLARVIEQVEEAQANRSGAERFADKFGAVYTPAMFALAIAV
+ALVLPLLGFEWREAIYRALVVLVVSCSCALIISVPVSVVTAIARGARDGILIKGGIYLER
+LADIKAVAFDKTGTLTRGRPTLAQVTPLDGISEDEALTLAAAVETGSEHPIATAIVAGAR
+DRGLTIPAVQDARALPGAGMEATLDGRTLHIGRPTDEDRTDGTAGPALAHAEAEGCTAVV
+LRDDTRPLAVVAVADQLRPDAESTLTELRDLGVERVLMLTGDNATVARSTAQALGLDDYR
+AELLPEDKSAAIRELREKHGVIAMVGDGVNDAPALANADLAIAMGAASTDVALETADVAL
+MADELDRLPAAIRLSRRARNNIKINIALSLTVVAILIVAALAGWMSLTTGLLLNEGSAAL
+IILNGLRMLRPGRGETRRAQVDFGTRQGSDLNSGRPCAPGSTTDGHSVAAGSSYDQREHG
+R
+>2_1949
+MSTAETTRTGERRGRTGPRLPHRWRRPALAGLLIVLSLILAPEQVAQGTAHPVAAALMLA
+AAVVAGAGIVRSAVAALRVKTIGIDLLVATAAIGATLLGNFWEAAAVTFLFALGHALEDA
+TLAKTRSALGDLVATAPETAVVLEADGTQRTVAAHEVPAGATVLVKAGARVPVDGVVLTG
+TGAVDEASITGESLPAEKSDGDDVYAGTVATAGLLHVQARGVGADTTLARIIHRVEEAQE
+ARARTQQFMDRFSRWYTPAIMVLALVTGLITRDVPLALTLLVIGCPGALVISIPVAIVAG
+IGRGAKDGVLIKGGEFLERSAKVDAVAVDKTGTLTSGTPELTDVVALEDGREDEVLGWAA
+RLEAASDHPLAAPIVAAGRDRGLLSGAMATDVDVVLGRGLTGTVEGRTVAVGNVALLRES
+GADADRTARVEAVAAELAAAGRTPMAVAVDDVPVGVLAVADTVRPEAAGMIRELHRIGVR
+EVVMLTGDQPGVAHAVARQVGVDRVRAGLLPEDKLDAITAMQAEGRVVAMVGDGVNDAPA
+LASADIGVAMGAAGSGVAIETADIALMGDRLELLPQALGLAQRTVGVMRQNIAVSLVTVA
+ALLAGVFAGGVTMSIGMLVHEASVLLVIANAMRLLRPAAGSGRGGSRAAQSRSTTSNSSS
+SAPVATGAGRPSDSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e315bf0154be47c8c5e9b72be56f6503be8ff7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001843.fa
@@ -0,0 +1,32 @@
+>0_970
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ
+RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS
+PAPTAAERHHRSAEPR
+>1_693
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ
+RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS
+PAPTAAERHHRSAEPR
+>2_1842
+MPPTDAPIRTALIGYGFAGKTFHVPLLHATDGLALTHVVSSRPDAVHADLPDVVVVPDVD
+ALLARHDVDLVVIAAPNDQHAPLARTALGAGRHVVVDKPFALSLAEARELRDLAAATGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL
+GPHLVDQALLLFGVPDRVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNIERAPAPTGAQQ
+RSYAGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVKPALTAVERAAYPGVS
+LAPTAAERHHRSAAAR
+>4_913
+MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD
+ALLAWHDVDLVVIAAPNDQHTPLARAALRAGRHVVVDKPFTLSLAEARELRDLAAETGRV
+LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRSRWREASVPGGGIWFDL
+GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR
+FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPTGAQQ
+RSYTGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAVERAAYPGVS
+PAPTAAERHHRSAAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001846.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9bc5291cfe007fb47473f208e9189a3d8a00086
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001846.fa
@@ -0,0 +1,20 @@
+>0_1019
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEVGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>1_747
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGRALDGLPAGGSLAVDGVCLTALDGPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
+>3_1679
+MFTGIITHLGTVLSLEERPETDTAVLTVDAGGALDGLPAGGSLAVDGVCLTALDDDAASA
+APGVFRADLMGQTLRMTSLGGRRPGDRVNLERCLRPTDHLDGHVVQGHVDGTGTVLAVSP
+HGDWTTLRIGLPARLARYVAAQGAIALQGVSLTVTGVSPADAREHWFEVGLIPATLEATT
+LGRLAAGDTVNLETDVLARYAERLAAIPAPTTEEPHA
+>4_966
+MFTGIVTHLGTVVALEHDAAADTALLTLDAGGALDGLPAGGSLAVDGVCLTALDEPTERP
+GVFRADLMGQTLRMTSLGDRAPGDRVNLERCLRPTDHLDGHVVQGHVDGTGEVLAVTPHG
+AWTTLRIGLPARLARYVPAQGAIALQGVSLTVTAVSDPGAAAHWFEIGIIPATLEATTLG
+ALRPGDRVNLETDVLARYAERLALIPSAPAAPTEEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c6f8488db1db0f0bbcb89980683bf2e30751b23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001849.fa
@@ -0,0 +1,36 @@
+>0_1032
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>1_760
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>2_2272
+MDPILLLILGTVVILVIILANGFFVAQEFAYMSVDRVRLAAAAENGDEAARRALAVTRRT
+SFMLSGAQLGITVTGLLVGYVAEPMVGEALTQLLGGTAIPASVVIAVSTVGVLLVATVVQ
+MIVGELYPKNLAIANPDPLARALARPTQVYLALFGWLIWVFDKSAEALLRLLRIEPVHDV
+DSTATAQDLDRIVEDSRDSGTLPAELSVLLDRILDFPERDAEHAMVPRSQTDEVGPETTV
+AEVRALMAAAHTRYPVISADHQPLGVVHLQDVLALGHAPAPDLLVTDVMRPATVVPTVMP
+LPDVTRALDDADDQLACVIDEHGGFVGVLTLEDLAEELVGDLRDEHDDEAHEEIVPVVVG
+ESWALRGDVHLDELERAIGHPLPEGEAETVSGLLIESLGRLPEEGERVAVDLPEDTRDYG
+GDVLYDRRLEVDVRRVERHVPADVEVHLVETPREDETEEDPR
+>4_981
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce65d11291fa5bd3d7d65e7794f46b2d93d3f76a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001850.fa
@@ -0,0 +1,26 @@
+>0_1065
+MKEAGLWIGFYVALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>1_793
+MKEAGLWIGFYVALALVFAGLLFTLGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQ
+VPRRYQQEVLMVGIIIALIARAVFIAVGAVAIEHLTWEFYIFGAFLLWTAWQQLKDDGGD
+EESEPGVVARLTRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPA
+IFGLTQNWFIVLTANIFALMGLRQRARRRPAPPAAGRGVVVRPGRLTGDVGEYPEHCGRQ
+HAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
+>3_1642
+MDVLTPAFEITTLVVLGVILLFDLLYVLKRPHEPSMKEAGLWIGFYVTLALIFAGLLYVL
+GDAQHGTEFLAGWVTEYSLSVDNLFVFLIIMAKFQVPRRYQQEVLMVGIIIALVARAIFI
+AIGAVAIEHLTWVFYIFGVFLLWTAWHQLQDDDDGEEAEPGIVGRLTRRLNVAEDFDGNK
+LRTTVDGKRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIVLTANIFALMGLRQL
+YFLLGGLMDRLVYLKHGLAFILAFIGVKLILHALHENELPFINGGNPVPVPEISTFLSLA
+VILGTLVVATVASLVWGKAADEGDARRAESATRMKQVSDAARRDGR
+>4_1015
+MALALVFAGLLFALGDAQHGTEFLAGWVTEYSLSVDDLFVFLIIMATFQVPRRYQQEVLM
+VGIIITLIARAVFIAVGAVAIEHLTWVFYIFGAFLLWTAWQQLKDDGEDEESEPGVVARL
+TRRLNVAPDYDGNRLRTTVDGRRMFTPMVVVFITIGLTDVMFAVDSIPAIFGLTQNWFIV
+LTANIFALMGLRQLYFLLGGLMDRLVFLKHGLAFILAFIGVKLVFHALHENELPFINGGH
+PVTAVPEISTFVSLGVIVGTLVLATVASLTRGPHQRARRRPAPPAAGRGVVVRPGRLTGD
+VGEYPEHCGRQHAAAAESAPPAGHRGPGRGRGGRRDLRHRPDP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001851.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4746b6eddc070fb3059025fba4466d07778b93aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001851.fa
@@ -0,0 +1,32 @@
+>0_1066
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>1_794
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLAEDADPAERERAAALMD
+RWTARAEALDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>2_1750
+MEINGLTWGLTITLIVGLLAFDYFAHVRKAHTPTIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTIFIL
+LGAAVIAAWSDVFYLFGLFLLVIAGGQLKGEMAGDADDAKDEADNIMVRMVKRFLPASDR
+FDGDKLFTLENGKRVMTPMLLVMIAIGATDILFAFDSIPAIFGVTTEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVTIPT
+TLSLVVVVVILAITVVVSLYSPKGQALRALQNAEKFSYRYSKLDETADPAERSRAAALMD
+EWTAKAEGLDQKWRDELLEHKDTWSGIIRTAHETRLADPRDDDARGVSERIVRQDGPTV
+>4_1016
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIATWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c0c267f684ca6b4f3215c42edc08867f9b274da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001852.fa
@@ -0,0 +1,13 @@
+>0_1099
+MIGAVPGEPGMDLLGALASGRLDPAAGASTARSPHAAVDGPERPVCSRRGCTAEAAWALE
+WNNPRVHAPDRVKTWLACTDHRPFLDDFLSARGFLRRSRPLDPAATQAPEVDTPETPQEP
+PRP
+>1_827
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
+>3_1609
+MTGPDLLGALAAGLDPSLPAVRREPSAEGPAAVTADGAPVCSARGCRAAAAWVLEWNNPR
+VHAPDRVKTWAACPDHREHLSDFLASRGFLRRTRPLHAAAGPAATDPTTPGEPRR
+>4_1049
+MDLLGALASGRLDPAAGASAARSPHAAADGPERPVCSRRGCTAEATWALEWNNPRVHAPD
+RVKTWLACADHRPFLDDFLSARGFLRRSRPLDPPATEAPEVETPETPQEPPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5297070891fb03010781d9bd67b7ebd22aad0313
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001853.fa
@@ -0,0 +1,18 @@
+>0_1109
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>1_837
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
+>2_1703
+MNALSLNPRGGAEHLARHAGLVAALRERPVVVETEAAGDRAALRAANELGLRRVGRELRF
+LVR
+>4_1059
+MPVGAATLRELPLVGETSPELAALVDRAHREARALNRLLGVHPLALGTVAPADVLGADAT
+AALRTGLAAGLGVAPTAWEDPGVVLAPAADADPELLHVVLLHTTAVVAGPPALVARLADA
+DVSDLLDDASLGAHLRGPVEDVSAAWLHAADRQALSLDPDGGAAHVARHAELTAVLETRP
+VVVERVGMRDRDAQRAADAVGLRRVGRERVLRVAAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ef9103868c07d810d71def22807bd97b2b59315
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001859.fa
@@ -0,0 +1,37 @@
+>0_1258
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>1_990
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>3_1452
+MAELRLTGTTEDGHALRLAAPDGTEHTLERTPFLRRLALDDVARPDAVPAAEPADGAAPA
+SPAQADEPSAEAPAPEVPRPAPSPAQEPAAPVTAVAEQADVRAAATAEAQPLSPRDIQAR
+IRAGASVEQVARESGNAFSRVRTYGYPVLAERGYIAQQARAVQVWVGGPDLYSGTVADGG
+PTTLGALAEHRVRELGTDPASLEWDAWRESGGVAWTVVARFPLPPRGRALTAEEPPARWS
+FRPAGGRLDPENAWARILSDAEAWDVFTAEEPLTREDDAAAPQQGGGEEASGGDAPAAVT
+PLGASPSSVGVDADLLEILRARRGRRVGQDAESDDALAHLIARGVAEREARQDGAEADHT
+EQAETEPAAPGRAARLLRGLPSLREEVAKDGADGRPPVEADSPAAEAAPAVDAAGREDAV
+TPQAPGKTDAGKTVAGPSGADRTETGQAGTMQADAEPSDAPVAAPQEEEPARTARRERPA
+MPTPRPRARSAARRASVPSWDDIVFGKKSD
+>4_1215
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPRADAEEPVDATTHADDAAEEGERAPDVPSGPARPDEDLALTPRIDPRPVADDST
+ADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRTYGH
+PVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLEWDA
+WREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAWDLV
+PRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDALAHL
+IAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADVADA
+GVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70f149835dfb8c7556a1a8c846fdfa7f999c8ab3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001860.fa
@@ -0,0 +1,28 @@
+>0_1267
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTAVR
+TLRARARHRDAVELVATGPADAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>2_1547
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTVVR
+TLRARARHRDAVELVATGPTDAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>2_2607
+MTAGILTMALCTGLVALAVFGPWLLRHAAPALVRVPRLAIVVVAGGIGVWLVTLLAIGPV
+LAWAGAGPALLPERAAEVCQRCLTAANPFSADTTETLIPAVLLLALPVALALALGAGLAR
+QMVRRSSRSRDAARTLLHGARRQLLHGHEVALVDAEHPFALTFPDRHGGIVLSTGAVRAL
+GPGELAAVLAHEHAHLHQRHHLITALVDSIAAYLRWVPLIRAVADALPHYLEIAADDQAR
+RHAGTRALVSALVKLGERTHPAMPQHSCPVALHAAGPERIRHLVHPSAGLAGALPAVAIA
+AYLVGMAALAALVHLPYVSAALTGCTI
+>3_1443
+MSFSVLVLAAVALCLAGPVPVLLGRAAWPSRSPGLAVLAWQAVALAGGLALVGTPLLWGL
+HPWGDGLLDAVPALLADLTSPDSGIARPGSAPAEVHLLAVGAGLTVALHLLLTTAVTALR
+TLRARSRHRAALELIATDPERADDWPGGPRGARELPVDLPLAYCVPGVPGGGTPLTVVSR
+GLLERLSPEELRAVLLHERAHLAQHHGLLRLAFASWARACAWLPSAETARAGVVLVTEML
+ADDAARRTAPAPVLARALALTVRPAEAPGASASGPDAEPDAESGGLGRRVARLLDPPAPV
+PGAVAGAAAAACLALPLAVLAVILGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bc298158ded68fc14b28a5f77e5eab0c8b6cc08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001864.fa
@@ -0,0 +1,36 @@
+>0_1360
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPTAAADGTVQFLLDIIPGSLPMLPTLFIALLVGFALQQMGPADAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLVGRWVGELDGERARRVLSGE
+LQFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFAMAADGDRNPAR
+>1_1099
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALVYFMAMSTFALAIGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGYLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
+>3_1368
+MTHASPAEAVPVKKKDRTHWLYISVIASVILGAAVGLLFPEFGKSLKPLGDGFVSLIKMM
+IGPVIFCTIVLGIGSIAKAATVGKVGGLALLYFITMSTFALAIGLVVGNFVHPGEGLKLT
+PYDPNKPKAPLDSTVQFLLDIIPGSMPVLPVLFVALLVGFALQQMGPAGAPLLRGLTLIQ
+GVVFRILMMIMWVAPLGAFGAIAAVVGSTGWSAIGAMLLLMGAFYLTCILFITLVLGTIL
+KVVTGLNIFSLLKYLGREYLLIFATSSSESALPRLIAKMEHAGVDKSVVGVTVPTGYSFN
+LDGTAIYLTMAALFVSNAMGMEMNLGEQVGLLLFMIIASKGAAGVTGAGLATLAAGLQAH
+RPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGQWVGELDGDRARRVLGGELKFD
+EAMVAGHGDAVLEDAKAHPSMVEQTGGSHAASTY
+>4_1309
+MAHTPPAETSAPPAPATKKDRTHWLYIAVIASVVLGAAVGLLFPEFGKSLKPLGDGFVSL
+IKMMIGPVIFCTIVLGVGSIAKAATVGRVGGIALAYFMTMSTFALAVGLVVGNLIHPGEG
+LKLTPYDPNKPQAAADGTVQFLLDIIPGSLPVLPTLFIALLVGFALQQMGPAGAPLLRGL
+TLIQGVVFRILMMVMWVAPIGAFGAIAAVVGSTGWSAIGAMALLMGAFYLTCIAFIVVVL
+GTVLKVVTGLSILSLMKYLGREYLLIFATSSSETALPRLIAKMEHAGVDKSVVGVTVPTG
+YSFNLDGTAIYLTMAALFVSNAMGAEMNLGEQIGLLVFMIIASKGAAGVTGAGMATLAAG
+LQAHRPELLGGMGVIVGIDKFMSEARALTNFTGNAVATLLIGRWVGELDGERARRVLSGE
+LKFDEATVAGHDGAAHDPQQSPTIAEQAYEGHPDSSLNFTMAADGDRNPTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acaa70c26a5e92734d01ee860a29f0fbe8dc04e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001868.fa
@@ -0,0 +1,15 @@
+>0_1393
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGEFDRPHVLCGVCRTELSVTAYLALEATADPACPACGAPFNPGCADHAPLYFDVP
+ASGSPAGDADPAAQP
+>1_1134
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGDFDRPHVLCGVCRTELSVAAYLALEATADPACPACGAPFNPGCAAHAPLYFDVP
+ASGSPAGDVDPATRP
+>3_1332
+MVTPADPGPAVRGVDADPQTRCAHYRTERDVVALRLDCCPEYWCCRECHDELAGHPGRPL
+PREAFGLPSVLCGVCRHEMDVPAYRAAMAHADPHCPACGAGFNPGCSRHARLYFAVDA
+>4_1342
+MTAPDSLDGTDPLLRGVGLDAQTRCAHYATARDVVALRFACCPAYWSCHRCHAELADHPA
+VPVPAGDFDRPHVLCGVCRTELSVTAYLALEAAADPACPACGAPFNPGCAAHAPLYFDVP
+ASGSPAGEADPPAQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dc1b3dc35a057d56b1164ebcd9e421e61b09d33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001870.fa
@@ -0,0 +1,47 @@
+>0_1418
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQSGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADADAVGRVADVAATAAD
+APPCARQDEQALTAPTRPVRRVPPGDPADGPAAGDRTGEDAAEEAR
+>1_1159
+MTVSGPDVSAAPAAESGAEPVEPAAARPRSWGPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQSEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPDSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPNPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRHVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVSRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYMVPMDRDRA
+DGHVAHVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AVQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVATAAPPSA
+RQAEQALTAPTRPVRVVPAEDPAHGSAPGDPTGDDPAEEAR
+>3_1306
+MTAPAEPPQPAETGDPDETGATSAPASAGPSTSAAPPRAGLRRRLRRRWNGSLQLRTAVL
+AGLLTLLASLMISGLITQQVAQALFDARHQQVEAEARRGLARVQSTFANAAATDQQATDA
+LVSQTMRALELDGGTTIRRRFRLEPLPGGTAASVGTVSSQGLDADVIPQDLRDAVASGPG
+VYDASIALPAADGNTRPGLAYGTQVVLPPGATYALYLVYDLSDVQESLDSVLGVLLMFGS
+GFLLVTVLVSWWAAHSVVRPVQQAATAAESISGGNLAVRMPVRGDDEMARLGTSFNRMAD
+SIQAQITQLAQLSRMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLY
+HQVDRFQAMLADLLEITRFDAGAAQLALEDTDLLALARDVVLTAAPLADQAKVPVYLVPL
+PLEEGLDCVAQVDPRRIERILRNLVNNAIEHAEGSPVDVLVAADEGAVSVAVVDEGIGMS
+PEQVQRVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGVGSVFMVTLP
+RRNGAESPVRRAVLPMPPSYDRGGRRLAADLHTPVTGPEGTGVHDAAALPERGREQEL
+>4_1367
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTRPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGTSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPARKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVTAAAADAP
+PSARQAEQALTAPTRPVRMVPPADGTAAGGWTGDDGAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f28c155b32755b3b8d1ce3416b091ff1ca4fecf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001871.fa
@@ -0,0 +1,20 @@
+>0_1424
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>1_1165
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>3_1300
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVALELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVSSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
+>4_1373
+MADLTRSLFAPRRGDRPTVAVLGLGRFGSGVARELMESDCHVLGVDADAEAVQALNGRLT
+HVVRADSTDEEAMRQLSVHEMDHVVVAIGGDLADSILTVSLMRRFGTHQLWAKANDDRHG
+EILRQLGVEHVVHPERDMGRRVAHLVSTSFQDFVEVEPGLAMVRATPPSRLLGRDLRATG
+LAGERGMRVVAVRSRGTWLYPPSHYVLEPEDTILLVGPTRDVERFLARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001874.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b8514737a3814b6fdf8146f8c425db24c340a33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001874.fa
@@ -0,0 +1,36 @@
+>0_1460
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>1_1179
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>2_1386
+MSNDPRTPGSDDGRDPLEEMLRQLFGGNGPDPDEIRRAMEGMGGPGGMPFDPSQLDPAMM
+QQAMAQFQAMMNPGPGSEGPVNWTLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGATQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASMLSGIQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGVPIAGHRLAMVPVNVEEF
+GDGLSVPDDQVRIYLALREAARMRLFLHSPWLERDLYAAIEQYAAGIRLDTEGIEQAARS
+VDPMDPESMQAVFDGSSFIAAPDATQRAALAQLELLVALVEGWVDVVVAEAATPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEQGKEYREEIWRHPER
+QPTAEDLEDPAGYAGRRTAADASTDSLDDDLRKLLEGGFGDAPKEG
+>4_1387
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWSLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAISMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYTGRRSAADASTESLDDELRKLLEGGFGDAPREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001878.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02e904bf36c33ac2d959e1b5db6c5e33ab72cd5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001878.fa
@@ -0,0 +1,28 @@
+>0_1538
+MTRTPPAVAPPAAETGGESLLTVLIALGVNAVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>1_1260
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNTRV
+>3_1197
+MSHSDDIRPSVAAHPDDGDATSDPALAPPQAEDRPEGLVTVVIALAVNVAVAVVKSVVAA
+LTGSAAMVAEASHSWADAGNEVFLLVAERRAARPADARHPLGYGRAAYVWSMVAAFGLFA
+VGAAVSVWHGITAWSAPEEEGGGHLIGYVVLAVAFVLEAVSFGNAHRRVSAGAQEHRVSR
+SRFLARTSDPTLRAVWAEDSAALVGIGIAAAAIALHQLTGDARWDAAGSILVGVLLGAVA
+VFLLSKNMAFLVGEVADPAVRVRVLRWLLERPEVLSVSYLHLEYVGPGRLAVVGAVDLAA
+DEVESLAAVALQRVEDALLAHPVVAAAVLSLSNPSHAPLRLEDEEAAARR
+>4_1465
+MTRTPPAVAPPAAESGGESLLTVLIALGVNTVIAVVKSIVGAVTGSAAMVAEAAHSWADA
+GNEVFLLLAERRAGRAPDARHPLGYGRAAYVWSMVAAFGLFAVGSAVSVWHGITAWSAPE
+EEAEYTIAYIVLAVAFVLEGISFLNAHRRVRRDAERRHISDATFLRQTSDPTLRAVWVED
+ASALIGLAIAAAALALHQLTGDPRWDAAGSILVGVLLGVVAIFLLSRNMAFLVGEVADPV
+IRTRVLRWLLERPEVLSVSYLHLEYVGPEKLFVVGAVDLAGDERESEAAVLLQRVEDALL
+EHPRVAAVVLSLSNPAHAPLAPESQNARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2da4105a4402bd4d9380028d6f0fa21d83219bd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001879.fa
@@ -0,0 +1,20 @@
+>0_1560
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWSAATGAHFARRGNRFYPALHRAGL
+TRHLVDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>1_1280
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRATARADELTAEDLAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAVLGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
+>2_1260
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALHRAGL
+TRHLIDASDGYKAEDLAELHARGIGISNLVPRASARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQETPWPGTRLFVAPNPSGLNAHATVDSLAADYRAA
+GAAAGLVD
+>3_1165
+MRFTQAELQQFRDRTVPDLLPDPLRLLFIGINPGLWTAATGAHFARRGNRFYPALYRAGL
+TRHLIDASGGYKAEDLAELHARGIGISNLVPRATARADELTAEELAAAPARLDALVAAHA
+PAVVAVLGVTAYRQAFGRPKAALGEQQTPWPGTRLFVAPNPSGLNAHATLDSLAADYRAA
+GAAAGLVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dddd8ee12f13ddc89d4112df42d48c81b6792da5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001881.fa
@@ -0,0 +1,49 @@
+>0_1601
+MDTPTPPHPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAIVGLSVGYVSYRRGRVPLMSSIIAPLFGDSPRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIVSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSNWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTRGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIIMLAVFFITTADSAS
+IVNSQLSQRGDPAPRRMITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDDADGPAGAGPSGR
+>1_1316
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMVHAGWLFVLLAIGMVVFLLVLAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAGSEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAEGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDGDGADGPAGAGPSGR
+>4_1498
+MNWPVFAGTAGIVVGFALWAMLLPAQADSVISATVSWIAESFGWYYVLTAGVVVVFVVVV
+ALSRLGRVRLGPDHAVPQFSMFTWSAMLFAAGIGVDLMFFATSGPATNLLTPPDLEPMSD
+EAARMAPLWTIFHYGIPGWAMYALMGMAFGLFAYRYHMPLSIRSAIAPIFGRRVHGGIGH
+AAEIGATVGTIFGISVSLGIGVVFLNAGLALILDVPVTTGVQIALMALAVGITIISTVSG
+VDKGIRRLSELNVYLAVVILLWVLVTGRTTDLLNALVQNIGDFFASFPSMMMRTFAYTDG
+TAAYPAEQWMSDWTLFFWAWWIAWSPFVSLFLARISRGRTLREFVLGVLLIPFAFIMLWV
+SIMGNAAIGLFRDGDDALLQEAVTAPEAGFFSLLQQFPGATFLIGLAVFTGLFFYVTSAD
+SGSLIMAKMTSKGSVEDSDGAPWLRITWAVITGLLTLSMLFIDGVYTLQKATVIVGLPLS
+VLVYLVMISLWRVLHSESLAMDSRTASLPHVLSGRVRDANSRATWRQRLARRMNFATAKQ
+AAAYVDREVSPALSEVAAELREHGADVDVTRGTHPESGVPWVDLTVRFPGQTDFKYQVYP
+VAYPVPSFAGSLSAAQDTYVQLEVFSAKGSRGRDVMGYSREQLCANILDDYEAHLAFMTM
+TGDDSLLAARIDAEAPEVWTDADHSPATDALPTVALQTTDPETEGARP
+>4_1531
+MDTPTPPRPTGSHTTRTPARPRLRRFVREFSYPHGIHPALVPGVSVEDRRVRYGVDRVIL
+AVVGLLVVGFVVWGVLQPDAVLAVSSAALDWVMLHAGWLFALLAIGMVVFLLALAFSRYG
+EIPLGLDGEKPEYSTASWSAMLFAAGIGIGIIFFGPYEPLTYYLAPRPGAYEAASEEAVT
+GALAQAALHWGVNAWAIYAVVGLSVGYVSYRRGRVPLMSSIIAPLFGDSQRSDSVGARLI
+DGLAIIATLFGTAASLGIGALQIGRGVEIVSGWSAPGNTVALGIIVVLTIGTIFSAVSGV
+ARGIRWLSNINMLLALGLALFFFVVGPTAFLLNIVPGVLMDYVSSAPDALGASMAQGEDM
+QEFLSSWTIFYWAWWVSWAPFVGVFMAKISKGRTIRQYVLGALFIPAAVIVGAFTIIGGT
+TIWLQRTQGSVAPDGTAASLPAPAEIFWVVLDQLPGGGLVAPVVIVMLAVFFITTADSAS
+IVNSQLSQRGAPAPRRTITVFWALCMAGIAVVMLLTGGDTALTGLQNLITITALPFTVVL
+VLMAVALQRELANDPFAIRDRYQRAAVEKATVRGLVEYGDDFAFTVERTPPGSWYAAGEG
+FDSTAAEITDWYRRTDEDGNPVDYDYVLGEYLDEGDEDGADGPAGAGPSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71b5d2e2f8aba814b32624a5b903072032472dbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001883.fa
@@ -0,0 +1,34 @@
+>0_1625
+MRPTRRQFAQGMAAGLAGLVLPPAVASSAVAAPQGPNPRSGRGRDERAIQAALDAVVQWP
+AVGAVCSVVGPARRFDTASGTRGLHANAPARANSVARIASVTKGMVATVALQEVERGTLS
+LDSTIGGVLPGLWPDVEDRVTLSMLLNHTSGMPDAIWVIMRGQSLFELDFDELADVVSRS
+YGQRELVELAKQADWWFEPGTDYGYSNTGYVVVEMMVEAVTGRRMPELIRDRVFRPAGMH
+RTRLEHGTLVRGAEMQDAAVRPHEAKALETIDQSIFASAAAVNTTAADVTRFYQALMRGE
+LVSQQTVDLMVTPVGPATQAGYGYGLFLVADPAPEHAGEVLVGHDGAGFGSVSLALCSRD
+GERAFAFTYIGRPYWQEGWDEVFAKELALMRTAFVVNAADAPASRDRLVRGGAAASRRAV
+ADMAARGARLV
+>2_1174
+MSTSRRRLTQGLAAGAACLALPAGLSAPAAAAPSARSSRTPDSAALQAALEALVQWPVAG
+AVCAAASPAGLVELAAGRRSTASPAPARPQSVARVASVTKAMTATVAFQEIERGTLRLDS
+TIGEVLPGLWPGRESVTLGQLLNHTSGMPDAVWVLMDHVSLWDLPLEHVRDVVARSYPPR
+ELVELAKQDGWWFEPGTDWGYSNTGYVVAQLMVEAAAGRPLSSLIRDRVFRPAGMHRTRL
+EEGALVRGAEMEDAAVRPGQTMRLQTIDQSVFAGAAAVNATAGDVVRFYQALMRGRLVGQ
+ASVDAMVTPVGAARAAAYGYGIFQVPDPVRAGEVLYGHDGGGFGSASLAVSSRDGSRAMA
+FAFVGRPYWAAGANEVWPRQTAVLRAAMSLSGTAGRPGGSAGRAAAGAAHAAVGGTRLG
+>3_1193
+MTRDTPSADRPPLSADALRPIAAALDRWLATQTEVRRVPGVQAAVRLGDELILSTAHGVA
+DESTGERLTTRHLFRVASHSKTFTAVAVLRQVELGTLRLDDTVGALLPGYADTPLAGVTL
+RELLSHTAGAVRDGADADHWILDRPFPDAAALQALVRDHGTAYAPQEHFKYSNIGYGMLG
+AVLEHVTGRPYAEHVRASVLDPLGLTDTHADLTDDVAARAATGHTRAGGRARARVTVEQT
+TTGALAAATGFVSRAEELSAFYASLALGARGVLSDRSLRLMHRAEATFRRGGGTGTYGLG
+LLGQEVGGRRLLGHSGGFPGQITRTLFDPATGLAVSVLTTAVDGPAEALAVGVVQLIDLL
+TAPAADWQALPGGVTAADLDRLAGRYVSLWGATDVLRGGTAERPRLVLLDPAAPAPADAA
+EELRALDATTLRVEDADGFGACGEPIPFDLDAAGRVTRMRVTGVSAWPEEAYRARRGDAW
+RHADGVDGAEAEPDAHEEAAPVLVQAAAFADLDPATAYRLWALRQAVFVVEQDCPYQDMD
+GRDMEPATVHLWVCDEEDAPIGTVRLLDDGDHARIGRVVVDRAHRGRGVAAALMEAALEQ
+VGERACVLDAQAHLEHWYGRFGFAADGPEFLEDGIPHVPMRRPEAGRRTP
+>3_2066
+MDFIVRPCTPEDEPSWLRCRVLAFLDTQNHDDVHAAHPVPDPDVADPADSLQWVAVVRDG
+PDAGTVAGILDASVGAADGDDAGLATIDTLAVHPDHRRRGLAGRLFEAVLERLPERVGHV
+DVWTREDEAANAWYRAHGFARDHVYLQVHLESWVDGDDVAALIRTPPALSAPVKGLFHAS
+LEDEAWIRERFHRVVRVSRYVRPVGMTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfef657f168bdc1f2ba643a07f92ff7819cf7775
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001885.fa
@@ -0,0 +1,44 @@
+>0_1709
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQAGDV
+AGRHAADPVAEGTWADFLAEAARVSDEDLAVREAATGPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>1_1426
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLQVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>2_1089
+MTPSPSVQESYTRGPSDVPMLEQTLAQNLDDAARRSGARPAVVECGPDGDPATDRSWTYE
+QLREESVTVAKALMAAGYEPGDRIGLWSPNVAEWTSLLYGAARAGVILVNLNPAYRAHEL
+TYVVEQCGMRGLVVAPADAHQDRPDIARDVACGGCPELRQLIILPTAGPITAESYAHAVD
+GVLDCRPEPTPVSEGTWSAFLAGADRVSDEELAARESAVSPEDPVNLQYTSGTTGFPKGV
+TLTHRNVLNNGFHIGELLGYSQEDTVVIPVPFFHCFGMVIGVIAAVSHGSLCVIPARGFE
+PVATLRAAAATRATSLYGVPAMFIAMLARPEADELDLSTLRTGVMAGSTCPVEVMRRVID
+RFHMAEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPVSGEVVPRGS
+TGELCTRGYSVMRGYWNDEEKTAEVLDAEGWMHSGDLASMDEGGSVRIEGRIKDLVIRGG
+ENISPREVEEFLYTHPDVQDVQVVGVPDERYGEQLMACLIMKDGTRPLTPEDVRAFCEGK
+IAHFKIPAHVRVLDAFPMTVSGKVRKVELRAEGAKLVEGGDRD
+>4_1638
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADELDLTTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGEVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d50d4dc046f71cc664c019fa0c250ee08848574
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001895.fa
@@ -0,0 +1,16 @@
+>0_1835
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
+>1_1542
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFGAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGG
+>2_943
+MTRQSDLKTLIRARMAVTGERYTAAAAALAHEWETAERFHATVLARFFDGERLRSIPALR
+KPRVAVLLELLRRFAPDRAYTEPEVNDLLRPAHEDVATLRRELVDYGFLDRADGVYRMAD
+AGPDVDPRFAADLPVDLERRLRQLRAGR
+>4_1756
+MTRQSDLKTLIRARMAVTGERYTAAAAALADEWQSAERYHATVLARFFDGDRLRSIPARR
+KPRVAVLLELLRRFRAGRAYAEAEVNDLLRPAHEDVATLRRELVDYGFLARADGVYRLAD
+AGPDLDPRFAADLPVDLERRLREIRAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e80acfbfb6590db5febfe658b079e0f6456538e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001897.fa
@@ -0,0 +1,35 @@
+>0_1852
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VQMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDSLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSVRTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPAWLLVMGALAWLVSVFIAVRGFVPMVTM
+ITGA
+>1_1559
+MSHADIPHAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
+>3_864
+MSHADPTAHARGDAAAGEAVQASSSNRRTALLGAMFLMATSAIGPGFITQTATFTVQLGA
+AFAFAILVSILIDIAVQMNVWRVIGVSGMRAQELANSVLPGLGWVLAVLVFVGGLVFNIG
+NIAGTGLGANAMLGVDPLIGGAVSAVIALLVFLSKRAGVALDRIVVVLGAVMILLMLYVA
+VTSAPPVGEALRQSVFPEKVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDDVEAIT
+RSSVLSILVTGVMRVLLFLAILGVVASGVALAKDNLAASAFQAAAGDIGLRMFGIVLWAA
+ALTSVIGASYTSVSFVTKSTTTTRTRNLLTVAFIVVCTVLYLALRQTPQTLLVFAGAFNG
+MILPIGFAALLWVAWRRRDLLGGYRYPTWLLVIGALSWLLSVFIAVRGFLPMVQMITGA
+>4_1773
+MSHADIPYAGPDGSTPSGTAPKTDSRAASATRRTALLGAMFLMATSAIGPGFITQTATFT
+VRMGAAFAFAILVSILIDVAVQMNVWRVIGVSGMRAQELANRVLPGLGWVLAALVFLGGM
+VFNIGNIAGTGLGANAMLGVDPLIGGGVSALIALLIFLSKRAGVALDRIVVALGAVMILL
+MLYVAITSAPPVGEALRQSVMPEEVDFFVIVTLVGGTIGGYITYAGAHRMIDSGVKGVDD
+VQDITRSSVASILVTGLMRALLFLAILGVVASGAVLSKDNLAASAFQAAAGDIGLRMFGI
+VLWAAAVTSVIGASYTSISFVTRSTTSARTRNLLTVAFIVVCTALYLALRQAPQTLLVFA
+GAFNGMILPVGFAALLYVAWRRRDLLHGYRYPGWLLVIGALAWIVSVFIAVRGFIPMVEM
+ITGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55f84a10684caaa382d18aa41f44d0d8a1441518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001899.fa
@@ -0,0 +1,20 @@
+>0_1854
+MRVPTRDGVTGDDLAPGAGDGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>1_1561
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAVFGDYLDEAEQFVLAHLAAVGD
+>3_862
+MTAPAAQGAADALRRRIGEARLQPGERLGEVALAAELGVSRNSLREAFSELAVEGLVVRR
+PHRGVFVAAPGAEDVRGLYRTRRVIQLGALQHGWLTPAAEERIGRSAELLGRPEPAVREL
+GDANHLLHLGIVDLAASPDLSRVMSSVLARVRLSFLPLDLETGLHQAFAERNRWIAGRLL
+AGDLDAVHAMLEGYLDEAEAFVLRHLDGAAHGLRG
+>4_1775
+MRVPARGGVTGEGLAPGVGGGESAPAPAPVAAAAQLRQRIAAAGLVPGERLGEVALAAEL
+QVSRNSLREAFTMLASEGLVERRPHRGVFVAAPGPEDVRGLYRTRRVIQLGALEHGELTP
+GAARQLRCAQDLLSGGPDTPARVLGDANHRVHVGIVDLAGAPELTRLMASVQARVRLAFH
+PMDEQTRLHVQFADRNRWIVERLLAGDLPAVHAMFGDYLDEAEQFVLAHLAAVGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..782127f849b5d2a3e28d9c4b49f57948cfcc0d4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001900.fa
@@ -0,0 +1,44 @@
+>0_1856
+MSAPHHPAAEPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPERGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGEVTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASVTSGTDAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAARQANRLVGNRSREAVL
+ETVLGGLTLAAHGHQVMALAGAEAGGTITAADGAARRVPARSPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAARPTA
+AGAPASEEAGVVMVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFVPHPRPGAETVVDSASPSEETPA
+>1_1563
+MSAPHHPAAEPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPERGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGEVTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASVTSGTDAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAARQANRLVGNRSREAVL
+ETVLGGLTLAAHGHQVMALAGAEAGGTITAADGATRRAPARTPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAARPTA
+AGAPASAEAGVATVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFVPHPRPGAETVVDSASPSEETPA
+>3_860
+MSGTQAPGAATPRPIRAVGTQAFLVECASLADVMAVHAHLVAHPERGQRQVLSAARTVLV
+TFTSQAAAQHAAPRVAALDPDAQDRDAGRTVEIPVVYDGEDVAEVGRLTGLSPEAVVRAH
+VETDWFAAFGGFAPGFLYCAAEAPPFDVPRRDSPRTAVPAGAVAVAGQLSAVYPRTSPGG
+WQLLGHTDAVMWDLGRERPALLEPGDRVRYVPVRAEAVRGAAPAAEAPAEDTLVAAHTPD
+AGEASAPGLTVADPGLFTLLQDLGRPGLGDLGVVASGAADRDAARQANRLVGNASGEAVL
+ETVLGGLALTARGDQVLALAGAEATGVVTGPGGVARPVSPRTPFPLLDGETLTVQEPTAG
+LRVYVGVRGGLEAPRTLGSRATDTLSGLGPAPLTAGQALARHADLDAPRAGVVPVGDPEA
+PLRPMPAPGGTAVLRVVPGPRDDWFGPAGLERLTAQEWAVSQQTDRIGVRLTAGEAGPLE
+RIRTGELASEGAVRGALQVPPSGEPVLFLADHPVTGGYPVIGVVARADLGLAAQLPPGAR
+VRFVLHPQPSQEPTA
+>4_1777
+MSAPRHPAATPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPARGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGELTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASLTSGADAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAAHQANRLVGNRSREAVL
+ETVLGGLTLTAHGHQVMALAGAEAGGTITAADGATRRVPARTPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAASPTA
+AGAPASAEAGVATVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFIPHPRPGAETVVDSASPSEETPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dadad37934f46d41e213b6f376a54b72fc7a3ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001902.fa
@@ -0,0 +1,88 @@
+>0_1871
+MTAMFSAQDHDDLDRVLSATGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRHMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASLTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATAHPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDGGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPVDPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGAEADGAGASWLETARALDTHAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEKLVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALILPATEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>1_1578
+MTATFSAQDHDDLDRVLGVTGGIPDPADLHALADDAVAQVRRWLAESRDHEADFAARQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAGRAPGFLPPALRAVLGVGGRAAPL
+VPRIAVPTARRVLRRMVSHLIVDARDRQLGKAIAALRDEHTRLNINLLGEAILGQGEADR
+RLEGIAALIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLFELARDRDTFINL
+DMEEYRDLDLTLNVFTALLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMERMQASVTGWPLATVGSKQEADTNYKRVLNYALTPEHLAHVRIGVA
+GHNLFDVALAHRLIERRGLDPAAVEFEMLLGMATGQAAAVRADVGALLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADADLFAREEERFRASLRHLDAAVPRPNRLQDR
+SRGEDGPTPAPVDGFANTPDTDPALPGNREWARRILAAVPGSDLGTDTVRAHRATTADDA
+RAAIAATADPGARWGALTGHERADALDAVGRALHAGRARLLEVAAAETGKTLDQGDPEVS
+EAVDFAHYYARLARGLDAVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+PAPQSERTGAVAWELIVAGLRDSGLFDDRGPLAGHDPADLVRLVTLADEDEAEVGAALVT
+DPAVERLILTGSWDTARLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVQSAFGH
+AGQKCSASSLVVLVGSVGTSERFHRQLLDAASSLHVAHPADPRAEMGPVIEAPGEKLRRG
+LTELGPGERWALRPRQLDETGRLWSPGIRSGVRPGADAHLTEYFGPVLAVMTAETLEEAI
+GIVNAVDYGLTSGLHSLDREEIDVWLRGVRAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWEDAPTWAGGEGRPGSEADGAGASWLETARALDTQAWTTVFGVAT
+DVSALEAERNVLRHVPTPVLVRRHSGPADHLLRIVSAGLRAGAPMTVSLRPTPTAEGPDA
+DGLSAEAVRGRVEELVRSARTEGAGTAAPVDVVVEDDAAFHDRARRLALVPPAAEGGGDA
+RIRLVADWTGDREAAEAARSALHAALGDTPDVAVYAGPVVSAGEVELLPFLHEQAVSVTA
+HRFGTPDHLTEGVL
+>2_909
+MTPTFSAQDHDDLDRVLTATGGIPDPADLQHLADDAVAQVRRWLADARGHEADFAAQQLA
+GALKEPGGLDFIVRFVDHVVRPEDPAIAARALRELAQQAPGFLPPALRAVFGVGGRAAPL
+VPRVAVPVARRVLRRMVSHLIVDARDRQLGEAIAALRDERTRLNVNLLGEAILGKGEADR
+RLEGIAGLIRRDDVDYVSVKVSAATAPHAPYAFDEAVADITERLTPLYELARDNGTFINL
+DMEEYHDLDLTLNVFTGLLEQPGLRDYEAGIVLQAYLPDALAAMVRLQEWAARRVAAGGA
+PVKVRVVKGANLPMELMQASLMGWPVATVASKQEADTNYKRVLNYALTPEHLRHVRIGVA
+GHNLFDVALAHRLMDRRGLGPEQVEFEMLLGMATGQAAAVKADVGSLLLYTPVVRPEEFD
+VAISYLVRRLEEGASPENFMSAVFDLDADEALFAREEERFRASLAHLDAEVPRPSRGQDR
+SRGEDGVRPAAVDGFANTPDTDPSLPGNRAWARGILEAIPGSALGAERARAHRVGTAEAA
+RAAIADTQAPGAAWGALTGAQRAEALDAVGRALHAGRGRLLEVAAAETGKTLDQGDPEIS
+EAVDFAHYYARLARGLDEVEGARAVPVRLTLVIPPWNFPVAIPVGGVLAALGAGSPVVFK
+AAPQSERTGAVAWELIVQGLRDSGLFDDGGPLAAHDPADLVRLVTMADEDEEEVGTALVT
+DPAVERLILTGGWDTAKLFKGMRPDLHLLAETSGKNAVIVTPSADLDLATKDVVHSAFGH
+AGQKCSASSLVVLVGSVATSERFHRQLLDAASSLHVAHPADPRAQMGPVIEEPGEKLRRG
+LTELGEGERWALRPRELDATGRLWSPGIRSGVRPGADAHLTEYFGPVLSVMTAATLNEAI
+DIVNAVDFGLTSGLHSLDPDEIAHWLERVHAGNLYVNRGITGAIVRRQPFGGWKRSVVGP
+TTKAGGPHYLHGLVDWVDAPSSTSESPAADRAGEGTAAGTPAAAERSWLDAARALDERAW
+AATFGSGTDVSALAAERNVLRHLPVPVLVRRASGPAEHLLRVVSAGLRAGAPMTVSIAPT
+PAAQAPGTDDLSAEALRGQVDELVRTAGAGRAEGAAPVSVVVEDAAAFHDRARQLAQIPP
+AAEGGGDARIRLVADWAQDREGARAAGAALHAALGDTPDVAVYAGPVVSAGEVELLPFLH
+EQALSVTAHRFGTPDHLTDAIL
+>4_1791
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd9116faf593d4e848e6ff01e67da6ce75dd4fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001903.fa
@@ -0,0 +1,16 @@
+>0_1880
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
+>1_1587
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQRRRSSGLGGALVGTLGGLAL
+RELSRRGAGGTTRGRGSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTVGGGF
+>2_899
+MGILSGITRALGGSRRRPTIGANTYGRRRSSGAGGALLGTLGGLALRELSRRSSGGTARG
+YGGQAGYGRTTGGYGRTSGGLGGLLGGLGGMGAGRSSSRGGGLLGGLLSGPMNSRSGRRT
+TGGRF
+>4_1800
+MGILSSLTRTLGGGGRRSSRPTIGAHIGRSPGFGRQARSQGRRSSGLGGALLGTLGGLAL
+RELSRRGAGSTTRGRSSGAYRGGFGPSARSTGGLGTGLLGGLLGGALASRGRSGAAGRRT
+AGGRRTMGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..717e2ab88f72c21044abbd0ddbf048ab46ffd35c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001904.fa
@@ -0,0 +1,16 @@
+>0_1886
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+>2_896
+MTEDHRAPSASGYWYVSSPNSVGPVEVLNVLRAYREAERRMRRRTRDSMRMGETDLLALR
+HLLRESRAGRPVRQRDLAAALEISPASASALVDRLIRDGYARRSPHPADRRSVIIETTAR
+TDDEVRATLGRMHRSMLDAVESLSPDELAAVAKFLTALTRSVDEAAEDALEHGTEH
+>3_829
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLQADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
+>4_1806
+MGEEHTTLTSTDGEPTSGYWYTRGAREIEPVDVLNLLRRYREAERRMRARTRDSMGMGET
+HLSALRYLLRADRRGHKVRQRDLASALEITPASASALVDRLVRDGYARRAPHPQDRRSVV
+VEPTAKTDHEVRATLGAMHRSMLAAVEGLTPAELAGAAAFLRALIRSVEEHDEDEADQPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001912.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b6541d2233cf6090baa4fbaa337eb005bbac9ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001912.fa
@@ -0,0 +1,25 @@
+>0_1976
+MVGITLRHMEYLVAVIDEGSMTAAAARLHVTQATVSMALAECERRLGVPLLVRQPAKGVA
+ATLAGHRMAVQARRILGLVHEMEASVPAMPGELAGDLEVGCVPSLSPQAVPVLAEHFSRR
+HPRVTLHYREGAATDLQREVLQGRLEMAVMFSRQQAPGLRSIEVARAQLKVMLPEGHRLA
+AAHEVAFADVAQEPAILIDLPPSTERSLEFMRAAGVEPTLRWSSNNLATVASLVGAGLGW
+SLRYTLPGEQPAARGLVEIPVADPTPPNAVCAVVPDGDRVDQRVRHALEVLRRVLSEEEG
+RPDVDCA
+>2_133
+MEPLNLSSPGLSPAVWRVTTVSRVEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIK
+QLEAALGVTLLERTTRRVDLTDAGRLLLDRSRQLLTDLASLEHDVREVGRGAAGILRVGF
+VGSATYRLMPAIVRAARDAMPGVRLQITGEKITPALEDALLENRLDVAVLRPPVRAAELT
+LTPVEAGRLLLAVPAGHRLAAEDGPVALADLVDEEFVSYPRDSALTAIVQEAARRVGFRP
+RLVQRAGETSTVMAFVAAGLGVAVVPDDVRRPGAVSGVAFRPLSDMPDVELAVAAKADAR
+SPLVPAFVELACRTAAALAEAGEDPTPDPDRPAQET
+>2_789
+MDVHQAKAFLAVAEELHFGRAAGRLQIAQPALSRTVKQLERSLGTDLFVRSTRRVELTAA
+GLALLEPARTLVQASQTAREAVQSALAGETGTVRLGFAGASTHGVVGQLARSVRRRRPGL
+TLEIHSSQFSHLGLERVLEGSLDVAIGRWDFIPHELASRVIAHEEAIVALPADHPHAQET
+GPIDVGLLRDEPWVTLPSGLGSALANRLTTLATSAGFAPRVVQQAPDSFTQMVLVAAGLG
+CAVTLDSVRDNSATPGVVYRPVAGDNPPLEVRMLWRSLDASPALRAVLDLAPAAEPAGVA
+PARTDAAD
+>3_95
+MEIRHLRSFVAVAEERHFGRAAERLHIAQPPLSQQIKQLEAELGVRLLDRTTRRVDLTEA
+GRLMLERTRSLLADLASLEHDDDIASAVKPELLLDVQQGADGNSTVYDFVLDPVSEKTHP
+TAIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001913.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c086e88ff2ed0bc44ebc21f408908b15e0024187
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001913.fa
@@ -0,0 +1,31 @@
+>0_1983
+MRRLAEVTGLVPVEYPTTRQLGASPESRARDLNAAFADPQIRAVIATVGGEDQITVIGHL
+DADAVRADPKPFLGYSDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAAL
+LTGGRLEITEPGESEDHGVDWLDPRALTEFGTREPVPGPHDDGARGVGAGASPWRWAGPR
+RAVTGRTWGGCLEVLPWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGES
+GVLGAVDAVLAARPPTRSFEVPRGAEERARRRAEQADVVLEEVGRYNPDAVVCVGVPFGH
+TRPQWVLPHGGVMTVDGAERRVWAEYC
+>1_1700
+MASRYAPGMTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEY
+PTTRQLGASAEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVRADPKPFLGY
+SDNTNLHQWLWANGVASFYGGSTQVHLGPGPAVDEVHAASMRAAMLTGGRLEITEPGESE
+DHGVDWLDPRALTEFGERDPVPCPHDDGARGVGEGASPWRWAGPRRAVTGRTWGGCLEVL
+PWVMAAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPP
+TSSFEAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTV
+DGVERRVWAEFG
+>2_754
+MEHTLVRPPKAAPGDRIAVVSPSFAAPGFAPEVHEQAMRRLRELTGLEPVEYPTTRELGA
+SPEDRARDLNAAFADPRIRAVFATVGGEDQITVIGHLDAAAVRADPKPFLGYSDNTNLHQ
+WLWAHGVASFHGGSTQVHLGPGPGVDAVHAASLRAALLTGERLEITEPGESEDVGVDWQD
+PRALAEFGQREPVAADDDGLGGPGASPWRWAGPQRSVTGRTWGGNLEVLQWVLAAGRGPV
+DVAALRGGVLLLETSEELPSATDVRRMLRVLGERGILGEVAAVLAARPPVSDFDVRPDAQ
+ERARLRRAQADVMVETVHRYNPDAVVCVGVPFGHTRPQWILPHGGEMTVDGVEKRVWAEF
+G
+>4_1918
+MTQPLVHPPKAQPGDRIAVVSPSFAAPGFAPAVHEQAMRRLAEVTGLVPVEYPTTRQLGA
+SPEDRARDLNAAFADPQIRAVIATVGGEDQITVIGHLDADAVSADPKPFLGYSDNTNLHQ
+WLWANGVASFYGGSTQVHLGPGPAVDEVHAASLRAALLTGGRLEITEPGESEDHGVDWLD
+PRALTEFGTREPVPGLHDDGARGVGGAPGAGASPWRWAGPQRAVTGRTWGGCLEVLPWVM
+AAGRGPADMAVLEGGVLLIETSEELPSAGEVRRLLRILGERGVLGAVDAVLAARPPTSSF
+EAPRGAEERARRSAEQADVVVEEVGRYNPDAVVCVGVPFGHTRPQWVLPHGGVMTVDGVE
+RRVWAEFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa882ae2576ea3dcda653f087a433307c5877b8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001917.fa
@@ -0,0 +1,18 @@
+>0_1993
+MLVLLILATRLPGVVAGERLSVWDVAYLLLAVVVLVSEWRDYRAAVRRARR
+>1_1710
+MTIRPHSDPVTPDATWRDVPVLGFTVAAGIAVLFCLVWLLRDGLTTDYTWGLLLSPVLMS
+VPGAAVMVLWERLLARVPRLAATLVAVAALLALGLVLAWWLVEVNAQTHLFTGSTFWLLA
+VAPVCAGLAWLAHRLLPPARRPVGEPPAALDDDAWARRLAGVLRLRKDLPDARVAEIVRD
+ARARGAAAGRPLAEELGSPESYAAGFQKDRVAAPRRRAWAVTALVLLILATRLPGVVAGE
+RLSAWDVAYLLVAVVVLVWTWLDYRAAVRRARR
+>2_748
+MSTHDHDHDPADPRRATTSAPASLEPEIEAMHAARGNEEDRDWALLLVGVLVVDGVSTAA
+ARRHLRRAAEAVAQSGEGPDELFGTPVEFAAQMRADAAEAGEPIVDSTPDASWRDVPVVG
+FTVAAAISVLFFVVWLVRDGLTTEYSWGLLAGPVLMSLLGVGAMTLWERLLPRVSRLVAV
+LAAGAAFVVVVGGLAGWLVTGGGTETLFTGSTFWLLALAPVHAALAWLANRVLPEARPVA
+TSSADPLDDDAWARELAGTLRLRMQLSDARIREIVREAQAHAADAGRPLAEEFGAPAGYA
+SRFAKDGVAGKRRMAWFFTALAGLVVLTNVAGAVEDGGIDAWSVAQILVLVLVVGVSWRE
+YRAAVRRRDAVAPGAGGR
+>4_1928
+MLLILATRLPGVVAGERPSAWDVAYLLLAVVVLVSEWCGYRAAVRRARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6ed1309dfefc426b49fcba474106afc85bc312b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001928.fa
@@ -0,0 +1,35 @@
+>0_2094
+MSTAAPAPARPTTATSRPPADSPLDSRLPAILRAEPVSRHMRIVLYVIVGLMVLGEILTL
+VLGPMVAAGLSADPELAAIFEEDGGLTGERREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGSAFGLAGLVEADHAHLTPQAFSGGVILGAAMVTRYSHRVFVWFALGALILLTVAGE
+ALTDGTWADEDSLKGVMVVTLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPEKRAASEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELEELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSELEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLMAGPLGGCWVVRAELPLR
+>1_1818
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+MLGPTVAAGLSADPELAGILEEDGGLTGEGREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGCTFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGTWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPDKRAAAEKAIEEAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEAQLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLGGCWVVRAELPLR
+>2_584
+MATVSIGRPDSPVWGPFGARRLSLRIRLIVWISLAVVFGIDVVLAFSGTGVTAAEALPQL
+AGEYLLIGLIAQHAPLGVIAYAIAFTAGARWWDYEALSIVFAGAALMLGLSAQRGLLLLA
+GGLFAAWFVIAGPVLGSFSTAAAVAFAVSAALGVAAGLGLRWLARRFDSALRLAEERQTQ
+LEQAQRDERHRLALELHDVVGHGLTVIALQAGMLPTVTSPVQRTEVEQAIADTARQSLTD
+LRTMLGVLRGSAPGLGPAEDAEPPRPVRELVAEYRDRLTAAGFDVHVRLEAEAEVPDSLR
+HTLRRIVQEASTNVLRHAEPGGRVDVEIRHDGCETSVLVRSPLPARRRQEPAPHSGYGLA
+GMDERVRILGGRITHGPVDGSWVLDVTLPSQERAAQA
+>4_2038
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+VLGPTVAAGLSADPELAALLEEDGGLTGEGREPLLRWVLFLAGVLVTLLFGWQPTLAAVF
+VLLGSAFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGSWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQKDPEKRAAAEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLDGCWVVRAELPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c7e6e4917499b9727f04d30e8bbe32401db95d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001931.fa
@@ -0,0 +1,44 @@
+>0_2111
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALDRFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSATGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>1_1836
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>2_562
+MSSAPPDPADASSGRGGPRPRRQSSLARRTGAGVVVILLITLTAFALFAGNTTRALTAES
+ASRNTTAAWTRAAEQLASLEAGTAFDAEPTAGDPQVPGTLGQPEGTVVALVSPADLEDHQ
+AGTLRGHRVGKAGESVPLDARQSHDIIHAIRGEPIGAPVDAAVSGEGYRFKALPMTSPGP
+WVGADQLLVVGVPTGALTAVSRRGLLMVVLGLSLTVVVTALAVFLWLRRGLAPLGEVAAM
+AERVAGMDLAHTGIDRRQTRMPKRLLQGPDEVVVVAEAMDRFTGAVEDALEERRRQEQQL
+RSFIADASHELRTPLASVRGYAEMIAMTEDLSETGRRSLDRVLHQAGRMSALVDDMLLLE
+RLESVSRGRAVGLAPSGEVPAADPVDLPEVLLEAVVDARAAWPDHQWVLDLPETLGEEGQ
+GCVTGDPAQLARLVGNLLSNGAKHTPAGTTVTTSLRIGRPLPHQVVVSVHDDGGGIPAEH
+RERLFERFARGASAGGPGREPSTGLGLAIVRSIARSHGGEASVASEAGWTRFDVVLPCAR
+WTARAQAEAAGRGGPEAPEGTGAPRE
+>4_2057
+MSSGLPETAAVPSGHGSTRRTQPTSLARRIGAGVLLILVATILAYSFFAAGITKALLAES
+ASRDASEAWIRASEQLTAPSPGGGGDARPGEGYLRAPGTLGQPEGTVVALVPLSGLEAHQ
+QDALTGHRVGDTGESVPLTAQEAHDLLHAVRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVARQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72d296567dab308afb2898df4b08e720f7311784
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001934.fa
@@ -0,0 +1,8 @@
+>0_2131
+MPHATLASVTRRPDAPPPADPRARAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>1_1855
+MPRATLASVTRRPDAPPPADPRTRAALRAVLTVLAVMAVLFAAVVLTLAYGPAR
+>2_532
+MPRATLASVTHHPDAPPPADPRTRAALRAVLTVLAVLAVLFAAVVLTLAYGPAR
+>4_2076
+MPHATLASVTRRPDAPPPVDPRTRAALRAVLTVLAVMAVLFAAVVLMLAYGPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5c991c7b165d193b49f07245f7471ac1f4d1f21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001936.fa
@@ -0,0 +1,12 @@
+>0_2142
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>1_1866
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
+>2_522
+MTHHDDDRSALAAGETYLVHILETSTPPGNPEHYRITDAVEAHHAETGSWDIEAAGPDAA
+RELLARHGR
+>4_2087
+MTHHERDDRQALAAGETYLIHVLETSDPPGNPDHYRITDAVEAHHASTGSYDVEAGGLDA
+ARELLARHAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001943.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f453694a98512cc1ca6bed8f2df0da72fa5e094e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001943.fa
@@ -0,0 +1,36 @@
+>0_2161
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARLGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>1_1888
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAANPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAIGAFTAFLDDADVALVGVEPGGRSAAKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFASVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDARILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>3_444
+MTHRNPEDNALRAADAARPEPRTLAEATDLVHTPDLTAGADGMFGTYGGAVLPPELAGPM
+AEVAEAYEEARHDPEFYAEYRRLLRDVVGRPSPLTPLDRLSDELGGARIVLKREDLNHTG
+AHKINHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGSIDVAKQHP
+NVVRMRLLGATVVSVDREGRSLKEAVDSAFDVYASDPAHYLFAIGSVVGPHPFPTIVRDF
+QAVVGREARAQFLERYGALPSAVVAAVGGGSNAMGAFTAFLDDADVRLIGVEPGGRSATK
+GEHAMSMAQGVDGVLHGMATKVLQDEQGVPDPVHSIASGLDYPGVGPQHARLAQLGRVEY
+VAEDDAAVLEAFQRLTKLEGIIPALESAHAVARAIRMAPGLGTDQRILVNLSGRGDKDVD
+YVAETLGLTGDADEVVR
+>4_2101
+MTHRNPEDNALRGAAEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a8418068612c65df295a2811bf7683254888b9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001944.fa
@@ -0,0 +1,20 @@
+>0_2163
+MTLMWGAVAASSLLVGAVLATLHRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKRRRHLLIQWSLVTVVCALATWGGGLIADVAS
+PALTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
+>1_1889
+MTLMWGAVAASSLLVGAVLATLRRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKTRRHLLVQWSLVAVVCALATWGGGLIADVAS
+PTLTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
+>3_1205
+MTQILLWGVVSASSLLLGALLALARDWHRPTIGRILAFGAGALIASVSLELAEEGVNTGG
+AVAVGVGLALGAAAYFTANRVVERRGGGSGGGSGAALTVGALLDGIPEQVVLGVGLAAGG
+EISLALVVAIFVSNLPEAIGSSADLLRAGKTRRHVLTQWSVVTVVCILATVVGGLLAELA
+TPGMTAGVQGFAAGALLVMLIDTMIPEAREQGGETAGLVTVVGFALACGLSLLG
+>4_2102
+MTLMWGAVAASSLLVGAVLATLRRWHMGTIGLVLAFGAGALIASVSFELAEAGVQAAGPA
+AVGIGLTLGAAAYFLGDRAVERSAARSGGSSSGAALTVGALLDGIPEQLVLGIGLAAGEG
+VSLALLVAIFMSNLPESIAATADSLDGGKTRRHLLIQWSLVAVVCALATWGGGLIADGAS
+PALTGGIQGFAAGALLVMLIDTMIPEAREKGGEKAGLLTVVGFALGAFLSLVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4681d076ac65765709468f8bf8d6cd530bf5bc17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001948.fa
@@ -0,0 +1,22 @@
+>0_2212
+MPHSDPVPEPFVLTLGSVLDAAGLDPHEVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HLGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGGLQSMVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSNTPQAQIDAAEKHYKEALMTRRFGLNRN
+>1_1915
+MESTQPVPEPFVLTLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQH
+HVGKFPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERHRYYDVAPVPLLASLEE
+RLVVEWSADPVNWAKRGPLAARFPVLEIADPTTEAFPGFDHVLLSYGDLQSLVTETRYAG
+WRTALQAVRGIYLIADETAGQCYVGKADGERGVLGRWAAYARDGHGGNVALRDALELDPA
+QPERYTFSLLRVFGSSTPQAQIDAAEKHYKEALMTRRFGLNRN
+>2_441
+MESTQPFVLSLGAVLAAAGLDPHDVLAIRHTYKESGLPSRAAATPERVLAYTREQHHVGK
+FPKEPARHWLIFMGEGGRRSRLTAVYENRGEAVAERTERYRYYDVAPVPLLASLEERLVV
+EWSADPVNWAKRGPLAARFPVLEIADPSTEAFPGFDHVLLSYGDLQSMVTETRYAGWRTA
+LEAVRGIYLIADETAGQCYVGKADGERGVLGRWEAYARDGHGGNVALRDALELDPAQPER
+YTFSLLRVFGSNTPQVQIDAAEKHYKEALMTRRFGLNRN
+>3_391
+MPLLASLEERLVVEWSADPVNWVKRGHLAARFPVLEIADSTTEAFPGFDHVLLSYGDLQS
+MVTETRYAGWRTALQAVHGIYLIADDAASQCYVGKADGERGVLGRWEAYARDGHGGNVAI
+RDALELDPAQPERYTFSLLRVFGSNTPQAQIDAAEKHYKDALMTRRFGLNRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2f5652cee4dce66288a016f984d592b99d83436
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001950.fa
@@ -0,0 +1,32 @@
+>0_2223
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAETITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>1_1925
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTTGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMERQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>2_435
+MPSPTPFHAEADSFLGRADVVGLDALFSDQEKATALAVRAFVDEHLRPHIASWYEDAVFP
+REIVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIH
+KHGSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQETGGDWVIDGVKRWIG
+LATLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVR
+LPASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLAS
+HQLTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIARDAREM
+LGGNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
+>4_2163
+MTTPFHAEADSFLGRADVVGLDSLFSAEEKAVALQVRGFVDEHIRPHIARWYDDAVFPRE
+IVPELGRLGVLGMPYEGHGMPGRSAVEYGLAAQELEAGDSGLRTFVSVQGSLAMGAIHKH
+GSEEQKAQWLPRMTAGEAVGCFGLTEPGAGSDPASMTTTARQEPGGDWVLDGVKRWIGLA
+TLADVAIIWAQTGEPGDGRGVRGFVVPTDTPGFRAEAITQKLSMRASVQCEIHLDGVRLP
+ASAMLPADSAVGLKGPFQCLNEARYGIIWGAMGAARDSFDAVLDYAMQRQQFGVPLASHQ
+LTQAKLADMAVAIGKGYLLAHQIGRAKDAGPLTPAMISAGKLDNCRVAIGIAREAREMLG
+GNGITLEHSPLRHANNLESVRTYEGTDEVHQLTLGRHLTGIGAFAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b43af5f842771a78f8c1f96445a8f50dfc196d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001954.fa
@@ -0,0 +1,33 @@
+>1_224
+MTWVVTGGAGYIGAHVVRALQGAGMDVAVVDDLSTGFADFVPADVPLLRADVGDVGQVAT
+YLTRVGAAGVVHVAGYKFAGESVREPLHTYRVNVRGTLGVLEAMERAGVPAIVFSSSAAV
+YGTPDVERVTEATATAPESPYGESKLIGEWLLADQGRATGLRHTSLRYFNVVGSADPALS
+DTSPHNLFPLVFRALDRGERPRLFGADHPTPDGTCVRDYVHVADVARAHVAAARALAESR
+ALAPVYNLGSGAGTSVRQIMEAVGRVTGRDVDPVVEPRRPGDPARIVADGSLAARDLGWE
+NRHTVEDMVRSAWEARRPPETR
+>2_1199
+MPHDESMCMMNVSAPEPTRPQLPPLARHALLIIWDSVSWILALLAFLVVRYDFGLSPTQW
+DWVLAFTLIAVVGQVAAGLVTQFYLGRHRVGSFSDAGWTAVIVCAIALAIGLALSVAAPA
+FPRGVALTMPPLALVIMLAGRFLVRNVAAGRPRADASAAVPAIVYGAGNAGHQVSQLMRQ
+AEEPPYRIVGFVDDDKGKSRLRIHGLGVRGRGTDLAEVAAELGAEAVIYAISNADAEHVE
+WVSRVCTEEGLDLVVVPPLREMVGGKVTLGSLRHLSVTDLLGRRPISTDISAISDYVSGK
+VVLVTGAGGSIGSELAVQLHHLGPAKLLLLDRDESALHGVQLDIYGNGLLDTDDIILCDI
+RDEQALQAVFEHHRPQVVFHAAALKHLPMLERFPLEGWRTNVLGTRNVLQAAHSVGVQRF
+VNISTDKAAAPTSVLGATKRLAERLTAWHATTYDLPYLSVRFGNVLGSRGSVLISFRNQI
+EKGGPVTVTHPDVTRYFMTIPEACELVLQAGAIGNPGEVLVLDMGQPVKILDVAKRMIAE
+SGQNIDIHFTGLRPGEKMHEVLFSNAEANATSQHPMISEVQVPDLDPVVVAELPSDRESI
+LAMIDDEPPVERADDTQTPGLDQAGARP
+>2_2384
+MTWVVTGGAGYIGAHVVRAFRERGLPVAVVDDLSTGHREFVPDGVPFFHADVTDTAALTA
+VLRENEAEGVVHVAGYKYAGESVRVPLTAYRANVQGTASVLDAMAAAQVQSVVFSSSAAV
+YGTPAVERVTEDTPPAPESPYGESKLIGEWLLRDQERAVGIRHTSLRYFNVVGSGWADIT
+DLSPHNLFPLVFSALERGERPHIFGDDYPTPDGTCIRDYVHVQDVAEAHVAAARALTSGV
+GLHSVYNLGSGQGTSVHEIMAAVRDVTGVTDPPEVLDRRPGDPARIVADGTLAAQDLGWR
+MRHSVEDMVRSAWDAHRRLGISASGDE
+>4_811
+MRLLVTGGAGYIGSHFVSVARQQGRADIVVVDDFSTGLRQRVPADVPVYTIDLASDAAVA
+TLTTLLKEESIDVVVHFAAKKVVADSVVQPEDYFRSNVGATVNVLAAMRAAGAASMIFSS
+SAAVYGEPDSSIVFEDTPTVPINPYGQSKLVSELALANASRAWGLRAVALRYFNVAGAED
+AILADTTTTNLMPAIRDVITRGQRLSVFGDDYPTVDGTCVRDYVHVVDLAEAHLAALPAV
+QGSTDPATRIYNVGTGSGSSVLEVVDAFRRRPGVDLDYDIQPRRPGDPGALTANVSLIEK
+ELGWVARYTRDDIVTSVIDFPPRLVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2114fdc7098604bcc5b1f4f4e5e2f58a6efaf83d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001957.fa
@@ -0,0 +1,26 @@
+>1_307
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>2_2223
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLRFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYKTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>3_1786
+MIMGFIDQMRAKGHAVESICRVLRQEGCQIAARTYRAWRRRSASARDTSDAVLLNVLHDL
+VGTPEGLYGRRKMTAWLRREGHQVGAGRVDRLMRVAGMNGVRRGRPVRTTVPAKDGCRAG
+DLLNRDFTAAAPNTKWVADFTYVRTWAGFVYVAFVLDCYSQRILAWHAATAKTTPLVLTP
+LRIALWDRDRHGHPVQPGELIAHSDAGSQYTSLCFAEHLAAEGIAASIGTVADAYDNALM
+ECVIGLYRTECITTTIFHNGPYKTIADVEYATAGWVEWYNNRRLHSSLAMTTPAEYETAY
+YAALNRELAPT
+>4_567
+MRVAGMNGVRRGRPVRTTVPAKDGCRAGDLLNRDFTAAAPNTKWVADFTYVRTWAGFVYV
+AFVLDCYSQRILAWHAATAKTTPLVLTPLRTALWDRDRHGHPVQPGELIAHSDAGSQYTS
+LRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADVEYAT
+AGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68fb5a52bdf8b177c7781ec226b7150bf44db5ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001960.fa
@@ -0,0 +1,28 @@
+>1_1596
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKARLLISALGHRVFESADGSH
+AAAAAGRATQAPEAAPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDDA
+>2_883
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>3_823
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>4_1816
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKAKLLISALGHRVFESADGSH
+AAAAAGRATQAPEAEPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001967.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..157b2d5978e46a2d4682683740e84010ff36f540
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001967.fa
@@ -0,0 +1,36 @@
+>1_1652
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
+>2_830
+MTLADAYVFDAVRTPFGKIGGKLAGTRPDDLAAHVIRTIVDRAPGLEGLRRESAQDVADE
+LKGRPIEAGTDRARPDRIDEVVFGNANGAGEENRNVGRMASLLAGLPVSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVMLVGGVESMSRAPWVLPKTSRPFPLHNLEAVNTTLGWRLI
+NDAMPKDWTISLGESTERLRERFGITRERQDEFAARSHQLTAKAWEEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRKEDGTVTAGNASPMNDGASAALLGSEKGAEILGLQ
+PIARIAGRATAANEPDFFGYAPVEAVNLALKRAGIGWKDVAAVELNEAFAAQSLACLDAW
+GVDPEIVNAWGGAIAVGHPLGASGTRVLGTLARRLQDTGDRWGVAALCIGVGQGIAVVLE
+NVDAR
+>3_768
+MCVDRTSLARPRGRAYGEAMSLTDAYVFDAVRTPFGKIGGKLAGVRPDDMAAHVVRALVD
+RAPGLEGLRAESAQAVADAAAGHPIEAGTDAAAPQKIDDVVFGNANGAGEENRNVGRMAT
+LLAGLPLSIPGTTVNRLCGSSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTSR
+PFPMHNLEAANTTLGWRLINDAMPSQWTVSLGEATEQLRERFDVSRERQDEFAARSHQLT
+AKAWDEGRYDDLVTVVPGTDLERDETVRPDSTPETLAGLRTVFRKENGTVTAGNASPMND
+GASAAFLGSEKGAEVLGLPPIARIAGRATAANEPNFFGYAPVEAANVALRRAGITWKDVA
+AVELNEAFAAQSLVCVDAWGVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLQATGER
+WGVAALCIGVGQGIAVVLENVDAR
+>4_1870
+MSLTDAYVFDAVRTPFGKVGGALSGVRPDDMAAHVVRTLVDRAPGLEGLRAASAQAVADA
+AAGRPIEAGTDAAAPQRIDEVVFGNANGAGEENRNVARMATLLAGLPLSIPGTTVNRLCG
+SSLDAAIIASRQINTGEADVVLVGGVESMSRAPWVLPKTTRPFPMHDLAAANTTLGWRLI
+NDAMPPEWTVSLGEATELLRERFGISRERQDEFAARSHRLTARAWDEGRYDSLVAAVPGT
+DLERDETVRPDSTPETLAGLRTVFRRENGTVTAGNASPMNDGASAALLGSSTGADVLGLE
+PLARIAGRATAANEPDFFGYAPVEAVNRALSRAGIGWKDVAAVELNEAFAAQSLACTDAW
+GVDPEIVNAWGGAIAIGHPLGASGTRVLGTLARRLEASGERWGVAALCIGVGQGIAVVLE
+NVAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af7a43c28d586680471f995f412664fddad0ff4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001970.fa
@@ -0,0 +1,24 @@
+>1_1657
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
+>2_826
+MAQPTVTTTLLKAAKSPARVLLVGAGLGTGVHALWSLAAQRMAEDTLVIGYDLPGHGASA
+PHADPYTIAELADAVVAAVARLKDEGAIPADVPLAYAGVSLNGCVALQLALEHADVVSGV
+AVVCSAAKIGEAKAWHERAELVEKAGTPTMVAGSAERWFAPGFIERHPERTTDLLHTLQE
+ADRHSYARLCEALAGFDVRERLGEIRVPVLTVHGAHDAVTPPAAGEEIAAAVPGTTVVAL
+DDAAHQAPLEQPVATAEALAAFLTTVQEAAK
+>3_760
+MTTPEVAVTLLKPAEAPTRVLVAGAGLGTGVEALWSLAARELPADTLVVGWDLPGHGASA
+PHDAPLTVADLADAVAAAVGRLRAEGTIPADVPVHYAGVSLNGCVALQLALDHADTFASA
+TVICSAAKIGEKDAWLERAELVESAGTPTQVEGSSKRWFAEVFIAEHPERATGLLHTLQQ
+ADRHSYARLCEALAEFDVRGRLGEDTVPLMTIHGVEDQVTAPAAGEEIAAAVPGTVVHAF
+EHTAHQAPLEQPERTAEALAAFLAR
+>4_1875
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e80598bb0e75fc632345afc9d921e572545ca6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001974.fa
@@ -0,0 +1,20 @@
+>1_1809
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
+>2_597
+MTAMTLTPVSPEELLERTEAGTAFVIDVRTPAEFAVEHIAGSYNVPLDTLKEHVRDVAER
+LHGDVVLVCASGARASDAQQRLTGAGFTEAAVLSGGIGSYAQAGGDVVRRGTGWGMERQV
+RMTAGSLVLAGVIASQIGSKRLALLAGGVGGGLVYSALSNTCAMVSVLDRMPWNRQDRER
+PASEVLGALPAGAARKA
+>3_522
+MTVNVTPITPADLQRELAQHPDTVVIDVRTPGEFEAQHIAGSYNVPLDLIQEHAAEVAAR
+LDGKAVLVCQSGSRAGTALDRLAEAGFTQARVLRGGIGAYAQAGGRVSGTGSRWSMERQV
+RMTAGSLALAGAVASQLGPKRFGLVPAAIGAGLSWSAVSNTCAMASVLSTMPWNRPTEQR
+SADQVLGALPGADADGARG
+>4_2029
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bb1a2c5f87c4113e188eb565a2d80cbfa1a9147
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001978.fa
@@ -0,0 +1,23 @@
+>2_715
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQGGFNRSSQHPLGIIGGMGDGQQGLGEEDQ
+>2_732
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQGGFNRSSQHPLGIIGGMGDGQQGLGEEDQ
+>2_2277
+MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH
+AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD
+LVERRFAAERPHQLWVADITYVRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGREGLVHHSDRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETV
+NGLYKAELIHSKRVWESVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSA
+PVAS
+>3_398
+MIAFIDEHRDQFGVEAICRTLRATECGFITSRGYRAAKTRPRSSRTLRDEILVEELRRIH
+AENYSVYGVRKMHHAMVRAGWQVGRDQVARLMRAAGLQGVRRGRKPITTRPAGEPDARPD
+LVERRFAAERPHQLWVADITYVRTITGFCYVPFITDVYSRRIVGWAVSASLHTQGLPLLA
+LEHALLSTGASRGRQGLIHHSDRGAQYVSLAYSDALITAGVSASVGTVGDSYDNALAESV
+NGLYKAELIHSKRVWESVEAVELATLKSVHRPRPRRRRSALPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001980.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e450ec8367f3cee06a4585c757f02fc6f0f77bae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001980.fa
@@ -0,0 +1,31 @@
+>2_2197
+MSSLNTVKDTATAAGTAELETDILVIGWGKGGKTLARTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARSTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRSRAPRRRRLRPRPPRSSRHRRSARAA
+>3_385
+MSEQKTTTPDLDPTGQAIATQAPLAERYDHVIVGGGMAAAKAVESIRELAPEASVAVVSA
+DTAAPVYRPDLSKTLWADADAHVEDSILATPDSEGTAPGERTAYRLGAEVTAIDPQAHTV
+TVDGRTVGYGSLLLATGAEPVAAGIPQSERVHTYRTVADYRRLKEASGPGTTAVVVGGGY
+IGTELAAGLTMAGTDVTLVVPHRPLLARMLPAELSAAVEATFQEKGVRIAEGRLASAAES
+GDAVTARLEDGTELRADLLVLALGVRPRATLAEAAGLALADQGVRVDDRLRTSAPDVYAA
+GDIATFPDALLGERRVEHADAAETQGATAGRNMVGADQAYTHTPFFWADLFDYGYEAIGE
+LDTRHRTVVDLATGEDGRPDPSTAVVYYADEAGHVRGVLLWNVWDSVPQARALIERTAQE
+PVADLGSLKGRIPLG
+>3_697
+MTPQHVLILGSGAAGAAAARTLASRDDVRVTLVTRTGETPYTRMLIKGIAFGQTPPEMIK
+LPLPQIEVIADTVLKVDTSAKQAQLTSGAQVSYDALIVATGSMPRSLPADVFGGDDAGQG
+RVTALHSVGDALGIRKLLTGLGRPARVAIYGGGIIAAETASSLQADGHMVTLVSRSSVPG
+VGAFGAPVAERLAADHAAKVQARFGRTLQHVDETESGVTITLNDGNPVVADFLLLALGTT
+PAAPSPWTNGIDVDDHLRAAADHVYAAGGVATHHDEALDAWRIDHWEDAAAQGAHAARAA
+LHDLGVSDDPGAYLPRSPYMAMVYGQMISGVGYTAGADAHLEAGEEFIVRHEIDGIVVGV
+TGIDAVGTVYQWGQQLHGVRA
+>3_2069
+MSSLDTVKDTVTTAGTAELETDILVIGWGKGGKTLAKTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARFTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRTRAPRRAVVVGSGPVGLELASMLAGFGAEVTVLVRGEQILPDESDAVRDSLV
+EALQDRGVRLATGASATGFAEADGGLRVDLEEGEPIAADIVVLATGRASTAEALDPAAAG
+IELDEKGFIAVDEHLRTSAPDVWAVGDVNGGPQQTYISLDDHRIVTGQLAGDGAYSRADR
+VAVPTTVFTTPPLGSVGMTAEQAREAGHEVKVASKPVAKIAAMPRPKIEEDAHGVIEVVV
+DAATDLVLGARLHCVEAQELVNLVALAMRADVTASALRDGIWTHPSATEALNEVLGELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892a5506e9baa6735c183e6be252cf82828e0a32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001983.fa
@@ -0,0 +1,23 @@
+>3_406
+MGAMTDPTSRALRLLGLLEARAVWTGAELAERLGVTSRTLRRDVDRLRTLGYVVEADPGP
+GGGYALGRGQVVPPLLLDEDQAVAVTLALTRAAHAGDGVAAESALRALATLDALMPADLR
+HRLEGLRAASTVGAGDGPPVGPELLACADAVRRRVRLTFGYRDRRGARTERRVEPHRLVA
+RARAWLLVAHDLDRDDWRTFRVDRIVDPAVGTWAFTPRPDLAEALARLDEPTPPEAWRHR
+VSVRVHAPLESVRASLPATAGRLTALDARTTAFETGADDPAEAARWLALLGHEFEVLGDE
+PVRAAVAALADRLHRSTVQVLRG
+>3_627
+MASPCRRFRTPNVRNPRHAGVMADTSARILRLLSLLEARVEWPGGDLAERLGVSARTVRR
+DIDTLRELGYPVEAVPGPGGGYRLGAAGKLPPLVLDDDQAIAIALALQTAPATVTGIDDA
+VARALTTLRQVMPARLRAASEAFEVTALRNYWEFSAPPIDVATLQVVGSAIRTSSCLRFD
+YADPDGRVPGPGDADFRPPHDVEPHHLVVWAGRWYLVARDRNHGTWGTYRVDRIRPKTPA
+GRPFTPTPLDPDDLNRLVVQNPDRGDTPGQWQCVGTATLPLPADVVARWAPGGSAVAPID
+RQSCRLTIGGWSWAGVAGLFITFDTDLTNVEPSGLRDALATIRRRLEPAPLGGLRPTLQQ
+>3_1747
+MPSVKIPPLLLDADEVCSLVTGLLLLEAGGVNEAATVRTKLEQLLPPKLRQQAAATALAT
+QVITPVAAPVDWRLLGVLAEAVAQGQNLRFTYTDQHSKVSERHIRPYRHALRKGAWYLIA
+YDIQRTDWRLFRLDRIQHATPEPTATGIDVPVFPSPSIEEWLTTDFGRLPASAG
+>3_1783
+MLGYDIQSHPGPGGAYVLAPSIKIPPLLLDADEVCALVTGLLILEAGFADDSATTVRAKL
+ERLLPPSLRQRAVAAAAATQVLTATHAFDWPALGMIADTIAVGQHLGFAYTDQHGHASNR
+IVQPYRQVLRHGIWYLVAYDTQREDWRLFRSDRVHEPEPRTPAPGYEAHPFPDESIHRWL
+ITDFGRAAQHVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001984.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecd5a083df1f1f12812a38cdb5c3ed9d61be9f31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001984.fa
@@ -0,0 +1,24 @@
+>3_644
+MDTPVMASLPAGVITLRDARRSQTREVTLEAFEIAVHPVHDQGSGLPWAPFTWFDAVAYC
+NELSRASGLQEAYTWQGRTVDWDTAADGYRLPTEAEWEYACRAGTTSPTYGLVEDIAWTS
+LDDVDSPQPVGSKAPNAWGLHDMLGNVWEWCWDYADPARYGDYRSLRGGGWADEPWSVRA
+SVRRGSAPNAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLWEIAR
+>3_681
+MNQPSMATLSSGKITLRDARRRTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTRAGGGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+ISLDHLEGPQPVGMKKANPYGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLREI
+FA
+>3_704
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLRDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTHAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+TSLDHLEGPQPVGMKKANPHGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAICGPLPVGWTPLREI
+FA
+>3_1369
+MQGAIDDDMMLTGAVDEWRFIVQTLADRLDQAAHAAGTPVSTAADVDAGTPAGTVSSDHQ
+AGPDMVVIPAGTYTAGSTDAEHEAWGVPENRRDFELPQREVTIAEPFALGRTEVTVEQFQ
+AFVDDTGYQVCGGSRWWDPEDPSAMTFNPELSYLDPGFEQTPDSPSVALTRQDAQAYVDW
+LSETTGESDRLPTEDEWEWAARGGADTAFFWGDTLDEAARYANTYDTVSQAVNGFPWESL
+SVTDRFAHTAPVGSFEADGFGLYDVTGNARAFMADDWIEDLSGTAGDGSVHDGPVPFPVV
+RGGAWNYQPQNLRLDYRGAYLSAEVATTMFGFRVVRDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b46679bfcc084313e7a70bf8405ac77af809e6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001985.fa
@@ -0,0 +1,12 @@
+>3_657
+MAYLFLIIAIIFEVAGALSLRMATSGSKKKGLWLLAVLGGYGIAFFGITMALVEGLALGV
+AYGIWAASGVALTAVLSRILFKEPLTKVMAAGIGLIIVGVLMIELGAAH
+>3_658
+MKWVFLAGAIALEVTGSLSLKAAVDAPGFFALVAVGYIGAFTLLAGALKQGMPLGVGYGI
+WGAAGVALTAILSAVIFGEPLTALMTLGIAVVIGGVLCVELGSQAATKKREGTV
+>3_2173
+MQWLFLAGAVLSEVAATLCLRVAAAGRRGFYAAVAVGYVLAFVFLTLALRAGIGLGVAYG
+IWAAAGVALTAIASHVLFKEPLTRTMILGILLIMAGVLVIEIGSSSH
+>3_2174
+MTKWFLLAGAVGSEVIASLSLKAALTHPALYAVVLLGYVSAFTFLTLVLKRGMALGVAYG
+IWGALGVAATAVLSAVLFDERITAMMGIGIALVIAGVLMVELGSHHTPDTDEQQAGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f47bd926be34989e21eeb4b15fb5f6b46c541b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001987.fa
@@ -0,0 +1,9 @@
+>0_23
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVAVSVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>1_1992
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>4_23
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dff98f3117c4d34d092cf2713d25bcf186beb317
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001989.fa
@@ -0,0 +1,13 @@
+>0_25
+MSHASTVPPAADAPSRWGRAAGLSGLVMPAVLAAFSLYLLLGSLTMDTDGADFPGPDFFP
+LILSVAGLVIAAALAVEVVRVRQAPEG
+>1_1994
+MSQASTVSPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
+>4_25
+MSHASTVPPAADAPSRWGRAAGLSALVMPAVLAAFSLYLLLGSLAMDTEGADFPGPDFFP
+LILAVAGLVIAAALAVEVVRVRQAPEGQADADGEVGQAAGPLTLFHSDFGALAWCFLGFL
+AFAVLLPWLGWILAGALLFWCVTRAFGAPHPVFDILVALFVSSLAYLGFAVALGLTLPSG
+ILGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001991.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb48db94d1833be5a6da927455a189609b779500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001991.fa
@@ -0,0 +1,30 @@
+>0_34
+MTVDARRLVDKLWSYVHVLRDDGVGVLDYTEQLTYLLFLKMAHERATRPLKPEQVLPEQY
+SWQRLMDARGQDLEAVYTGMLQGLSREPGVVGTIFRKAQNRIQDPAKLRRIIVDLIGAQQ
+WSQSGTDLNGDAYEAILARSASDGSSGAGQYFTPRALIEAIVDAVDPTVEDTVVDPAAGT
+GGFLLVAHDHASREASSMTPTQREKLRDDFVHGYELVDATARLAAMNLLLHGMGRYDGDS
+LIDVRDSLTSAPSRRWSVVLSNPPFGRKSSMTVVGDDGREVREDREIVRQDFVATTSNKQ
+LNFVQHIMTILDVNGRAAVVLPDNVLFEGGAGEVIRRKLLTDFHLHTLLRLPTGIFYAQG
+VKANVIFFDKKPARPGEVWTDAMAVYDLRTNKHFTLKQSPLRRADLDEFVSGYRRPEAQV
+GERWKTFTYDELIARDKANLDITWLRDETLEDMDNLPSPDVLAREIVEDLTAALAEFEAV
+AVSLEEQLSSADGTQEDR
+>2_201
+MPYAVRVITGDLKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAQEKRAAF
+MNGPIEDPKFTPEQDHLRWSRFRDLDPDTMFLTVSDAVFPFLREYGRQVGGEDSTYSAHM
+KDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLASSGVNGQFRTPRHIIDL
+MVRMTAPTPADEICDPACGTAGFLVAASEFIREEHPQVLVDAQQREHFHRSMFHGYDFDS
+TMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAADLQ
+RVVKTKKTELLFMALFLRLLKPGGRAAVIVPDGVLFGFTKAHREIRRLLVEEHLLEAVVK
+LPSGVFKPYAGVSTAILFFTKTGTGGTEDVWFYDVRADGFSLDDKRNRVEANDLPDVLER
+WRNRGAEADRARTEQSFLVPRQEIVDNGYDLSLNRYKEIEFEETEHRDPLEIIAELEQLD
+DEIRAGLAELKEMLR
+>4_180
+MHPIAYADPVITGELKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAAQRR
+AEFTGRPIEDAKFAPHQDHLRWSRFKELDPDTMFLTVSDSVFPFLREYGRQVGGEDSTYS
+SHMKDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLQSSGVNGQFRTPRHI
+IDLMVRMTAPTPADEICDPACGTAGFLVAASEFVREEHPEALVDATQRRHFHRSMFHGYD
+FDSTMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAA
+DLQRVVKTKKTELLFMALFLRLLKPGGRAAVVVPDGVLFGSTKAHREIRRLLVEEHLLEA
+VVKLPSGVFKPYAGVSTAVLFFTKTGTGGTEDVWFYDVQADGFSLDDKRNPVEANDLPDV
+LERWRNREGEAGRARTEQSFLVPKQEIADNAYDLSLNRYKEIEFEEAEHRDPLEIIAKLE
+KLDDEIRAGLAELKEMLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5671957c4a8025cc1073391ef1a15d51470586ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001994.fa
@@ -0,0 +1,18 @@
+>0_159
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>0_2017
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPMPPPTHPDSRFYGTTEVPNRVEKLAGTVQDKLHRE
+>1_1731
+MYIHKQKLQHVSSPEKPDAVYARKLQEVIGGQYGEITVAMQYSFQAWNAHIPGKYRDLLF
+STAAEEFGHVEMLATMVAQLLEKAPVGITTDAIQDDPAVAAVIGGTDLQQAIVAGAGARP
+VDSMGNPWTGAYVTASGNLLADMTANLNAEMQGRTQVARLYHMTDDPGIRELLSFLLARD
+TMHQNQWAAAVKELQEDGLEEMPVPSNFPQKKEATEHSYTHYEFSDGQATAEGSWAAGPT
+PDGKGEFSYSSEPPAGVPLPPPTHPDSRFYGTTEVPNRLEKLAGTVQDKLHRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36a129a04d439b9ce82d5da376f5c1e097e5aaee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001999.fa
@@ -0,0 +1,21 @@
+>0_265
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVVGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARIE
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVAREVLG
+>1_2231
+MDTHRATASLPWIDGPAVRAALSPRAAVDALEAALAAGLDPEADAPRTRVSTAAGQLLQM
+PSTRGSEVGAKLLTLTPDNPERGLPAIQGVYVLFGAPGTPGQAPRAVLDGVELTGLRTSA
+VSALGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDAGRAAALAARIT
+AELGVTASAAGPEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDAL
+ARRATVAVESRDSAAREAGDVTLAIDSGALAGIEDTVTLAELVAGTARRREGAPALFVTT
+GMPWQDLVVASAVARVVLG
+>4_263
+MSTPISTAPGLPWIDGPAVRSALSPCAAVDALEAALAAGLDPEADAPRTRVATAAGQLLQ
+MPSTRGTEVGTKLLTLTPDNPERGLPVIQGVYVLFGAPGAPGQAPRAVLDGVELTGLRTS
+AVSTLGVRLLADASPRHLVVFGTGVQAWEHALTFQDVFGLERVSVVGRDADRAAALAARI
+EAELGVTASTADSEAVAEADVVVTCTAATAPLFDGTLVPEHATVVAMGSHTTDARETDDA
+LARRATVAVESRDSAAREAGDVTLAVASGALAGIEDTVTLAELVAGTARRREGEPALFVT
+TGMPWQDLVVASAVARVVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b02cf8c1c905474ada699be6c7e69c4dd5286dc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002001.fa
@@ -0,0 +1,15 @@
+>0_357
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGASMWVGLTGTEELA
+GVKRLLPGGAVTELIIEGWSGMALHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRT
+>2_2529
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGAAMWVGLTGTEELA
+GVKRLLPGGAVTELIVEGWDGMVLHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRA
+>4_363
+MFAIARSEMTQLVRNRLVAASSLFIPLAFSAVLIFNRENFGGTPVTAALILVTVTAMGTY
+ITATTTLASRRQNLFLKRLRSTSAKDASILSGLVLPIALVNLVQAGVIVAILSVVGTPPV
+GVVAVVAAVVVLELMFVGAAIATAGLTNSPDHAQVTTLPLFVVALGASMWVGLTGTEELA
+GVKRLLPGGAVTELIIEGWSGMALHEAVSLLLPSLAFVVAAFAMAKSTFRWEPRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f68b46789d459babe587f52d42a92078317f8099
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002005.fa
@@ -0,0 +1,15 @@
+>0_475
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>1_205
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
+>4_474
+MTYRDDLWDVAAGNHGVITTTEAEEAGVPAVEVRKLAQRGVLRRLAHGVYLHRQVPRDRF
+TDAAEAVATGGEDAFLDWDAVLSLYDLALVDPSVVRVGVTRRYRGSPRAHVRVTRRRPPP
+GDEDLTFHGGVRGLTINQALREALDRIPLERVAAAIEEARARGLLTVGEARSLKKDLEAR
+QNGGHRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcd4adceef4c9948e7bae99b9858d6a7953597c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002012.fa
@@ -0,0 +1,17 @@
+>0_575
+MTSPWVEDDELTDWEAPAAADDDGQTGTPLPYVDPEIAAELAGEGPPVWMGTRWREIEAE
+HQWEAWNTLRRWVDWFVAEYRLVTSVVPPCWYKHSDLTAELYAAMCMEYKVWEEQAPGLG
+PMMMWHPHVEMLTARLRRMVDEAGCAKIGQHKEPEAYGDRPAFNLDYDEDDFTAWAATTC
+EQHALERPEAGVKYVRARVFNGDGEEIALSNPVGLASRRTSTGVTAELMMTSSTPLAPGL
+RLTVPSATPGLEVGWQTSVNGHDWE
+>3_1765
+MSTHSPEPDDQYDDPGILDDQPDMFDTNALPEPPHPINWNLLSAQDLEAELLELNRWVDW
+LRHTYGLPASVIPPYWHRHPELLWELSALHLHWLCAYDPEQNGSAPLGWHRDFADARHRL
+RDWVTASGTRLDRDRPTRQTTWPGEEPQPTHGESVITDRDADFVQFIIDQVNERQAAEDA
+FYASLDDRIDPATGEVRDDVLGPEGG
+>3_2189
+MASPWVEDDEPDWSETAPLQDEGPTETSLPYVDPEVAAELAQEGPPVWMGTRWREIEAEH
+QWQAWNHLRRWVDWFVAEYRLGTSIVPACWYRHPDVTAELYAAMCMEYKVWDEQAPGLGP
+MMMWHPHVEMMTARLRRMVDEAGCAKIGRHKDPEAYGNRGAYELDYDESDWTRWAATERE
+EELIERPTEGVKYVRAKVVDSDGNVLGHSAPVGLRPVPNVVGVEAKVRVTSSTPAEPRMA
+VAVSSGRDDLGIEWEMSPDGAEWSTRPNDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f310ea840036d6383e0b7672051879174b43a01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002013.fa
@@ -0,0 +1,13 @@
+>0_582
+MNHRRRYPLVLLTVAIGAGVVVLDQGTKWWAENSLSTGERVPVLGDLLGLQLAYNPGAAF
+SLGATSTWIFTVISAVAVAAAIWFSLRVRTVSWALLVGCLGGAVTSHLGDRLLRPPSFGQ
+GHVVDFLAYGNWFIGNVADIFIVGGAAAAVLLTATSPDRDTADTPQ
+>1_1717
+MNHRRRYPLVLLTIAIGAGAVVLDQVTKWWAENSLSTGERVPLLGELLGLQLAYNPGAAF
+SFGANSTWIFTIISAVAVAAAIWFTLRVRTVSWAIVIGCLGGAVTSHLGDRLLRPPSFGQ
+GHVVDFLAYGNWFIGNIADIFIVGGALAAVLLTATVPDRGTVDVAR
+>2_2312
+MTAQDAVVVESTGGAPTRSRQALVVALVVAALALAIDQGSKVLAAAQLTQGERIPLVGDL
+FGLSLVYNPGAAFSIGSGATWIFTISGLLAAVAVVVFAARMRGARWGVALGLVLGGAVGN
+LVDRLVNSPAFGQGHVTDFLAYGDLFVGNVADVFVVAGVGLVCLNLLTQTPRTTAEGERT
+EEAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86d282bf73d5696da7ec2dff16b8ec719cc2412d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002017.fa
@@ -0,0 +1,11 @@
+>0_780
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESHDVEGDELRAFVRFQSRDG
+>1_521
+MTDSPIAADRDGIRYLSGVIPAADGGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIAS
+ELLRRVFARFGQVRQHVLLTDTEERQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
+>4_749
+MTDSPIAADRDGIRYLSGAIPAADDVRALYDAVGWSAYTADMDTLMGGLQGSATVVTAFD
+GGRLVGLARVVSDGHTIAYLQDILVDPGHQRRGIASELLRRVFARFGQVRQHVLLTDTEE
+RQRAFYEAHGFRESRDVEGDELRAFVRFQSRDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01c0e3862bc38f72ea851dfb87853c1b7e5049f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002021.fa
@@ -0,0 +1,15 @@
+>0_910
+MRMDLPLAPMDEPEPCAARVPLFTGLDLEQLRRVSALARPLVLEAGDALHLAGDRTDRLC
+VVHSGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVAATRLCTFSHAE
+VARLLAEHPGIGGRVMRTLAVRLAEAEQRLAREHQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLDPDALEALAAE
+>1_638
+MRMDLPLIPVDEPEPCAARVPLFTGLDLEQLRRVSALARPIVLEAGDALHLAGDRTDRLC
+VVHTGRLALTLGSATGRERVVRMVEPGDSVGEHEFLTGEPARHGARAVVATRLCTFSHAE
+VARLLAEHPGIGGRVMRALAVRLAEAEQRLAWERQPVTARIAGHLLGLPALRDEADLVVV
+LAAPKKDVASLLGTTPEAFSRGLRRLADDGLIAIEGPRVTLLNPDALEALAAE
+>2_1951
+MRRELTLTPVGEAEPCAARVPLFAGLEPDQLRRVSALARPFALEPGDVLHLPGARTERLW
+VVHTGGLALSLTSPTGRERVVRMAGPGDSVGEQEFLTGAAARHGVRAVAPTRLCTFSHEE
+IAGLMAEHPGIGRRVMRTLAVRLADAERRLAQERQPVAARIAGHLLELPAVHASGTPTVL
+LTAPKKDVASLLGTTPEAFSRGLRRLVDDGVVAVDGPRVRLLDADALEGLAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9121d3739aae8a3a0277a48b902190cd2b0bec68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002025.fa
@@ -0,0 +1,9 @@
+>0_997
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>1_719
+MARHGRDEDEAHEAPAGAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVIGCA
+MMGFALGIAWMYVERGRDGRDR
+>4_939
+MARHGRDEDEAHEAPAGAGTLAQWRIPLVGLLIGVGLGVVFGLGTERPWGTVLGCAMMGF
+ALGIAWMYVERGRDGRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f08921e192b31149492042202c54136664454fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002029.fa
@@ -0,0 +1,9 @@
+>0_1266
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>2_1548
+MTRARLEGAVMDLLWDHAEGLTAAEVRTLLHREGAPPALTTVHTALTRLAAKGRVRPAEG
+GRPRRFRAAVTREAHTAELLRDLLGSAPDREAVLAAFVGGISETDSAALRRLLD
+>3_1444
+MARARLEGAVLDALWDHPDGLTAQELRVRLEREDGAPAVTTVLTALSRLTAKGHVRRVGA
+RRPQVFAAARTREQHAAGLLQDILGSSPDHEAVLAAFVGGISDADAAALRRLLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eab8b1f9869abd1b276cc62c1ff5db19e31114bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002032.fa
@@ -0,0 +1,9 @@
+>0_1343
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>1_1084
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
+>4_1293
+MRITAFATNAPRGQLPVLELRHRRRARCEDRIRNAKDMGLMKFPLQGFAQNQVWCQIVQL
+AGVIVAWMQAIALAGHDARRWEPKRFRARLFEIPATIVRRCRHKILHSRLIAFEGVARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a801314ae16bc50ed86cd927508389d0a23896d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002035.fa
@@ -0,0 +1,10 @@
+>0_1454
+MRESGVMSRDVISDEVWAVIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPER
+FGNWNTIYKNVNRWAAQGVWERVLEKTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRP
+TGGLDELQEISGRAG
+>3_1710
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
+>3_2183
+MIGPLFPAPKSTGRPPVDRRAVVEATAWRFRTGAPWRDLPERFGNWNTIYKNFNRWAAQG
+VWERVLERTQSMAQQAGELDWVASIDSTIVRVHQHGATLPRPTGGPDELQEIRGRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eaeb03abb4a564e3219df3dd1d6f2d1bc05a67a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002036.fa
@@ -0,0 +1,24 @@
+>0_1539
+MTDSPLHLDRPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLAAGRALEAGVVSPIQAFG
+LDDFETACAAVGLVRA
+>1_1261
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAEAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVGALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRIVADVHLSGPNAYTLTGDLMAWGARQLAAGQAREAGVVSPIQAFG
+LDDFETACTAAGLVRA
+>4_1466
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEIGFVKD
+LKADLDATARRTGATLLPALGFEYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLVAGRAREAGVVSPIQAFG
+LDDFETACAAVGLVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8749e1c3dc4c3a333bea0d8ef27b35ec9d9ed1c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002037.fa
@@ -0,0 +1,21 @@
+>0_1542
+MRALVLQSYGGREAMALTDVPAPTAGAGEVLIRTRAVGLNPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDAVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
+>1_1264
+MRALVLQSYGGREAMALTDVPAPTAGAGEVLIRTRAVGLNPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDAVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
+>4_1469
+MRALVLQSYGGREAMALTDVPAPTVGAGEVLIRTRAVGLSPVDAMHREGDFKAIAPDDFP
+TVAGNELSGIVETVGAGVTAFAPGDTVITRVDPSGHGAFAELAAVRADWVAAAPARMPLT
+DAAGLPLAGLTAQQALGPEHLDLQPGERLLITGAAGGVGLIATRLAHLRGAHVTVTASAA
+GEPYVREAGADAVIDYRARTVAEGGERFDKVFDLIGGDQMAELLGSIEPGGRLVTIAGPP
+SPGSLRETARPSRRPLAAVVSRVASAKVRRAAKKAGVTYEFFLMHPDGAGLAELVRLVDA
+GELAVTVDSRYPLADWEQAFERLESHHAKGKVLLEF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2decb5b849c78f576dc5c1cbd44b1f6e4ec1291e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002040.fa
@@ -0,0 +1,24 @@
+>0_1564
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIAYGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGAGRVIVGAGGSATTDGGTGAAAALGVRFLDAAGEEFVPTGHTLTRIARIDSSPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDTDTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPAGLRR
+>2_1253
+MQRIIVIPDSFKGALSSREAGSAIAAGLASVTDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVIVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLTRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGPQGAAHVFGPQKGADPAAVASLDTGLVHLAGLVERDLGVAI
+DALPGSGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAADRAIPVIVLAGSVGQDADTLYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDVGRLVMACSPARLTR
+>3_1161
+MQSIIVIPDSFKGALSSREAGSAIATGLASATDAEVLVVPIADGGEGTVEAFVAAAGGAL
+RSATVCGVFYGERVPVHYGLIDPDVAVVETASCAGLPLASGREDTGRATTFGVGEQILDA
+VSAGARRVVVGAGGSATTDGGTGAAAALGVRFLDVAGEEFVPTGDTLIRIARIDSTPARD
+RLRDVDVEVMCDISNPLTGSQGAAHVFGPQKGADPASVASLDTGLVHLAGIVERDLGVAI
+DALPGAGAAGGLAGGLHAFIGATLKPGIDVVLETAGFHDLVKTADLVITGEGRIDGQSLA
+GKVPIGVAQAVRAAGRAIPVIVLAGSVGQDADILYDEGITAIVPIGRGPQDLATAIRRTA
+EDLTATARDIGRLVMACSPAGLTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88e935623d1eadd84b02f38652ca08b64c41ff1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002045.fa
@@ -0,0 +1,12 @@
+>0_1885
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCARLAMSAARAVTVFPEVAEARFAI
+TGTPSAPELEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>3_830
+MTATLEAPQAMGRTLSAAPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
+>4_1805
+MTATLEAPQAMGRTLSAVPPVLESPAPQPAAFRQRCALLAMSAARAVTVFPEVAEARFAI
+TGTPSAPALEVDCILRDGEDTAAVIETITVHLVEDLEELLGARFHERRLELVVDRSLPRV
+GVGVVSAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8e542d0e9286a4429d6c2b4dac05c924dd7767f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002046.fa
@@ -0,0 +1,18 @@
+>0_1901
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTPAPLDVRVDVLRDALDLTLPTRLASAHLLGTLRWCRDSAEVAALKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCRHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDAEPLPEPPAHALDADEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>1_1605
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTLAPLDVRVDVLRDALDLTLPTRLASVHLLGTLRWCRDSAEVAELKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCCHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDTEPLSESPAHALDVDEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>4_1828
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLMTAVHGVSADGRLVVA
+HAPNLLGSLGAFHTLAPLDVRVDVLRDALDLTVPTRLASVHLLGTLRWCRDSAEVAELGL
+RGRVADLVADVGPRVRVGVIETQRILLHDVDGVAVFCRHTLPLTSRGLIDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVGTGPLPESPAHALDADEAGVTLLRVRDGEA
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2602e5b90104cd689b6cb2dbddfd746b17d3e86a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002048.fa
@@ -0,0 +1,18 @@
+>0_1904
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPEEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAKRRHRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>1_1607
+MSTHRLSSTALGFAAGLGTAAAVTAARRIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAQRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>4_1831
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMGAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEKRRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTTAKRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8075812d199777da87baa1cbe8c1a19a7b432718
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002049.fa
@@ -0,0 +1,24 @@
+>0_1905
+MTEQYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTSTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVHLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAVDPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILTQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRLGQPRIYWHRLLKGKV
+>1_1608
+MTEQYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTTTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVHLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAVDPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILTQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRFGQPRIYWHRLLKGKV
+>4_1832
+MTEHYDILIVGGGNAGVSLAAALRRKRQGRVAIADGQQLHRYRPMLNYAAGGQADMARFE
+RPMRAVIPDGVEWIPDHVVAVDAEERTAVTTTGLTVGFRHLVLCPGLTPWWGAIDGLREA
+YAAGWAASAHVPEHVDAARALLSRVAAGDRVVANVPAEPSSCGGTVLKALFLACAAWERT
+GILPDVDVRLVTPYGRILDRQTIDPALAEAVARYGIHVHAGAEVNAVDHEAREVVLNTGE
+RITDVAAAYITPVVRAPEFIAEAGLADDGEAGLAAADPATLRHPVHPHVWALGDAAALGT
+RPSGGALRRQVKILAQNIQAADAGKPLQKYDGYTVIPVMVSRDELVLDEHVRDGSEDRSI
+PGVDLTKPRKSTAAFDRFGQPRIYWHRLLKGKV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f0fd118cf9716ef5924d4d2947af2dd3828175f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002050.fa
@@ -0,0 +1,20 @@
+>0_1980
+MPRPLAPLATSLPTILTVPEGREAGLSRARLRAPDLVAIGHGLRMSRDVEATWTDYLRAV
+QSLNPSGVFSHATAARIWGMWIPGRLLEDPRVHLAKERGHGGRTSRSGLVMHQLQPDAPV
+IEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAEARRLGHLPPRATTVDEMR
+RLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAGFPEPQVNPPIRLSSGETV
+RVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDWAVTWVAGEVFTRGGRPRF
+VGDLSRLMRRQATRRGAVLPPGLPGE
+>2_759
+MRMSRGVEATWTDYLRAIQSLNPSGVFSHATAARIWEMWIPGRLFEDPRVHLAKERGRGG
+RTSRPGLVMHQLQPDAPVIEYRGLRLTAPAWTWVDLAHHLSVEDLVVAGDSLLPSPHGAE
+ARRLGHLPPRATTVDEMRRLAHARKNVRGIVRARAVLDLLRTGADSPPESRLRHRLHEAG
+FPEPQVNPPIRLSAGETVRVDLAWEELRLCLEFDGDQHRTDRAQWQRDRARRRGLEADDW
+AVTWVAGEVFTRGGWPRFVGDLSRLIRRQAARHGTVLPPRLPGE
+>3_727
+MADPSRATPPRLVTTATLRSRGVAPWELRRREYTGRGRSLWGAAGVEFTLLDHVRALQEL
+HPTGVFSHATAARLWGMWLPRDLLQEPSVDIAKVKGRGGWPSREGIRGHHLDPAAQVVRL
+HGVRVTSPAWTWVDLAARLSVEDLVVAGDSLLPDEHGATARSLGRLPCRASTVAELRRTA
+ATRKNVRGVVRARHVVGLLREGADSPAESRLRHRIVEAGFPEPEVNPALRLHDGRIVRPD
+LCWRALRMCLEFDGDHHRTERAQWQEDRARRRGLEADGWSVTWVAGEVFTRAGWGRFRGD
+LAATMRRQAHQEGVVLPPSLPGEEASLW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3de13262d41a4c71a80f4ab69728f775ac5181e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002056.fa
@@ -0,0 +1,21 @@
+>0_2104
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRADGRRAAGAPGSAPANRLRN
+>1_1829
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSTP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
+>4_2050
+MTAPDPAPTDARRAEDRSARIAVTVFPLLVLAAALVGFLAPTAAKTLLPQVNLFLGIIMF
+GMGLTLTLPDFGLVARRPLPVLLGVVAQYAIMPLLGLGVAVVLQLPPELAAGVILVGSAP
+GGTSSNVVSYLARADTALSVAMTSVSTLLAPLLTPLLTLWLAGQYMAVDGGAMAKSIVNI
+VLLPVLGGLVVRLLLRRVVDRVLPALPWVSVVFIALVVAAVVGNSASRVLSAGLLVFAAV
+VLHNGLGYLLGYGAAKLFRLPTPVARTVSIEVGMQNSGLAAGLAAQYISPAAALPGAVFS
+IWHNLSGAVLAMAYRRSDGRRAAGAPGSAPANRLRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eebfa070569504cbaff3e3d5047e0e62543aec5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002060.fa
@@ -0,0 +1,24 @@
+>0_2143
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>1_1867
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>4_2088
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..267c2e92f7ca419cc0a335e220430c18676f3946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002061.fa
@@ -0,0 +1,9 @@
+>0_2144
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>1_1868
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETPLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
+>4_2089
+MTNAPNRDELPLPDYDHIPNGTLPTRITGLDESQVEQLLAYERAHGDRLPVVQVLETRLE
+ALRSGAQPSGDQVPDTPEVGGSRTGSPVTPETSGPPVEPLSRGIPADPQHPGNR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11772a7f3c88626fc773b5f30a1f2139c6794bfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002068.fa
@@ -0,0 +1,21 @@
+>0_2197
+MTTKVGFIAAASHALQNGPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLIGPEDYIGSW
+>2_454
+MTTKAGLIAAASHALQNGPQLFARVEDGGVVIGGRGGEVVPDSTGLYAVVAQDPDAVWAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVERLGLEPVAV
+ASAGRFTLTQESGEQLTTWMRCHLAVRVWQAPAGFAEVTPLGGIEKPVIDTHTPPLNLTY
+GGTSPEAQQLRRRIREARTAMAEQAKRGVDVVEADSSARATVGDLFRRRPRQYGLRGSVG
+LWEELAERLDDTPMPTSEHELGRLLHDALERSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTQGLLGPEDYIGSW
+>4_2129
+MTTKAGLIVAASHALQNSPQLFARVEDGGVVIGGRSGEVVPDSTGLYAVVAQDPDAARAE
+LRLDTSVSRSDVLYIGKAEGSLRARLERKHFADGGTAHSTLRRTLAALLVDRLDLEPVAV
+ASAGRFTLTPESGEQLTTWMRRHLAVRVWQAPAGFAEVTPLGDIEKPVIDTHTPPLNLTY
+GGTSPEAQLLRQRIRKARTAMAEQAKRGVDVVGADSSARATVGDLFRRRPSQYGLRGSVG
+LWEELAERLDDTPMPTSEYELGRLLRDALDRSLEGAEPYDEDKVNVERFNRGGMSQGLVH
+LPWWEDQAIPLLLDRWGAWADTRGLLGPEDYIGSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc2274570735dd76ba9010289f7f56023a0344f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002073.fa
@@ -0,0 +1,24 @@
+>0_2227
+MPSAPPPSDLAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLAALTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>1_1930
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>4_2168
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTALGYDA
+LFRACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVVAAVGIPVMYLLSGGVGVALLLYYRLVHGGRAIARRLSPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62e277fa824282d9141bdd2fbe118d1a31ad6d23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002075.fa
@@ -0,0 +1,16 @@
+>1_221
+MHHHGGAFTGIKKHHHAWAPLIEEMQEDVDAWVTGYRVPRSSEAAYFHGPLGRDVRKNFS
+LLLGFSGKIVRPGSPLTSEWLAEVERRLDYYGSLLAQAPGNIYGDNPGYPVPWTRIGSQV
+FEPLTLKYREHIRIDPRLKPQLWGHR
+>2_2376
+MALNAARRAKHQVWTLRKVSAQQARELLDTTAQRLRPLSFNPHRYPLHRFLRFDAPMQET
+LPAPERIFVLWTGLNEMPAIRAANLGRIRTIVGVPVEFVTPATLHEWTVEHHPLHPAYPH
+LSLTHSSDYLRAYLLHHHGGGYMDLKAPAGSWADMFTRLNGDPEAWVLGYPEDSKGRIPP
+YGGHMERDLRIHFARVMGTMAMIARPRSPFTAEWFHEVERRLDYFLPLLRDHPGGVRDEI
+DLYPVGWTQILADIAYPLPLKHHDHIRLEKGFTPPDEAYR
+>3_2259
+MRLMYSARQAKHAAFVANKRTRRVLGAGKWRALTMVTPALSRVWPFRYDAQRYTGPNRGK
+EGHDLSFLQLPPPIDAASSELPRRVFVLWTGNNPLPPNRSRNLAHLRKVIAVPVVLVTPQ
+TLGGWLIPGHPLHPAYEHLSLVHRSDYLRAYLMHHHGGGYIDLKAPVGSWAPAFDRMERD
+PSAWLSGYGEINANASARFPGPMGRDIATHWKSLVGTAAMIVRSHTPFTGEWIREVDRRM
+DALAPRLAASPGLVRLGGPGYPVSWTDLLGKVYQPLQLKYFEHIRVDDDLLVNFTDYQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3334214367b9a2050a7cf129c46ca286378d0709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002078.fa
@@ -0,0 +1,25 @@
+>1_341
+MTAGVDRPADGKVAVERVDRPGRRGMRLLGPAFVAAVAYVDPGNVAANLTAGAQYGYLLV
+WVLVAANLMAMLVQYLSAKLGLVTGRSLPELLGHRLPRGRRLAYWVQAEIVAAATDLAEV
+IGGAIALHILFGIPLLAGGVIVGVVSMILLGVQSRRGQQPFEFVVVGLLAVITLGFVSGL
+FYGPISWGEAVAGMVPRFEGTQTVLLAAGMLGATVMPHAIYVHSALARDRHQGAHAHPGT
+LGRLLRATRWDVGLSLLVAGSVNIAMLLLAAANLSGVSGTDSIEGAHAAITTALGPAVGV
+LFGVGLLASGLASTAVGSYAGSEIMGGLLRWRIPQMLRRVLTLIPALLVIASGVDPTWAL
+VLSQVLLSIGIPFAMIPLVRLTGARAVMGRHANSTPLQTVAWVVVALIVALNAVLLWLTL
+TGQG
+>3_654
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
+>4_1953
+MAAVAYVDPGNVAANLTAGAQYGYLLVWVLVAANLMAMLVQYLSAKLGLVTGRSLPELLG
+HRMPRGRRLAYWVQAEIVAAATDLAEVIGGAIALHILFGIPLLAGGVIVGVVSMILLGVQ
+SRRGQRPFEFVVVGLLAVITLGFVSGLFYGPISWGEAVAGMAPRFEGTQTVLLAAGMLGA
+TVMPHAIYVHSALARDRHQGAHTNPATLGGLLRATRWDVGLSLLVAGSVNIAMLLLAAAN
+LSGVSGTDSIEGAHAAITAALGPTVGVLFGVGLLASGLASTAVGSYAGSEIMGGLLHWRI
+PQMVRRVLTLIPALLVIASGVDPTWALVLSQVLLSVGIPFAMIPLVRLTGARAVMGRHVN
+SAPLQTAAWVVVALIVALNAVLLWLTLTGQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5371d15642caf595bf386281fdc213ac8284c8b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002081.fa
@@ -0,0 +1,7 @@
+>1_354
+MSRFQMLSDAQWELIAPMLPTHTGRPGRPFSDARMMIEAIIYRYRCGIA
+>3_2151
+MSRFQMLSDAQWELIAPMLPTHTGRPGRPFSDARMMIEAIIYRYRCGIA
+>4_105
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QRSVDLASALGRKRHMGHGAGHADRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a7ac1a30748e3189135191506a895cb2c15e16e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002083.fa
@@ -0,0 +1,9 @@
+>1_875
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
+>2_1664
+MTIVTDKRDRPLHATIAILLAILTGGYLAPWAVAATRGKSNVWTVFWVNLLAGWTVIGWA
+IALYMSLTSHRTARVWGARR
+>4_1097
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3875b958ef9e57354945efdc299cfb199eb745e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002090.fa
@@ -0,0 +1,15 @@
+>1_1659
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD
+>2_824
+MRIDENSERDAQGRLIPTPGQTIGPFFGYADGYEQVHLPFRDGQNLVPPGRADALRLTGT
+VYDGNGDPIPDAMLEIWQADAQGVISQEDGSLVRDGFTFTGWGRATVDNVGTYTFSTVEP
+GATGEGTARFISMVVFARGLLNKLHTRVYLPEDTEALAADPLLQSLPEERRRTLIAERLD
+DGSLRFDVWIQGRGEHADKETVFLQFPGIEYPQHD
+>4_1877
+MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT
+VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP
+GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND
+DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d387f9b86e0516ab6473f8dc18c1a26d9cbb6d19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002092.fa
@@ -0,0 +1,24 @@
+>1_1661
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
+>2_822
+MTQQPVTRTRVGIVGGGPAGLMLSHLLSKQGIDNVVLESRDHETIANTHRAGILEQPSVD
+MLTGTGVDGRVKTVGDEHRGIFLRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARER
+DGGDVRFETEVVEVLDIDSDTPGVRFRSVAGGEQGPVEELRCDILVGADGSRSTVRKALQ
+AGTEGKDYFTAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPAT
+RVEDWSDDRIWERLQKIVDGPDGLTLKTGPIIDKTVLGFRSFVRTPMDHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLFEALDSWASTGSRDLLDAYSDTVLARVWKAQNFSSWMTTM
+LHARPEASEFEDMRVRGELLNVVSSRFGQQYLAEQYTGWPHR
+>4_1879
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002093.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6fab4d664d412a9b7f6187c7fc7284a49f44b6a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002093.fa
@@ -0,0 +1,18 @@
+>1_1662
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLLDVQAVLHQHTQLAVLDAEGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
+>2_821
+MSGTLDRLIRILSSFDAERPAMTVAALARRADLPLPTAYRWVERLVGAELLQKDDDGLVR
+PGLRLWEMASRSAPSMSLARTAMPFLVDVQSVLRQNTQLAVLDDEGVLVLERLSSQGAVV
+NQAAVAGRLPPFTTSLGLVLLAHSPADVAERFIARHRRQLGVAVEHHPSEAGGAAPAGAR
+VRVTAPTEPHLRALLAGIRREGYAAVDGALDEEARGIAVPVTRADGTVVAALGAVVPCEA
+PYTPGVPPLLMTAARGIARAVGGDSH
+>4_1880
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLVDVQSVLRQHTQLAVLDDDGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002097.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6485619918a807983f30e4e8f0b44db0bb1aa1b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002097.fa
@@ -0,0 +1,32 @@
+>1_1745
+MVSNRLETESGWRRSRLHGVRADDTLTTATLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFASDRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALSVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRCLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPPVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAAMAAQVHGASAPMFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTVAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+>2_675
+MVSNRLEAESGWRRSQLHGVRADDALTTTTLDVRARAAALDHAVATTLADVARDFAGLDL
+FLFAADRSGRLIRLVGPWKSALGEQIRRRGLDVGVCLAEEAAGFNGIGAALELGRGVAVD
+GEEHYLDAFRAFSCFGVPLAHPGVGRVHGALNVVTFAGATPTLVEGLARHLGRQIEQALG
+AATYADELRLLTEFRRLTRGRGSAVVGVGEESILLNAAAERLVRHLDGSELRALAVRARR
+GELDGGDVGVAGGFSVADVSEASGMTLMRLERAATETTPRPTPGAGRGTWAPAVEAAREA
+RGSVSVIGEPGSGRTAAARRIAGPDAVILEVGRAQTPEDTTWLRGLEALVRRPGPAVVVD
+DVDALEPRLLPGLRRALRQGRCRIVMTAQVQPTTDVSAVLALTEHRVQLSPLRRRLAEFP
+ALLAALAAQVHGASAPTFSPEAVRVLAQQHWPGNLVELEYVVGRVGRRAGGGRVTAAELP
+ASHRGEGTVPLLGLERAEREAIIDALESAGGNKVRAAAALGVSRATLYRRLRTLRITQEG
+>2_792
+MAPEPPQADPERIRRARHELAARGLIAGSVPPALVGEQIEQSWRRSVAHEVSLDAVPQGG
+ADLDPALPLRRAAETVVRRWAEGLGQLRVSLVVADATGRILVRRALDTRDEDALDAARAA
+VGYGFGEQDLGTNGLGTPLQVKGDVYISGAEHFTDGLAGLTCAGTPVLDPVTGRAVGALA
+VASRADEAHPLMLGVARQAAAEVMEALRDETAGPDLEIARAFRGLRGPDRAVLVMSADTV
+MTDLPGLARIDAQTQAVLWETLRRRSPGEEPVRLSLPGLEGEALARRLPGAEAAYALEFD
+AVPAPEPALGRAAAAPRSGPPAGGGPERGAGTAPSVGVHPSEMAVAYDGIGDALTAAAEQ
+TGLVELTGPRGSGKRFQAVRWLRDRALAAGTADAPDPLHVELADVTGPQGEDLLRRVAAR
+GRAVVVAGTLPTAAETAQARAGLRTTVARVVLEHPEAPRVVLLRSVDASAEDDVAGQVRL
+PALAEVPQDIPALLARLSERLHPGAPPPRFSPEALQRILAWPWPDNMAGLSRLVSLLPGL
+RRGATVQVEDLPAALRAGPGSRLTRMEQAERDAIVAALREHGGNRSAAAAALGIGRATLY
+RRLKALRITV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..501aed54e9d4601db60448513d6d25b8fa65a907
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002101.fa
@@ -0,0 +1,33 @@
+>1_2078
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
+>2_255
+MATRLRQRLLSAAALTAAGALLITGCAESQRDSGGSAGGSGSNGDAAQVDGSFIFAASSD
+PKTLDPAFASDGESFRVSRQIFEGLVGTEPGTADPAPLLAESWESSEDGLTHTFKLKEGV
+TFHDGEPFNGEAVCANFDRWYNFTGIQQAETVSYYYGKLFRGFADAPENAVYESCEANGD
+AEATVTLAQPFAGFIASLSLPAFAMQSPKALEEYKADEIGGSAESPQMSEYARAYPTGTG
+PYKFDSWSVGEDIKLSAYEDYWGEGGDVTDITFRVIDDPVARRQALEAGDIDGYDLVAPA
+DTQALSDAGFNVVARDPFTILYLGLNQQQEELKDVKVRQAIAHAIDKEALIGQTLPEGTE
+PATQFIPKSVNGFSEDVTKYEYDPEKAKQLLAEAGYADGFTIDFNYPTGVSRPYMPTPEQ
+VFSNLSNQLSQVGIQVEAKPAKWSPDYLNQVQGTADHGLHLLGWTGDYNDTDNFVGVFFG
+QEKPEFGFDNPELFSALEEARGVPTLEEQTPMYEEINKQISDFVPAIPLAHPAPSLAFDK
+RVASYPASPVNDEVFTEIDLTE
+>4_119
+MATRLRHRLLSAAALTAAGALLVTGCAQSQRDGGGSGGSGGGDAAQVDGSFIFAASSDPK
+TLDPAFASDGETFRVSRQIFEGLVGTKPGTADPAPLLAESWESSEDGLTHTFQLKEGVTF
+HDGEPFNGEAVCANFDRWYNFTGIQQSETLSYYYGKLFRGFADKPEDAVYKECEATGEHE
+VKITLAQPFAGFISSLSLPAFAMQSPKALEEYKADEVGGTAESPQMSEYARAHPTGTGPY
+KFESWSVGEDVKLTANEDYWGEGGEVTDITFRVIDDPVARRQALEAGDIDGYDLVAPADT
+AALSEAGFNVVARDPFTILYLGLNQEKEELQDVRVRQAIAHAIDKDALIAQTLPEGTEPA
+TQFIPKSVNGYSEDVTTYEHDPAKAKALLAEAGYPDGFTIDFNYPTGVSRPYMPTPEQAF
+SNLSSQLAEVGITVNAKPAKWSPDYLDQVQGTSDHGIHLLGWTGDYNDTDNFVGVFFGQE
+KPEFGFTDEELFSALEEARQIPTLEEQTPKYQEINEQISEIVPAVPLAHPAPSLAFDKRV
+ASYPASPVNDEVFNEIDLTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18621eaf023bbc0a92650e63fe6a95c71d8d4397
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002107.fa
@@ -0,0 +1,18 @@
+>2_573
+MSEHTATPARAGSPAWIDYSATDFAAQQAFYEALFGWTFTDSGEEFGHYRMIAKDGASVG
+GAMDADQMTAMTGEAPAPAAWTVYLRTEDMAATLAAVREHGGTVLVDAMPVGDLGTMAMV
+AGPGGEAVGFWQADTFEGHDLPLTPGTSVWFELLSTRFDEAVEFYQAVAGWQPTLMGDDG
+APEDGHAAADAEDAAQDGPRYATDHPGEGATAGLCDATQWLPANAVGYWRMYIAVEDTDR
+ALEVIREHDGKVLDGPQDSPFGRVTTVQDPAGATFQINEALPGQE
+>2_1297
+MSITPGQPVWIDLGTTDLERSKAFYRDLFDWNFSDTGGEFGHYHMVDAGVPVGGLGPNVD
+AEGNIDASMPVWWTVYLKVEDVDATLAAVREHGGHVHVEPMQIGDMGRMAIVAAPSGAAF
+GVWEVGSFEGFDTEGRPGTPVWFEALTKDFDADAAFYAAVLGWKNVPMREGSSDEGAAEE
+DGAGMRYVTDAAGDDASAGLFDAAAFLPAEVPSHWRVYFAVPDTDAAVEKVLALGGAVVE
+PAQDSPYGRVAAVADDLGGTFMVIA
+>3_497
+MSAQHTAIPSGSPIWIDYSAGDFATQQAFYSALFGWTFQDQGEDYGHYTMVRAGDAVIGG
+AMDGELSAQFSGGPVQPAAWTVYLKTEDIARTLGLVAEHGGQVIVEAMPVGELGSMALAM
+TPGGEAVGFWQPGEFSGHDLPLTPGTSVWFEVMSKDFAADAEFYRAVCGWDVVPMGPDGQ
+QDDAAPDEDGMPAYATDHTGEQATAGLCDAAAWLPEAVPSHWRVYFQTTDMDASVKVVEE
+KGGRIVDGPMDSPFGVVASVVDPAGATFQLNQPPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08f0e8eff922a065dec8032cdb000bd12ede82b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002110.fa
@@ -0,0 +1,15 @@
+>2_878
+MTLTTRDAQTWEQMWLPLWPLASDDLRAGIYRTARKDARGKRYIEANPQALSNLLVVDVD
+HEDALMRALWGRHDWLPNAVVENPTNGHAHAVWALAEPVTRTEYAQRKPLAFAAAVTEGL
+RRSVDGDAAYSGLITKNPQHASWHTSWTSDRLYSLGELASRLEEAGHMPAPAWRRSRRQN
+PVGLGRNCSIFETARHWAYREAKRIRQRHEHATAEDSRDYYAAVLAHVHELNAAFSEPLP
+ANEARDIAASIHRWVTTRFYGWTDARTVQQATLSTLQAVRGRKGGTKSGEKRRSTVEDRA
+RLIVGEDA
+>2_1289
+MDARETQAWGQMWLPLWPLASDDLKAGIYRTPRATARGRRYIEANPQALSNLLVVDVDHE
+DALMRSLWDRRGWLPNAVVENPENGHAHAVWALGRV
+>2_1291
+MVKTIVRHALAEPITRTEYARRKPLAFAAAVTEGLRRSVDGDKAYSGLMTKNPEHTSWNT
+SWISNELYSLGQLAEHLDTAGFLPAPSWKRTRRRRPVGLGRNCSIFETARVWAYRELRHH
+WGDPEGLRVAIVERVHELNAEFSEPLPAREALDIAHSIHRWITTQSRMWQDGPVVYEATF
+TAMQSARGRKGGAKSAEKRRAVVEDRARLIVGENA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..173a5cce6e3378515638a15095dee8fd5878e59f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002111.fa
@@ -0,0 +1,28 @@
+>2_1055
+MTARADRDDVALIILGATGDLTSRLLLPGLAGALAAHDLPRITLVGSSHSEHDTQEWQGI
+VREALKGTALDAAAVDDLVERAVWRTADATDADDLRALFAAAREAAGPEAVPVLYFALSP
+GIARESVDALAGMDDLPDRLRLALEKPFGEDEASARELNAVLADIVEEDRVFRVDHFLGE
+SMVTALLGLRTANRLLGRVWDGRDVERVDVVVDEAIGLEGRAEFYDGTGALEDMLQSHLL
+QVLAMTALEPPARVAADELHDAVVEVLRATRVWQDDPVAASRRARYTAGEADGRPVPAYA
+DEEGVDPRRRTETLAEVTLAVDTDRWRGVPFRLRSGKALERTRWEVALTLRAPEDVPEGL
+SPAAGRDRIVVGLQPRGVRIELAVDGADTPFDAERRALTAGLGEEHVDAYGEVLRGILTG
+EPLLSVRGDAAEECWRILAPVIAAWEADEVPLDEYPAGSAGPEGWD
+>3_991
+MASADTAARDVALIILGATGDLTSRLLLPGLGRALAAHEMPRVTLVGSARSEHGEDEWRT
+VVREALAETPLDADAAEDLAGRAVWCAADASDPDDLRGLFAAAAEAVGSDDVVPVVYFAV
+GPGVAEQAVEALGGMDDVPEGLRLALEKPFGRDEESARRLNAALAEVVDEDRIFRVDHFL
+GESMVTALVGLRTANRTLARVWSAADVERVDVVADESIALEGRAEFYDGTGALQDMLQSH
+LLQVLAMAALEPPARVDAAGLQGAVVEVLRTTRLWDDDAAASSRRARYTAGVLDGTRTPA
+YADEEGVDASRGTETLAEVTLAVDTDRWRGVPFRLRSGKALAETRWEVILTLRAPEDVPE
+GLSAAGRPERIVVGLNPRGVRVELAVDGADTPFDARRTPLAAELGAERVDAYGEVLRGLL
+TGDPLLSVAAEASGLGWKILEPVIAAWEADEVPLEEYPAGSAGPEGWD
+>4_1661
+MPDVQNPCPAGASPAPDDDRAAASVALVIVGATGDLTRRLLLPGLARALTVHDLPEVTLV
+GSAHSDGHSLEERRGVIEEAVGETDLDADARAGLVERAVWRTADASDPEDLGALLVAARE
+AAGEEAVVVLYLALDPDLAAEACAALEQVEDRPTGLRIVLEKPFGSDQRSARELNALLGR
+IAEEEDVFRVDHFLRESMVSGLLTLRTANRVLERVWSAADVEHVDIVADESLALEGRAGF
+YDGTGALEDMLQSHLLQVLAMVALEPPRRLTPDALQDAVVEVLRATRVRDDDAVASSRRA
+RYTAGTVGGQDVPDYVAEEGVDPENGTETLAEVELEVRTDRWAGVPFRLRSGKALEPRRW
+EVVLSLRPPEGVPAGLEAAAGRERIVVGLDPRALRVELAVDGPDTPFVAERSVLAADLAE
+EDVDAYGEVMRGVLTGDRMLSVGGDAAEECWRILAPVIEAWDAGRVPLDEYAAGSSGPGD
+WPER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af309db360527369de23a2e404817f120bf063ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002115.fa
@@ -0,0 +1,37 @@
+>2_2278
+MDGFRRSLDGQFVTVDGHDYSEVTRPKLAQADQQERLPDGSERPLPTRTLHLMAAEDGTA
+PVDLNDWERQVLDSEAAEPSLRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFVFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGMPSVGSRPSLRSRGSCGCWT
+>3_332
+MRYTLKDYQADAVAEILANIERAQRLRREGHLPTMALTATTGGGKTVIAAAVIEALFFGS
+DTFDFLADPGAVVLWFSDDPTLNAQSRHRLEAAAPDLIGRMTDLNAGYTKPALDPRTVYF
+INTQKFAKTSRMVRGFQPSGTEGQDTFAGLDPRVRPDMVPQTIYDIIAATIQNPDLTLYF
+FLDEAHKGMGTTARAQAEQKTIVKRLIAGQPGVPPMPVVFGISATLQRFTNAMDGIRGRL
+GLDPVQVDPARIQKSGLLKDNILLNIPHPDEVGSFETVLLRSAVRQLLESEAAWDAYVAE
+QRADHPGAEIERVVPLMVLQTPNSVTPSDIAGYLRTIMDVWPEMPAGAVAHVFGEKEAIQ
+AAGLFIPHIDPEKVQDTKRVRILLAKEAVTTGWDCPRAEVLMSFRTVSDLTKITQTLGRM
+VRTPLARRIPGNDELNSVLCLLPNFDEKAARQVVKDLTNDEVPNPIIDPVVDPDPRPEVT
+PPSGGAGASSGGGTEPANPEVPGHGTHATDRVAEPSADGQGTPARPGGLHQGETRGASGG
+GQGGAVGPVVLTDRVKVTPIENGPLWDLFDSLPTETTPSRGLGPVPLLTALGQYLSEDGL
+RPDAGEEAHRHLHGTLDYRAGQFREDVDKAVKDILEVRVRTILADRATGKERIGMFTERA
+DLAVVREAYQRAARAFTADVSRTYVNHIVGPDADEDDLREAYARVAGMASVPDIVADVKE
+EASRLVGRWFQEHRTDIKALADDRQAAYKALMEQSTEPQRGNLAKPVNWQESPVDVDKKP
+LPTRTDHILTAEDGTYPLTLNRVESSVVDQEMRRRGAIAWYRNPSRVKDESLAIAYRDGN
+AWRTMRPDFLFFHEDAQGRVRASIVDPHGHHLSDALPKLRGLARYAEQYGDEFMRIEGLT
+EVNGKMRALDMQDPKVREAVEVATSARALYESDAAVDY
+>3_676
+MRYTLKDYQAQAVEQVLNRLHRARKNYQDDGVLSQFSLAAATGAGKTVMAAAIIEALFFG
+SDQYTEDIAPDPGATVLWFSDDPDLNDQSRARIHAASSELDGRLRTVENSFAETTFAPGQ
+VYFLNAQKLREGARLVRGAQDPTNAATPVMAAPDMAQRTIYDVIANTVATPGRTLYFILD
+EAHRGMKTTKKNDQERATIVQRLINGTALAPTMPIVLGISATVERFTQAMAHATDRDALS
+PVQVDPALVQASGLLKDDVVLTIPEEAGAFDTTLLREAVARTKASTRAWAAYAAEQGEPN
+PVVPLLVVQVADKPSDEHLSRILDVIHQEWPELRPQDIAHVFGTHTDRHLPGQIVNYIAP
+QRVQETTHIRVLLAMEAISTGWDCPRAEVLMSFRTYKDATYVHQLLGRMVRTPLARRIPG
+NEVLNSIDCFLPHFDKTTSTAIAQTLMRGQSDMDDTTSDPGKQAARRVLFDPVTLTPNPA
+VGEDVWAVFDALPSMNIPQGATKPLKRLDILANALSHDELLPGAVKTAAHTMCKLLDGCR
+VQYSEQIAAARQDVLTLSAQRLTGRLGTTTLSTTSLELLADDRAIEEAAAAAARTLTGWI
+AGAYIDHIVPEDEEDLDLREGDIIIASLARTSEVVADLEAKADKLVQDWLSQYRVQINGL
+TDERQAVYDRVREMARQPERVALTRPKLTQADQQERLPDGSERPLPTRTLHLMAAEDGTM
+PVDLNTWERQVLDSEAAEPSFRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFLFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGDAFGRIEAVAEIEGQLRVLDMKNDV
+VQAGVHAAQDAESLYKAAPAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..504a45acc292d099e993d1fe4bb71689fbe40588
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002118.fa
@@ -0,0 +1,4 @@
+>0_156
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
+>1_317
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6cb91ee3366494069569cd4950c5aafe6dd5487
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002121.fa
@@ -0,0 +1,8 @@
+>0_180
+MTAVPETYVFDTGPLRHFTLKGWLGVLKFLTAGHAVIPESVEQEIRDQQYQHPDLRQILD
+AEWIVVDRSEDLEFLAAFARYEEHLVAGGRNRGECGVLALGRTHGYRIVIDDNVPRVLAK
+REKLECTGTLGLLCEAIRKEQLTVPMVESLADDLIMGDYRLPFGPGGFKCWAEQQGLLG
+>2_203
+MTHVFDTGPLRHFTLNGWLGVLKFLTGGRIVIPESVEREIKDQQHQHAALRQILDADWIT
+VDRSDDLEYLAAFARYEEHLVDGGRNRGECGVLALGRTRGHRIVVDDNVPRVLAKNEELD
+CTGTLGLLCEAIRADKLTVSMVESLADDLLASEY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea85a946afea082502d8ed6a1b03275b5e0fa409
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002126.fa
@@ -0,0 +1,18 @@
+>0_381
+MTRREVESVEDRIREHLRRDDLNSAVELLRALSPGDALELLDRSEPRMVPVLFRLLDKST
+AVRVFAAMETGQQSDLVRQLQDGQVQDLFAELRVSGQARLLDEMPATVARKMLAGLDAGA
+RGEVGRLLGYPADSVGRRLRMAPVRLREDWTVAVALENLRDHGGREQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEESTEDAARAGGVEPLGRPYLATSVLALMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVIAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
+>4_387
+MTRREVESVEDRIREHLRRDDLDSAVELLRALSPGDALDLLDRSEPRMAPMLFRLLDKTT
+AVQVFAAMETGQQSDLVRKLQDGQVQDLFAELRVSGQARLLDEMPANVARKMLAGLDAEA
+SGKAGRLLGYPADSVGRRLRMAPVRLREDWTVSTALENLREHGGQEQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEGSTEDSARAGGVEPLGRPYLATSVLSLMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVLAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81498ae004a1b520d856861df2b8f82f8de897eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002130.fa
@@ -0,0 +1,12 @@
+>0_562
+MNVHSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRAPASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKNRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVEGESQAEIRSTLRDAVDDLDEVLKKIEEGTR
+>1_305
+MNGYSLQLAYTPEAAREVTDQIKTGLESVYHLIRSAYRGRAWEVLGYRSWDEYVTREFGN
+LHLRPPLEKRQDIVLSLREVGMSTRAIASATQISEATVRRELKHAGASKDAPGRALASVV
+GVDGKTYEATRPARIGNLEPSMGVRGGQSDVDAVLDMPAEDFGIEPLDLVRHDEEQKGRA
+RRVLTAFNGSGAAAVPALIKAATPVASLVSPATGKALVEDEDLHGVVWDSVRCVRTLAHV
+IRSVGHVDGQSQAEIRSTLRDAVDDLDEVLKKIEEGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3a76d23c8ca75d2026c6d9c7e3840ae88bfdc2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002131.fa
@@ -0,0 +1,8 @@
+>0_568
+MLNGINPDGLSGWSQISGWVVGTALVVLILAVGAGVALAVWGRALFSPGGMRKGWTMVAL
+AAVGATVLGAGTAGTSWGAGLGTSELMPAGARPQSVAIEKNAPKQTCNRQAVRDFDKEEP
+SPDRAERERVISTLLGGQPALDGYEWGKEPTGTESSYTVVTSVKWYATGEVNGSGEPDCS
+AQNEATAECSPVEVHVARQSLTNGAQTGRTLTLTRGQNCS
+>0_569
+MSNLIHAATTVAAGVPDIAPRFDGPWMPTIQNVTGLALGTFLVVLIVAVGIGVLVWIFGK
+LSSSGRAQDVGISFVVWGIVAAALIAGAASLIGWGAGLPLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a2155a604528f788134ce4741c629a0e7478c32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002139.fa
@@ -0,0 +1,18 @@
+>0_854
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
+>1_585
+MKIAVVALGKIGLPLAVQFASKGHEVVGVDVNATVVDLVNAGTEPFPGEAHLQEKLSSTV
+ADGRLRATTDYGDAVPGADAVVLVVPLFVDDEARPDFGWMDGATTELAKHLTPGTLVSYE
+TTLPVGTTRTRWKPMLEEGSGLTEGEDFHLVFSPERVLTGRVFEDLRRYPKLIGGLTPAG
+AERAREFYEAVLDFDERPDLSRPNGVWDLGSAEASEMAKLAETTYRDVNIGLANEFARYA
+GANGIDIYRVIEASNSQPYSHIHRPGIAVGGHCIPVYPRLYLWNDPAADIVRTARAVNAS
+MPDFAVDLLAQAHGDLAGQRVVVLGAAYRGGVKETAFSGVFATVGALRTRGAEVTVDDPM
+YSDEELTALGFTPHSSGSEVDAAILQTDHAEYRALTPADLPGVRTFVDGRNVTDADAWSG
+VTRRVIGLPQDAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc58cb590d68e40155fd868022be8c2ce866056
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002145.fa
@@ -0,0 +1,8 @@
+>0_917
+MFHPWRALRTLTHVVVVWARPHPTAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLADALPWSMSLDELADELWVTPLVLTDRLAGLTR
+TEREHLAALATEHSA
+>2_1893
+MFHPWRALRTLTHVVVVWARPHPAAPAATDGATVIWLDPRMTQAERRCALTHELVHLEHG
+HRGCQPPAVEHAVRAAAARQLITLEQLSAALPWSMSLDELADELWVTPLVLTDRLAGLTR
+AEREHLAARIPEHRDTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5062f26864c42cf46461dd56158f02ffb669f0ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002150.fa
@@ -0,0 +1,6 @@
+>0_1000
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAALGAGLVLMARGRVRRV
+>1_722
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAAVGAGLVFLARGWVRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f4c5274694a5c081141f611a33af12aa7d3a4c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002151.fa
@@ -0,0 +1,6 @@
+>0_1340
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
+>1_1081
+MGRPPSIPAEKKTRIVLSVLAGEMSIAEAARKEKVSEQSIGRWKAEFLEAGKTALVAGRS
+GPSSREEQLEAEVAELTQALGEAHLEARVWKKSAEGRLGPSRTSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9ec3b0c1ee0dfc95294395277f62dbf4ff6cbbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002153.fa
@@ -0,0 +1,16 @@
+>0_1436
+MANTRAPNSKLAPGEHSIDRVKPTKQADGTYVLRWRVCLPDGTVKPGRSQGPTVAEVRRR
+AREKVGDLLATSADGSWKPSSSIVDYIDKVSIPAVDAARLAEASRRRYRVALNQWKTVLG
+SKTIAQTARVRTLEAALKRIAEEHGSESARHCKTVWGKYIAQQLVRDEVLSGNPLAGMSV
+DLSSSKPARPRAERTLTREELGAAIDWLLSLDPAAGVEKPARGRWSREDAVAKRRNVIDL
+ALLQAASGLRVQEANALTWNVFDRSADVRRTKTGKGRRVPLLFPDVVDHLAERRSLGGAY
+VIGAPTDPDKQWDRDACRKACATFYPEIGAAIDCEVFEHGRTHLWRGTLNSLLVAVPVEV
+RAAFLGHDEDTNRRYYTDVTDPAPMVEAAKALR
+>3_203
+MPRPPLAVGTWGRISDPLEVAPGVFRAMAKVRDVDGVTRKVEARASSKERARRTLEARLR
+ARTAPPAGEVTPDTRVRDVARLWLAEVEARGRAANTVKRYRITVDLHVCKARGGVGELRV
+RECTTSRMEAFLRGIARDHGAPSAKVARTVMSGVLGLAARHDAIQGNPLREVSPISIPRK
+EVRALSPADVRVLRRRLAAWQSEPPVNGRRRRPDDLLDVVDVMLATGCRISEALALRWQD
+VDVDARKLAITGAVVVAGRGGAVRQDHPKSAGSVQTYTVDAHTADMLRGRWERSMDLGLV
+SPMVFPSSTGTVRDPSNYRKQWRTAREAIGFEWVTPHTFRKTVATRLADAEGLAAASAYL
+GHSGEAVTRTHYRAKAPEAADMTAALAGFWGDAEGGEGEVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7981bc10ac651e27472811f115b3a4e6e2d3878
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002160.fa
@@ -0,0 +1,12 @@
+>0_1551
+MMHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHD
+AASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEG
+QTRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVD
+ATTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEG
+MTVADFRSSGVAIAAGEEATRARAEKLVELSRGRMA
+>1_1273
+MHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHDA
+ASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEGQ
+TRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVDA
+TTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEGM
+TVADFRSSGVAIAAGEEATRARAGKLVELSRGRMA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..daa85ce9fe5605a199723fb59e2d2cc03e373018
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002165.fa
@@ -0,0 +1,6 @@
+>0_1562
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRMDGDA
+>1_1282
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRLDGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a50a02e736c6b62305dd706bcab451f3b17d87cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002173.fa
@@ -0,0 +1,14 @@
+>0_1889
+MVPASSIHTAATARTGTTYSGPMPVSAQGPRVTVVGDSSALGSTSLMNLEMPGITVDAKE
+DRTFAEGLTRLGQLKAAGRLRDIVVLGLGVNTGGTAAAQARQAMDLVGPDRELVLVTASG
+PVAWRAFTEQAMRDLAARYPGRVAVTDWEAASRYVTDFRADRIHPRAQGLSVDAQLVRLA
+ADRATGARTVTVQAGQTLSGIAVAYAVPGGWSAISRATGVPLAQLPSLNGPTLSTVLHPG
+QVLRIRCPLT
+>4_678
+MNRSTLGTRLGASVLVVAALVSAAPAAPAVTSASGTTTTTATTGLAPGTYLAQSGDTWAY
+IAPRVGVELADLLRANGATTSTAIRAGQPLVLPAVSKHLPATSRTGTPYSGPMAPSSAGR
+RVTVVGDSIALGAASLMNLEMPGLTIDAREGRTFAQGLTRLAELKQAGRLGDVVVLGLGV
+NDGGATATQVRRAMDLVGTGRTLVLVTASGPVAWETSTNTAMRNLAATYPSRVVVADWKR
+ASAYVTDFREDRIHPRGQGASVYARLVRLAVDTAPVLRSTTPRTVTVQAGDTLSLIATRY
+GVTGGWQALATLNKISDPHMIRVGQTLLLPATSTTTTPATYTVLPGQGWYAVSRATGVPV
+TQLLSLNGATLSTEIHPGQRLRLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..904c82d96dda3de56005354e430a98cfa5f3d42c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002174.fa
@@ -0,0 +1,17 @@
+>0_1890
+MVVDYAQGVTLNAIGKKWGLTREAVRQIINRKSEFTVPELKEYRRIVAQEERSLLRAGLL
+AWSEGNRGVGLEVAAREFGVPQHRVAELLGKRADLHRANPRRRTTALRATEEELLDLLRQ
+FHAETGQATAAGYTAWAKTRGVPGHQTVAIRFGRWNAALAAAGIRQAEPVPRESRYTTDD
+LWAAAVEAFSAPDGPVTHLEFVAWLQEREGMPSDALIRNRLDVSFENLRHTALRMAATRE
+LIPGVTGGVFERRQWKAKTDEGDDAASAIDVVRRAIEDLGPTLSSGRYSAWAKEHRCPSA
+TTLQRRAGLQWGDLVAAAGGLPNARKNTGYSDEQLTEWMRRFLTETGSSSSTLYTSWQAA
+NGAPSYITVATRFGGWPQAVAAARW
+>4_1810
+MEFEVPSVSPGSESLNAPFTSKRRRELAALASMTILPSTPRAVRMAREYFEGSTLAEIGE
+RFGRTRERVRQLIRDEAGYSTKELKAYRELLADEEFRMKRAAAVSWSERHVGVPLSVASQ
+DLSLSQQELRRLLGKRVEFHLGDAKPRKTSSATPDEVLLSALREFYEETGETAAQSFTQW
+SRSHGVPTHQTVANRFGGWNAALERAGIAVTDRRRSRSKYSDAELVEALVDAWSSATPPR
+TYLELSDWLSARPGMPSAALIRNRLGVGFEEMRARALRVVAGQSMGFPGRKRTRVDWKGK
+LDPGDDPLTLVRRAIEDRGPRLTVAAYNSWAAEHGVPATPTVLRRAGTNWVQLVEAAGGT
+PNPPKPANPFTTEELRVWMERFMTESATHSQSAHEEWRQAHGGPSAQTITTRLGPWREVL
+ENLGGGQREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99cfa4557d41a01501c2f66dab38f4983275b15d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002175.fa
@@ -0,0 +1,8 @@
+>0_1941
+MTRLPGLRPPRFLDPWRRPLAPRLPWHVVLAASIAGALTIATLSLGEDLASVPLLVGAFG
+SSCVLVFLVPHGPHSHPANVLVGHVVSAACGIAVISVLPLAWYSLAAGMGLAMAVMAGLR
+VIHAPAGATALAVMLSNADWHYLVTPVLAGALVLTACALLYRRLMWRVIGPAE
+>2_828
+MSRLSRAPGLRRPRLLDPWRRPLLPRLPWHVILAASLAGAATIATLSIGQDLTSVPLLVG
+AFGSSCVLVFLVPHGPHSHPANVLVGHVAAAACGIAVSSVLPLAWYSLAAGMGLAMAVMA
+GLRVIHAPAGATALSVMLVEAGWDYLLAPILSGALVLTACALLYRRLMWRVIGPPPPPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d83e653c8a43fd97650559efe7e55d549ca8e8a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002178.fa
@@ -0,0 +1,7 @@
+>0_2005
+MSEKLPVVAEHLDAARADILAFTTFPKDVWTQIWSNNPAERLNREIRRRTDAAGIFPNRA
+AIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTTVSNTGSEVNPDTAPALEFSA
+>2_371
+MYDQPDATAVNAQFDRLIDYVTEKLPAVAEYLDAARADILAFTTFPKDVWTQIWSNNPAE
+RLNREIRRRTDSVGIFPNRAAIVRLVGAVLAEQTDEWAEGRRYLGLEVLARCRLTPVSNT
+GDEVNTDTDPALELSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c957c445d37d3b5ebba05dc6db740412e093fcdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002182.fa
@@ -0,0 +1,34 @@
+>0_2174
+MNVNDKAALTVAIDEFDEFFAAVNHGREPYAWQRALLRQVVTTGRWPDAVVAPTGAGKSS
+VLEVHVFAVAMTHAPGWEGARAPRRLWHVVGRRALVDDMASRAEAVFDQLAEITDVPIEA
+PLSRVAAALRRISPAGQPGSVTTLRGGIAPERGWQDDPVSCQVICATPDMAGSRLLFRGY
+GSTAGMRPREAGLIAYDSVLILDEAHLNRQLLTTARRVASLAGESPLAAHVPVLQVVETT
+ATPAGLAPAQTSIGVELSDIRTGAVGEALLRRLDRPKPVHLHLDGPWLAGGIARETTQGA
+QEIARMVTDAVQAGHTPVGVVMNRVASALAVHRALRGLNGGLDVVLVVGPRRRWEQALER
+SRTPDVYVATQAIEVGLDLDFGFLITDIASGSALAQRAGRLNRTGARESAPMHVLCPSAD
+PTAKTAAPYEVQDITDALEWLRDRAEDPKGVSPAALLENPAPSSTPARPVLSEIEAARAA
+LFSRTSEALAVEPDLTLWLRDSLDAETDVAVVGRRLPRLGEDAGEDWSGLDQAESAALLA
+TAPPQPHEAYPVTLSRLRLLLAGGRRGRATPAFVRRGRQWTLVDPDASGHGIVPGDVVCV
+PHDWAATHHHVLVEDGREPVGDVLDPRSADGTMLSLEPVKASQRRVVFMTGVASPGVQDH
+LRCSLLEVCADLQEADVPLTLLSVLDALDDRGQSAWLTAYLGQWADPDLVARFDVRVHVG
+GRAPGSPQQAAWVVFELLDAADPDDAQLSATTGRSPVSLAEHQRDVADRAGEFAQVLGLP
+EGLKRTLTVAGAHHDDGKSDDRYQAWLTQGVAGVDEPMAKSLLSALPFRQSRFLPAGWRH
+EQLSAAMLHAHADGADALAVRLVGTSHGHGRGTFLMGAESLVHPEAPPHVRMAAEELFDV
+GVWDALVLSVEQTWGLWAVAWLEAVLRAADVTISKEGR
+>4_2107
+MNVNDKAALTVDIDEFDEFFAAVNQGREPYDWQRALLRQVVTTGRWPDAVVAPTGAGKSS
+VLEVHVFAVAMTHSPGWDGARAPRRLWHVVGRRALVDDMASRAEAVFGQLAETTDVPGDA
+PLSRVAAVLRRISPAGQPGSVTTLRGGIAPERGWQDDPVSCQVICATPDMAGSRLLFRGY
+GSTAGMRPREAGLIAYDSVLILDEAHLNRQLLTTARRVASLAGESPLAAHVPVLQVVETT
+ATPAGLAPAQTSIGVELSDIRTGAVGEALLRRLDRPKPVHLHLDGPWLVGGTARETTQGA
+QEIARMAADAVQAGHTPVGVVMNRVASALAVHRALLGLNGGLDVALVVGPRRRWEQALER
+SRTPDVYVATQAIEVGLDLDFGFLITDIASGSALAQRAGRLNRTGARESAPVHVLCPSAD
+PTAKTAAPYEVQDITDALEWLRDRAEDPKGVSPAALLEHPAPSSTPARPVLSEIEAARAA
+LFSRTSEALAVEPDLTLWLRDSLDAETDVVVVGRRLPRLGEDAGEDWSGLDQAESAALLT
+TAPPQPHEAYPVTLSRLRLLLAGGRRGRVTPAFVRRGRQWTLVDPDASGHGIVPGDVVCV
+PHDWAATHHHVLVEDGREPVGDVLDPRSPDGTMLSLEPVKASRRRVVFMTGVTSPGVQDY
+LRCSLLEVCAGLQEADIPLTLPSVLDALDDRGQSAWLTAYLGQWADPDLAARFDVKVHVG
+GRAPDSPQQAAWVVFELLDAADPDDAQLSATTGRSPVSLADHQRDVADRAGEFAQILGLP
+ESLKRTLTVAGAHHDNGKSDERYQAWLTQGVAGVDEPMAKSLLSALPFRQSRFLPAGWRH
+EQLSAAMLRAHADGADALAVRLVGTSHGHGRGTFLMGAESLVHPEAAPHVRMAAEELFDV
+GVWDALVLSVEQTWGLWAVAWLEAVLRAADVTISKEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9bfcbff277a3e8a0bebc129201af4f0ef69eb79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002185.fa
@@ -0,0 +1,14 @@
+>0_2187
+MAATDHTLNPRAGANPSAAPNRLVRRRAVIGLLTGAPLLAACGGDPLSSDGGGQGSGGSG
+SGGDGGGTVRVGSANFPESEIIGELYAQVLEAKGLTVERKMQIGSREVYLGALKDGSIDL
+IGEYTGNLLAFYDKQAKAKTSEEVFAALQKALPDDLEVLAEAKAENKDAWCAAGDWAKQH
+GISSYADLKDYDGTLRVGGPPEMSQRDYGAGLARVESVYGVPADRMEFTPISDGGGPLTV
+KALKDGDVDLANIFSTTPAIEENGFVMLEDPEGMVTPQNIVPLMAKDRVTDQIREAVESV
+QKVLTTEDLMAMNAENSGEQKKQPREVAGEWLKEKGLV
+>3_442
+MATSPRPSAPLSSALSRRAPRRAVLGLLAASPLLAACGGDPLAEGSSSPAPGSGGTDAGG
+AVTVGSANFAESEILGELYAQVLEAKGLQVERRMQIGAREVYLDALKDGSIDLIAEYTGN
+LLGYVDKEATATSSADVEAALKAALPDHLTTLAVAQAEDKDSYNVTKAFSEENGITSLAD
+LAAHPGTLRVGGLPELAQRDYGAGLAGLEEVYGVPQDKLEFTPISDGGGPLTVRALVDGD
+VDLANIFSTTPAIKDNGFVTLEDPKGMITAQNVVPLMAKDKVTDRIREAVEAVQAQLTTD
+DLLAMNAANAGEAKRQPRQVAADWLRQKGLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adc24c62da62c576cfb8e70bc63d6088ffc53155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002188.fa
@@ -0,0 +1,25 @@
+>0_2218
+MSTFQTPQYTIVELLQKARSGELQLPDFQRPYRWDDERIRSLLVTILRGHPMGVIMTLRT
+GGQNVRFKPRPITGVPAEGLKDPELLLLDGQQRTTSMVQALTGDGIVDTEDVRHHKLRRR
+YFVDVVKALGDVREQEDAVVSLPDTGIVTENIGRDVVLDVTTEEKQWELGLMPVTVLFDS
+ADCFAWMMKYQQALPERMEITQRFLSSVAQAVQTYKIPAIELDKDISKDAVATVFEKVNT
+GGLRLDVFELLTATFAGDRAYYEETGEDFRLAEDWALTEEVLRTYPVLTDMKSTDFLMAV
+SVLATLAKRREALAAGKTGQQVPQTSARREDILGMSLEDYRVWAPRLRKALPTVARHLRD
+LHIHDSRGAPYSSQVVSLLIITTLLGDRAEEHAVRARLNQWFWCGVLGELYGSTITTQLA
+KDAEQIPEWSLGKSAETPEAIIRASFSESRLGSLRTRLSAAYKGVYALIMAQQPPAKDWM
+LDQTLDFQSYDDLQVDIHHVFPRKWCDENGIEPWRRESIINKTPLAKKTNIRLRGDSPAV
+YTERLDDKGLTPQQVDAQISTHAIDPALLRAGDFDAFFNDRRRRLVSMIENAMCKPVVRD
+WEVDSESTDAPENFNDPAEMEADEPAGDEEAANVAD
+>1_1969
+MPDTFGHHPWTVQDLVSAVDSGHVRLPDIQRPFVWSNAKARDLMDSMYKGFPVGELMFWE
+NADPEHSRAIGTLEKSQSGSMQVIDGQQRLTSLYAVVKGKRVVREDYSQENIVIAFNPLT
+ERFDVPDNRIKRSSEWIQDIKTVFASPIDARSDYLDGLEKARGGERLSREDERRIEEAIN
+RLSRVLAYQFQVVQLKKEVSRETVADVFVRINSEGVKLSSADFILTWLSVFWEEGRQQLE
+DFARGSRFTPQELARMDETTVRWTPKNPYLTLDPGHVLRVVVAVGNRRAPLQDAYNALRG
+RDPRTREIVPANRERELAKLKDGQARALDPKNWDEFLKVIERAGMRTSAMVTAKNAVIYG
+YALWLIGRTEFGVPVDDLREVMARWYFMAQITGRFSGSAETRAQEDLNRLDGLERTPEAF
+TTAIDSLVSTTLTEDWWTVTLSEDLHTSNMSGPAYTGYVAALNILDADVLLSTLKVKDWI
+DPNRRPVKGVEKHHLFPKDYLKGALGLKSTRQINQVANQALVEWSDNIDISNEAPSAYWP
+AQVTEKAIQGERLAKQTWWHALPEGWTEMSYTDFLAARRKLIAGVTREGFRKLSDPNYQP
+SPPAHPVPASEPVLPTFEQLVLAGALPVGTHLLPTDGRTDSIAEVTPDGTILLDDQEYTS
+PGLAAKADGAEDEDGWLYWSADLAGQATILDEVRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc2f67c5e1cd264fbe4181d199709b4873741fbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002192.fa
@@ -0,0 +1,14 @@
+>1_225
+MPSPLDLARQAKHRLFLLRRAREVVRQAAAVRGSERFAREYALASAGFDLPGLPAMSGPC
+AVAMVRDEADVIERSVRHLADQGIPHIVVVDNGSKDATPDILRRLAGEIPGLVVGADREP
+AYVQSAKMTRLADLASAAGATWVVPFDADELWFGAEGTLAEALAAADAPVLRAVMHNAFP
+AADGSGPLLDTIAHFNVKVAFRPRSGAVVEMGNHEVLRPGVRADGLRILHLPWRSFEQFA
+RKSRTGAQAIALADTPEDKAYHWRRLGALDDDALRAAWEALLAGQPLTDAAWYPRGTLRP
+LRSDTPTRWDEV
+>2_2381
+MDLLSPARALKHRAFLARKDAELRAEARRLRADPVFRAQYSAAEAGLKVPPLEDHPGPWA
+IAMVRNEADVIETAVRHLVRQGVDHLLIVDNLSEDDTPQVLARLAQEFPHLHVGTDHEPA
+YYQSAKMTRLADLVSAAGARWIIPFDADELWFAPQGRLVDALTRSGVPVRRAHLYNLFPT
+PDGQQWHLDTARHFDDKVAFRAWDGAVVVMGNHEVSRPGPRDGEGLRILHLPWRSFEQFA
+RKTRIGAAAVAQAELNEGEAYHWRWLGSASEDELRAVWRRLLSGEAVANAAWYPRGTLRP
+IGDTLPSSWADVQALLGPGPAEGNALSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..504755af3b8906c837cf3a6cfc4520edae01ab4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002199.fa
@@ -0,0 +1,11 @@
+>1_309
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFVSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAHSAC
+LQYRRTGW
+>4_1946
+MSTLTLSSKPLTDDRRAVLHRRIRWIVAGTITYNVIEAAIALAAGTVASSSALIGFGLDS
+IVEVLSAAAVAWQFATPDPHRREKVALRLIAFSFFGLAAFITVDAVRTLFGAGQPEHSTV
+GIVLAAVSLAIMPFLSWFERRTGRELGSASAVADSKQTLICTYLSAVLLVGLVLNSTLGW
+TWADPVAALVIAAVALKEGVEAWRGDACCTPASALIAGDQNEKDGDGCGADCACCAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b08eb761c2b4414aa9be229b52661b2bca0818b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002204.fa
@@ -0,0 +1,11 @@
+>1_658
+MQNTEQTPRDASTEAGGRLWRHRIVENDTLRMTVLSMLAAAVAIGLSTLLIATPLGDALG
+VGAARRASWMTGLMTLCLMWSIYSALDTVVLYRWLGRRDSTDLHALLRTRSRGPKESVDP
+VGWRALMLGASSTLGNTATFSVMAMLVVVISMWMPEVRSVPAMRLLAVATVLASWASIVL
+AQALRYARLAAQHDPKRSRPEGESPAPPIRFRGSDSPVFSDYVALSLTLSTMMGAQDVVL
+SGRAARTAVREHALVGFLFNSMIIAALASLLLTVA
+>3_1488
+MDSDDGRLWLATLPALAAGASGVLIGREAAAEFPSADWRVMFYGTLGVTQVVMYVVYLWL
+TLRRFHGLDARTLERDLRTVSRGPRPGSWAVRMGLPYGSTLGWMTSVSVVALVIVVVVML
+DPATAGQPLLRVLCALVVVSSWAVLWVSQALAYARMAAQHGGIEFTGEEPPVFEDYLTLS
+AFVSALFGTGDVTLTGRRTRRAMRSHVMVAFGFNSMLVASLATLLLSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d31fbaf3cfb8a91e529a9c947109eec5bd532ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002209.fa
@@ -0,0 +1,20 @@
+>1_738
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAEAVEREVAAGAVPMA
+VVATLGTTDRGAIDPLPAIADVAERHGMWVHADAAVGGILAASAATRHELPGLHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVVSLFAGARERTRQACGILRARPTFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAATHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEELVDVVEEAALRHV
+DAVRASRHRWRGVARTRPHGPSVAVSCTLPASAGPRPSAARVDEHGEQVCA
+>4_957
+MLPRLFGLGDPAAYLDATGRAARVAVDTAYDRAGVHPDTPSTHLADAVGAVDFSQPTGSL
+DDALAEVAELYAHQTTAYHHPRYAAHLNCPVLLSSTAADTVLGALNTAVESWDQARSAAL
+MEQRLLAEVGRWCGFAAGDGVFTSGGSASNLQAMTLARGRAVQRLTGHAGLADLPAEVLG
+SLRVFVSAATHYSIAKAAGLLGLGRHAVVVVPTDAAGRLDPGALAAAVEREVAAGAVPMA
+VVATLGTTDRGAIDRLPAIADVAERHGMWVHADAAVGGILAASAATRHELPALHRADSVT
+MDFHKTFYVGLACSALVVRDAESLRHVTVHADYLNPEDSVHPNLADRSLQTSRRFDSLKL
+WLTLREHGAEAVASLFAGARERTRQACGILRARPMFAVLEDPTLVTVLFRVRAEGLSEEE
+CTAVQAAMHRELVAGGRALIATTVVDGVPHLKFTILNPAVTSGELEALVDVVEEAALRHA
+DAVRAGRHRRRGAGRNRPHAPSASVSCTLPSSAGPRPSAARVVEHGEQVCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002213.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61ad9f96690006e8c2e3066f18f6d049f0eda989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002213.fa
@@ -0,0 +1,10 @@
+>1_1655
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
+>4_1873
+MARKSNPVYYDANGNVVQPPAKKKGGCLKYALIGLLALIVIAVLASMMGGGSNSTSEGGG
+EAASQGETSSSDEAAKVGLGQEFTVGDWATTVESVDTPVASVGPSGFSTEAQGEFVPVQI
+SAKNNAKEERTFFADSVKLVSADGAEYSYSTDASIYGTENGMNIEPTNPGNVASGYLWFD
+VPAGTEITQVKVSGGGLSLDQPVVVELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf25ba7fe609f25b20c76317471b64bd89ec9881
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002215.fa
@@ -0,0 +1,12 @@
+>1_1697
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
+>4_1915
+MNVFGPDILARTMSEPADPTKYGIRWQYHSRSDRHGKVASWGVAFDLLRSSSVMRQHARD
+GKIVLGVNLKLSDFETKKSKVLDLVIARPGGAATSARGESLVSLAQRYNMNLSGEEMGEL
+TSLPDIPVAPVGSVLVALEAKATMTAHVKSLPRLHDELTSSHISVHGESQTALAIGYAQV
+NVADVFVSSNPANVERIHLGQEPVVTSHKQPGDCQRVLDTLNTLRTRSSSIGIGFDAIGV
+TVLDLRNDDSPVKVVHSRPAPQPGDAFHYDSMIMRMATRYDTQFSGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eebd8f271382bb6cdf3266120cabcfc0130da01b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002217.fa
@@ -0,0 +1,8 @@
+>1_1732
+MADDLAQCYLMSYPPDVAASDLDEAREEMNATFRGDYGKLRADASTTAWVGGRLAGAIMV
+VTHSIWDEHLTGPFIIDLFIDPHARGKGIGRALVQHAIATCCDAGDHTLSLRFGQGTSDA
+AMRIYQRLGFRPVG
+>3_1271
+MSTDLLTLRLPAAHAADHVRGDFEFRGLDTGTTDDLARCYLMGYPPGVAASGLAEAREEM
+DATFRGDYGELRADASATAWVDGRLAGAIMVVTRSIWDADLAGPFIIDLFTDPAVRGKGV
+GRALVQHAVDTCSAAGDAAVSLRFGEGTSEAAMGIYRRLGFRPRTGTQRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5eae6621e08f3a6a5c7fbc61f27f6a9fbce60611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002224.fa
@@ -0,0 +1,23 @@
+>1_2115
+MSTAEAGAATSTPADPWSSWLGSRAAVRARRGLERRAEPPEPGAPSSDVVDLAANDYLGL
+AAHPDVRAAAARVATEGPVGARASRVVTGTHPAHADLESAAAALAGADAALAFSSGYTAN
+LGVLGALAGPGTAFLLDEHAHASLRDGTALAATARSGAFAPLPGASVTTVEHNSVPAFRA
+ALGRLRAEGRARRIVLVVESLYSVLGDEADLPALAALAAEHGALLVVDEAHSLGVVPGGS
+RTGALGLWAGQAPVVVTATCSKALGGQGGLALFGGPAARSWRDHVLNTARTFVFDTALAP
+VLAASAAAACRIAATGEPAARLARARETAVDVFTRRTELAGHVEVGAGAVHSIRMPGPEQ
+AVAAAAELRAHGVLVGCFRPPSVPDGIARLRVSVTTAVPEPRLRAALEAVASVAARAWGA
+STGCPFAHGDPRPEAVRGDHLRISDPADLRRVLTDPGTFASDNALTAVVPLSGPARRILA
+AARFRLPPVLASAGGEEHRAVRRVVAPFFSPAKVREARGRILATTRTALTAALADTGRAG
+GAVDLATTVAAAVPARVMSALTGVPNPPEAQLHRWSADSLELFWGWPDEDRQLRLARSAA
+DFHRWLRGAVVEARGDDAQPGNLFAALHEAGVDDERIVSLGYFLVIAGQETTRLLISTAL
+TRALADPARWAALGAGADGGAGADAAEAAAAELVAECLRTSSSVPTWRRLATADVRVGEH
+EVRAGDELLLHLSGEQHDDARLAFGFGLHRCLGAGLAELETALVVREVARLLPDARLTGP
+PATWLRLLSFQAPQHVLVTPGPWHGGEDIRIEQSGVDTCASRS
+>2_2334
+MYAFKDQLAAELDELRESGLYKRERAITTPQSAHVKATAAGAEDGEAREVLNFCANNYLG
+LADDSRLIDSAKRALDERGFGMASVRFICGTQDRHLELERRVSRFLGTDDTILFSSCFDA
+NAAVFEPFFGREDAIISDALNHASIIDGVRLSKAHRFRYANRDMADLRAQLEATKELNDG
+AGARRTVIVTDGVFSMDGYLAPLAEICDLADEYGALVMVDDSHAVGFMGDTGAGTPEHAG
+VSDRVDVYTGTFGKALGGASGGYVAARQEIVDVLRQRGRPYLFSNSIAPSIVEATITALD
+LVEDSASLRAQLFENAALFRRRMTEEGFELLEGEHAIIPVMLHDAALAARMADAMLDQGV
+YVTAFSYPVVPKGQARIRVQLSAAHSAEDVEAAVAAFVAAREAVQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26a25bf872f556fbd79b2c25b46775036952a548
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002225.fa
@@ -0,0 +1,10 @@
+>1_2130
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLAGGG
+RGLQVPAISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLAAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDAAGARAGVLALHDFLARSALDYAARRADHGSAEPPAPWAEGR
+>3_146
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLVGGG
+RGLQVPPISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLPAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDSAGARAGVLALHDFLARSALDYAARRAAHGSAEPPAPWAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86f9eed96fa9d4ab40bb475289de26c91382f062
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002227.fa
@@ -0,0 +1,6 @@
+>1_2167
+MYSVYAQHWQRDTEAAASARVYQVSRLRHDAAPAPGVSIFRHGRPVLTLTPDDARRIADG
+LHDAAERAERVPTTPTRKEHHS
+>2_35
+MTRRTFITNRDRWTRDLTTATKSRANAILREHPDGGTVPGVMIFRDRLPVLTMTPDQART
+LADQLHDAADTCLEAANG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e052cdc9d3d87203e959f4257879dc1d23deaea2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002228.fa
@@ -0,0 +1,5 @@
+>1_2170
+MTTENTASTDRASTEENLRAAVRFHVGRNDRIRKRAERAETEAAELRAALAQAHAETDRL
+RAQLTELPEAHT
+>2_33
+MSANERPTEADNLRQMLRFHMDRAERHRLRAEKAEAELAELRKKKEAHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..838b6e8cde02c11390dbe7db6bc548cfb01652f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002230.fa
@@ -0,0 +1,6 @@
+>1_2172
+MNGPTCRHCADWAYGYAEGYAQGHASGLAAGRVQGAAEGPAHPAIADSVARMFAGWDGAE
+AAHARSAAGFRDWYAQARQEENAHDIAA
+>2_30
+MSTLETVAERVAADRALYAAAYAQGHADGLAEGLAQGAAHPAITDSVARVFAGWGGAEAA
+HARSVAAFRAWHTAARAELKEAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002233.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce3fe7945b69fa8a70ae4aaedd4d5279c85589ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002233.fa
@@ -0,0 +1,12 @@
+>1_2244
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA
+>4_277
+MTEPRIAVVTGAARGIGAALARRMAEDGFAVAAVDLSAEACADVVGQIEEAGGTARAFAA
+DVAREESVAQVMDAVVAELGAPAVLINNAGVLRDNLLFKMSAQDWDTVMDVHLRGHFLMT
+RAAQRHMTEQGWGRIVNISSTSALGNRGQANYAAAKAGIQGFTKSVAIELGRFGITVNAI
+APGLIETDMTRATAERIGVPYETYVAKAAEQIPVARTGTPEDIAAAASFFARQEASFISG
+QVLYVAGGPKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d25a3c91f166f6dae96a9ff99f50d0cd6c78d199
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002237.fa
@@ -0,0 +1,14 @@
+>2_69
+MRLAAVNPIPGLFTIAPADRDHEVGLRVGVTVLVPLLVLLAAGRMDLAVYAVFGAFTGIY
+GRNLRHGPRLQAQLRGGGLMLAVLAAATLAGRLGVSEQADPWGLVLWTTVVAGVAGVVAT
+LLAAPAGVHHNYWAMVAAVVPLVGHSTRYRVSRGLQRVIGTFLGLVLTAGIILLDPPVIV
+LVLIIAVLQVAAELYIARQYVIAQTVVTPLALLSTMLVGVTAGGAGSLMAAGGLQHLADR
+GVETVIGAAVGIVCVLFPWAWRRWVWGSPDPARAIPVVRGPGS
+>3_53
+MTTQAPGIPLTMGRIRARRPRRKDPRPVRLADVNPFPAMFTIGPPDRGHEVGLRVGVTIL
+VPLLLLLALDRMDLASYATFAAFTGIYGRNEPHGVRLRTQLRAGLLMLGVLTAATVAGRF
+GISEAHDPWGLVLWTTVIAGAATVATGWWNLRPAGSLFHIFAFAAAASVPVKPPVVEGML
+MAVAVVVWAIAVGLSSRVLPSHRTPLTWPPSDRPDRGRRRLILLEAMWYVIAAGVAGSVA
+TLVAAPQGVRHNYWAMVAAVVPLAGHSTRYRVNRGLQRVLGTVLGLGLTALIVLLDPPAV
+GIVLVIAVLQVLAEVYIARQYVIAQTVVTPLALLSTMLVAVTVGGAGSLAEAGAFRNLQD
+RAVETVIGAVVGIVCVLYPWAWRKWVRRSPDPTREIPIVRPEQIQRPVGGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f1182f33b1f313d7dbcc4280621f9ed911fb678
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002238.fa
@@ -0,0 +1,8 @@
+>2_72
+MLLLDADTLIQAKNTYYAFDFAPGFWDWLDRGHAAGLLASVEAVGQELKRGHDELADWAS
+ARPSFFVQPGTAVPGSIAQLAAWVHGQAQYTAAARQEFLAGAGDLFLIAQAHGGSHTVVT
+SELSRPESKKRVMIPDACQAVGVPCVDLFGALRATGGLMLVLSPAS
+>4_1487
+MYLIDANAFIEASRHYYSFNLAPRYWSWLYEQSVAGTVGSIKAVYDEIADGDDDLSAWVR
+DNTPEEFWLEEDDDSVAAIIDLATWATGPTRQFTQAAIDEFMASADLRLVAQARALGATV
+ITREVPNAESKKRVKLPDAAAAVGVSCVQPFQAYERLGLRFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9aa2561c7a473b31229288c21a2cb7b63be94851
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002239.fa
@@ -0,0 +1,16 @@
+>2_73
+MTVRVAAAPDVLSWAAERAGWDDALAEKHFPRFHDWLTGTQQPTLKQLEEFAHKTHTPFG
+ALFLPEPPRMDLPIPDLRTVGGAGVSEPSPDLLDVVHECQLRQDWYRDEALRQGEEPVAL
+VGSATVDDDPEAVGARLRHELAIQPVQNKAGAESFRRRLVARLEGLGLLVMISGIVGGNT
+SRALDPQDFRGFALSDPVAPLIFVNGTDAPVAQHFTLLHETAHIVLGHSAVSGSRMRGGT
+GEEAWCNRVASAALVPLDEVRRARRDSAGVPLAELVEDLAARYCVSRSVIYLRLRVAGLV
+SEDVVSRHFEEQDADAPGRTPRRRRESGGDYYRTATVRLGKPLIRAVLRSTREGHTSYRE
+AMRLLGTHKIEVLHEMGRQAGVE
+>4_1488
+MTVRVSVSPDVLLWALDRSPDPDAVATAFPGVDRWVSGEAEPTVKQLHAFAARTGTAYGY
+FFLQAPPAIELPIEDFREGFEGERYRDPSVNLLAVLHQSLRRQDWYRDYAIENGFADVSV
+VGRGAGMSPLEAAADMRRELNYEVRSRVGNWSDQRKRLLAAFEALGGLTVVTSMVENNTH
+RPLDVDEFRGFSLIDDMAPLVFVNARQTINGQLFTLAHEFAHVWRGVGGISDEDLRYEPR
+NEVEQWCNDVASEFLVPSNDLRERYAGVSSLRLTEQIERLASIYRCGTLVVLQALRRNRL
+YDFEDFQTDYDAEVERLRRFERADSGPGGQFLYNQPYRIGTRLSRALISDAMAGRTRFTD
+AARLMSFKSMKNFDSYASYLGTVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4ed03e490f07bd40a490a62c6ad1696990c2d82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002242.fa
@@ -0,0 +1,11 @@
+>2_95
+MTTALPDALRLTDEARERLHADCRHLHRHPELSMQEHATAAWIEEQLDEIGVERFRCGGT
+GVVGVMRHPGGAEGPVVAFRADTDGLPIEEDTGLEYASTARGTLPDGREVPVMHGCGHDT
+HVVSALAAARLLAAAPDTWGGTIVWVFQPAEETGAGAAAMLEDGLWDRAPRPEVVLGQHV
+MPLAAGKVQLIPGMAMALADSQAITFHGRQAHGSQPQDSIDPILMAAHAVTRLQGVVSRE
+TDPRDPAVVTVGTFHAGLKENIIPDSAEIALNVRTFSAASRDTVLGAIERIVRAEAQASG
+APEPSFRTIARFPRCHNDDEQSARVAAALRAELGEDHVLDGRPLMGSEDVGALADAIDVP
+LVYWFFGGFEGEDPAAFPGNHSPHFGPAMAPALDAGHRAALAGLLAYVGR
+>3_65
+MAAVAAELGEENVMEIGPLMGSEDVGALTDAIDVPLVSWFVGGFEGEDFGDNPANHTPQF
+GPVMEPTLTTGVHAALAGLLHYVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c78c7ab85636b34236fbd3443450eca088a357d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002243.fa
@@ -0,0 +1,11 @@
+>2_106
+MTPTSALSSRAPGLAACLALGLAALGTATAVRPWAPALSPLLLAILAGLAWRNLAPVSER
+LAPGVAFAATSVLRAGIVLLGLQLLLSDVLALGPGVIALVVGVVGVTFAATLALGRVLRL
+PWDLTVLVASGFSICGAAAVAAADSVVRARREMVATAIGLVVLFGTLMIPVMPLLTGALG
+FEEQAAGLWIGAATHEVAQVVAAGGLVGGTALSVAVTAKLARVVMLAPVMTGLAWWQRHR
+DALEPATLDDGAPTAVERPPLVPWFVVGFLLAVLVRATGWLPAGVLDAAALVQQLLLATA
+MAALGLGVHLRSIAAVGPRPLVLGAASTAVVVVVGGFGATLLA
+>3_74
+MPARLEPGIAVAAKPVLRAGIVLLGLQLLLSDVLALGWGAVGLVVGVVALTFAAALALGR
+ALRLPWDLTALVASGFSICGAAAVAAADGVVRARREMAATAIGLVVLFGTLMIPLLPALT
+GALGLGERAAGLWIGASTHEVAQVVAAGGPRPLVLGAGSTAVALAAGRAGAALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3e1d8edefba8efd2c4e8e7db2160dfa17769a74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002245.fa
@@ -0,0 +1,14 @@
+>2_139
+MTAQTPATAPADDAPLEVPVLDLSGMRRPDGSFDPDFLARLRHAAHHVGFFQIVDYGAAP
+GQVDDLFRVTAEFFARPEAEKLALHNQDSPHWRGYSAVAAERTQGRPDSREQLDFSPDRA
+PVPAERIGEGEEYWHLQGPNRWPADMPELERSAMAWTALMDRVGEDLLKALSVAIGLEED
+HFAEAFDGDRAWMAKLAHYVGGVAEAGTQGVGLHADYGFITLLLQDEVGGLEVRPHGQDA
+WLPVEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFYSPRLDAVIEQ
+VELSAELAADARGASDDPDNPMLASFGSNMLKGFVRAHPKVTERFHPELLDR
+>3_97
+MTAPSPDSATPARVVPVLDLSIMRRPDGSFDPDFLDALRHAAHHVGFFQIVDYGAAPGQV
+DELFRATAEFFALPEEQKQALHNQNSPHYRGWSAIAAERTQGRPDSREQLDFSPDREPVP
+VERIGEGQEYWHLQGRNQWPAQMPELERIAMDWTALMDRVGEDLLKALSVSIGLDEDHFS
+AAFDGDRAWMAKLAHYVGGVAEAGAQGVGLHADYGFITLLLQDQVGGLEVRPYGQDEWLP
+VEPIPGALVVNLGEMLEVATDGYLMATIHRVQSPPEGVDRYSVPFFFSPRLDAVIEEVTL
+PDEYAAEARGVSDDPTNPMLASFGSNMLKGFARAHPTVTKKFHPELLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0b41781bf8827532991162ed71ede5694043c08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002246.fa
@@ -0,0 +1,6 @@
+>2_160
+MSTKQTRISPISGGRRPVSPLGPALLAAAAGVVLAGVRRMRARSRRREEVAARVAADRRA
+GR
+>3_111
+MILARIPRRSARRAVPVVEATQPPVRDRSREVSPLGPALAVALGGVVAAAARGLRARTRR
+AEAADRARVARDADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a89652fb241ddb070c768345e8a1c4df47519f69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002248.fa
@@ -0,0 +1,10 @@
+>2_239
+MRHFDDPVLQAMASRRSVSQVGPSTPTDKELAGLLAAVTPVADHKALRPWRLILLRGEDR
+RRLGEALDAAAGTERERGEVNPKPYRAELLIAVVASHRPHPGVPGWEQDATAAGAAHLLE
+LALWQAGWGVMWRSGLYTDAPAVRAAHGLGDRERLLGWLYVGDVDPAFRARLEASKKPAL
+DPAPFLGRMPQG
+>3_173
+MVCMKHFDDPVLQAMASRRSVSKVGPTTPSDEELARLLVAVTPVADHKALRPWRLITLRG
+EDRAVLGAALDAAAGVERAEGERNEKPYRAELLIAVVARHVPHPGVPEWEQHATAAGAAH
+LLELALWQAGWGVMWRSGLHANAPQVRAAHGLADDELLMGWLYVGDVDPEHRVKLAASRK
+PALDPAPFLGTMPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dad0c8c9a23bdfcb2278acdf49721860cb8f3dc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002252.fa
@@ -0,0 +1,9 @@
+>2_330
+MAALTAVVVLGVAGCTGPEGRTGTTTDGPGTSTSPPPVVQQSEAAAHPADNLPLGGEPWA
+VVTLTRGGEALDPGPWRQVRIVTSEPFILAAPELCPQPRFGITAVTESAWEATPDVAQPA
+IGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEMRLRRADVELVLSEEG
+>3_269
+MRPSAPPRRPRVTRMAAMTAVVVLGVAGCAGPEGRTGTTTTDGPGTSTSPPPVVQQSEAA
+AHPADNLPLGDEAWAVVSLTRGGEALDPGPWRQVRIDTSEPFILAMPELCPQPRFGITAV
+TESAWEATPDVAQPAIGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEVRLRRADVEL
+VLSEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5921f29bf9f34d7f0559f5ae3419cfa8bdf94cca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002253.fa
@@ -0,0 +1,17 @@
+>2_332
+MGDDNARMIRRFRSSSTRRPLHRSLTRRGTRPRRRLHTDDRVSLPPSSVAGLFVVPFLAT
+HLFAWGLFASVYLIAHPGGDSVFTASMWRLTTDVAVNAGLAMEDSLLALTSTGVAVTVAL
+YIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPASMIPELLL
+QGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIQGKFGGDFTLP
+PMRQWAKAARTLTFRRILRLLIWFFGYLLAGAFLGALTFACTSLTLEREWDARTLALGAL
+IGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLTTGLVLLSASPSQGSASLGTAV
+LGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPRPLLGTTC
+RTSPLRDAAR
+>3_271
+MVPFLATHLFAWGLFASVYLIAHPGGDSVFTASMWRFTTDVAVNAGLAMEDSLLALTSTG
+VTVTVALYIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPAS
+MIPELLLQGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIRGKL
+GGDFTLPPTRQWAKAARTLTLRRILRLLIWVFGYLLAGAFLGALTFACTSLTLEREWDAR
+TLALGALIGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLATGLVLLSASPSQGS
+ASLGTAVLGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPR
+PLLGTTCRTSPLRDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b949706457b8d4d1a7d4671df17f6dd790164f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002255.fa
@@ -0,0 +1,8 @@
+>2_353
+MVRVTEVDPATSIDELSDRAELIVRGAPGEVDAPGDGRTRITVDASETLAGEGRSASSST
+CSASPTRAPPTARRARSCSGS
+>2_1719
+MVLIARSARPVVALATALALALTGCAAEAAGPVDGDSAAAPAPTSTGASPSAEEAFWARY
+QATMVSEVDPALSFDDLTEKSTVIVRGPVMAAAGVREVDGRVVVAPADGDQTSSLLTVRV
+EERITGEAGDTVRVWVAGPAPTAEPPTESYLWYLMPADTPDALFTVSRSGVIGPDAGGTL
+STVMVPGDGEFILPDGAVTLADVQRRTEELLER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfee1cee9b41f73908e8148c867b2c77de72996a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002263.fa
@@ -0,0 +1,18 @@
+>2_479
+MRGGVDAAADPNGGPRPRRWWDGPLDVERLAWDAVVAARDAVRELAAARGQDGVAGTTPE
+LVAASFAALDHLRVEGAAVPAWAPMSGFLRAADGWVRTHANYPHHAAALTRALGAVDRPG
+LEAAVARRTAAEVESAVHAAGGIAVAVRSAAAWAAHPHGTATRDEPWASVAPGGPRRRLR
+GGRLPLEGVRVLDLTRVIAGPAAAQLAACLGADVLRVDPPGRPEILAQHLSNGMGRHSAV
+ADLTERAAEVEDLLAGADVVLLGYRPGSLDRFGLDPEALVRRHPHLVVGSVSAWGEAGPW
+AQRAGFDSIVQAACGIADACGRDGEPGALPVQALDHATGHRLFAETVRLLAQGRAGVVRI
+SLLGAARTLLGLSPPPPGPAAELPVPRVEVGSEAGRLDAVPPAIALDGEVLARDVGAYGA
+AALRWL
+>3_395
+MPRVSAPVPSPRRWWAGPLDVEQLAWGAVEDARDAVQALVDARGQGWRVGTSPELVAASF
+AAIEHLRVVGEPVASWAPMSGFVRAVDGWVRTHANYPHHAAALGRALGATDRASLERAVA
+GRTALDVEEAVHDAGGIAVAVRRATQWAAHPQGVATSGEPWVSVDAGRERAPLSGGALPL
+DGVRVLDLTRVIAGPAGSQLMACLGADVLRIDPPARPEIDAQFLSNGMGKRSATADLAEH
+RTELEALLAGADVVLLGYRPGSLDRFGLGPDALAQRHPHLVVGSLSAWGERGPWARRAGF
+DSIVQAASGVALACSPDDGATPGALPVQALDHATGYALAAGVVRLLVEGRAGVVWASLLG
+AARTLLGFAAPPEERVAELGVPHVTVRSAAGTLNTVPPPLTLDGASVERDVAGYGAASLR
+WA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7e7173900785df09560e955548fed5a02db3421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002264.fa
@@ -0,0 +1,10 @@
+>2_489
+MTLTAALLSFALLALLITITPGLDNALVLRYAGRQGSGAAFAASAGICAGLFVWALAASL
+GISALLAASEVAYTALRWIGAAYMVYLGVRMLISAIRGGYGAPGGSSVATVRSRDAFRTG
+FTVNLLNPKVGAFYVALIPQFMVTGVAPAAMGVLLAVVHIAVCMAWFVVLIALVGVVSGW
+LQRPSVQRGLDGVVGTALVGFGARLALAKA
+>3_426
+MTLTVALLSFALLALLITLTPGLDTALVLRYAGRQGSGAAFAASAGICAGLFVWAVAAAL
+GVSALLAASELAYTALRWIGAAYMVYLGVRMLIAAVRGTSGDHDGDAAPALVRRGQAFRT
+GFTVNLLNPKVGAFYVALIPQFMVPGVAPAVMGVLLAVVHIAVCLAWFVLLIALVGVVSG
+WLRRPAVQRGMDGVVGTALVGFGARLALAKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94e0b024a2235296516e52b8814b1812fde8430e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002267.fa
@@ -0,0 +1,10 @@
+>2_499
+MTSVLFVVSAADAWTLKDGTTHPTGFWAEELATPHRLFREAGWDIVFATPGGVPPTVDRA
+SLGEAAGSEEERAALTAHLESIRAELDAPLRLEDVDDREFDVVFYPGGHGPMEDLAADPV
+SGALLSRRVTAGDPVALLCHAPAAALAAKDADGANVFAGRRMTAFSDEEERAGGLAEQAP
+WLLETELKEAGVVYEKADEPMAPKVVVDGAVYTGQNPASSAELAERLIADLG
+>3_449
+MTKVLFVVSAADQWTLKDGTVHPTGFWAEEFVVPHQTFTEAGWHVDIATPGGRVPTVDQL
+SLGMMAGSPAKREQLRAALDRLRPALERPLVLADVDDSAYDLVFYPGGHGPMEDLAYDPV
+SGALIARRLLDEAPLALLCHAPAAVFAAKRADGTIVAEGRRMTAFSDLEEKLNPFARKAK
+WTLEAQLKHGGVQYEKARFPMQSHVVADGALYTGQNPQSSAALAERLVHDLSARVER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fd3433d50f63413155e4f93583cbe0b60d273ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002268.fa
@@ -0,0 +1,7 @@
+>2_503
+MVVIAGLAVRLAFDGAWTGPVGDALYAVLVFLGVAWAEAFPPARLVFGTTFTAADLGLYA
+VGVAAATAADALASRARHGSGLARGPAGS
+>3_459
+MSAPAAPGPTTTTPRRRSRLALAAAATVAAGLLVRVGLRGVPGAAAWTGPLGDALYAVLV
+FLLLAWIAPRARTLPLAAAAFGVCAAIELFQLTGIPAALGRAFPPARLVLGTGFLWSDLL
+LYLAGVLAAAAVDAALRRRAALSPRGSGPRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..903de4762828457360ffb2e1727ec21f458ae37a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002272.fa
@@ -0,0 +1,8 @@
+>2_553
+MSQYLISVWHAPGVHAAGTAYESEDQMRLAFERVAAFNARLEESDSLVGAGGLTPPEEAV
+VVDASAAQGPEEVAAQRRIAEGTASPEGAQLGGFWIVEAPDEATARTLAGEASYACGQPV
+ELRRLQG
+>3_481
+MSQYMITVWHAPGVHAAGTAYESEEDMQAAFARVDDFNRMLMGSGAFVAAGGLTPPGEAR
+VVDAVAASDAGQAAAQAEVREGTLAQGDMALGGYWIVEAADDAAARGLAAQGSYACGQPV
+EVRRLQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..963e5d8b44a046b2b28223c030e2a902abe506d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002273.fa
@@ -0,0 +1,15 @@
+>2_563
+MNKDAQPSTELLSSIPEGHVEFGLHTFGDVTLDAEGRRLSHPEVLRDVVAEGVLADQAGV
+DVIGIGEHHRPDYAVSNPEMVLAAIGARTERIKLISAVTVLSSDDPVRVYQAFATLDGVT
+GGRAEVSLGRGSFIESFPLFGHDLKDYERLYEEKLDLFMKLRTEEPVSWTGTVRAPLERQ
+SVFPTTAHEHGLPAWVAVGGSPQSVVRAASHGAGLELAIIGGAPRRFAPYADLFRREVAE
+RGLEPRRVAVHVHGFVADTDEEAMELYYPHWEAAFTKLARERGGPLPTPEQFRQEAVHGA
+QHIGSPETVARRVADTVRAIGASRFGLKYSNATLPHGPMMRSIELYGSRVIPLVRDMLSE
+G
+>3_781
+MDVKFHIDTFGDRTSTLDGELESHAQGVRHVVELAETAEQAGVDGITIGEHHRDDYTVSA
+PDMVLATIAGRTERLTLGTGVTVLSSDDPVRVYERFATLDALSSGRAEAIVGRGSFTESF
+PLFGYELSDYEELFEEKLALFAELRAEQPNPVSWTGKLTQNLEDVVLYPPLEGAEPLKAW
+VAVGGSPQSVIRAAGHDLPLMLAIIGGPSARFAPFAKLYRDAREKFGHAGETQVGFHMIG
+HIAETDEAALEQFAPHYLEHHKRLGAERGWGSMGMEGLMHEVRHSLMGVGSPETVAKKIA
+RGIADLDATRVNFKVQHGPIPHEYNRRSVELFGEKVIPLVKDMLAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fea82f6d08c11f220f6979da25b87a817871a89d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002274.fa
@@ -0,0 +1,15 @@
+>2_574
+MPTPSSATPDPASARSASGARPADALPDDGAPVRVRLGVLVARPADPAVLDTAALAAQLD
+AAYPGLTWDVTVRQEELGDEDDDALDLLEITRDRMLDEDWDIAVGVTGEPLQQGRHTLTE
+QVSPVHAAGVLSLAHLEEAPVDAVARVVGEVLGIDPDDDAPSAADRRAAAGWARQLADDV
+EHRDREAPAAYALRVAVRNARMLLGTVRANKPWTLAVSLTRSMSTALATGALTLITTDLW
+MLSAEYNGVQTAVLGAVSVLAVTLSLIVGAHLWERPRRRAEREQVMLFNMATVLTVLIGV
+VVLHVMLMLAALAGALLLVDPDVFHVVTGEPGEFVQYVKFAWFVGGLATIGSALGAGLED
+DDAVRAAIFTRGASR
+>3_498
+MSPARPHSPSAAAYPGLAWDVVVSAEEVGDADDDSLDLLEITRDRMLDEDWDVAVGLTGH
+ALVQGPHTLRSQVSPVHAAGVVSLDLADGGAREAVEDVVARVLGLDPDDGAPSAGERTAA
+VARARQRAEDVEARADESGASFTWRVLRANARLLLGTVRGNRPWLLAVSLTRSMSTALAA
+GALTLLTTDLWMLSAAYDGVQMSLLGLLAVAAVSLSLVVGAKLWERPRRAAEREQVAVFN
+LATVLTVVIGVLVLHALLMLAALAGALLLVDGDVFTEVTGEPASPWQYAKLAWFVGGLAT
+IGAGLGAGLEDDDDVREAIFTRGATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dddb5df498a273b7cc4eff5c26bb7ce7b0a8671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002275.fa
@@ -0,0 +1,15 @@
+>2_600
+MTEQRRHEVTLRFLAAPTDQGHTGTVDAGRVLEWVDKAAFAAATAWAGSYCVTAYVGNIH
+FRQPVLVGQMVEVTGTVLHTGRSSMHINTVVSAGDPKTGELTEAARCLVIFVAVEEGKPV
+PVPEFVPRTLEQELAAEYAVSRIAVRDEIQAAMEGQRYTDAGTADRTVLRFLAAPTDVNW
+GGKVHGGIVMEWIDTAAYLCSTRWAGRETVAVFSGGVRFYRPLHIGDLVEVEARLIYTGE
+KGMHVAVHVRSGDPKTAQLELTTYCLTVMVARDDDGDAVPVPAWEPVSQEDKALWQHARD
+LLEIRGRAPGNRLPNHLLAERGED
+>3_526
+MTDDAARTPASTDAARPSPGPVPAPASPTEPATPVVERRREVTLRFLAAPTDLGHSGTVD
+AGRVLEWVDKAAFAAATAWAGRYCVTVYVGNIHFRQAVEVGQMVEVTASVLHTGSSSMHI
+STTVRSGDPKTGELTEAARCLVVFVAVGEDGRPVPVPEFVPRSLEQELARDWAISRIAVR
+NEISAAMKTQRHTDAGTAERVVLRFLAAPTDVNWGGKVHGGTVMEWIDTAAYLCSSRWAG
+RDTVAVFSGGIRFLKPLHIGDLVEVEARLIYTGNKGMHVAVDVRSGDPKTDDLQLTTNCL
+TVMVARDEHGDAVPVPAWKPVTDEDRALWAHARTLLEIRAKAPGNRLPDHLLRERGEGPD
+RGEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d47a384fc4555745bc6e283884b596f5091b101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002276.fa
@@ -0,0 +1,8 @@
+>2_621
+MAARGGTPADHAPAARRLLDRAPVLLLAERAGSNSPRVVGRSGATLAALHPGAQPRWLTA
+GLTVTPEARRTGVVRRLLHAVIGAVADRGGGDLHSVVNAGNAPSLALHASLGLEIVETGP
+RFAGIEFASGVGVLLSRPTCPESAPACA
+>3_1936
+MIASYARWQPEDHGTPRADVLIRPVRPHDVPALARVMAARGGAPETHTDAAALLLDRAPV
+LLLAVAEDGGGDALGWSGALQTSVHPGEHPVWLTAGLTVVPQARRAGVGLRLLHAVAEAV
+RTSRIETGPLHSVVNTRNRASLALHARAGFQETASGPRFAGIEFDGGDGVLLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38e53c5c4f5a44aad95005fc5ab19385d67d84ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002278.fa
@@ -0,0 +1,7 @@
+>2_627
+MTAPHAIPPSGLPSAAEVRRVLSALVQRCFSRETHARLLDADVSEGVLTVVAWQAGPSPV
+VPGRVIGHRTDLGMRLAECEGDLEAVLLDVLQFQEFEPSAPGRAASGAEPAWLLERYPEA
+TWYAQGASGT
+>3_1268
+MPSTEAVLSILRRLERRHFSRDAYARLLDADVTGEVLTVVAWQGGPSPSDPERVIAHRTD
+LRQRLTECRGDLEAVLMDALQFGVYEPSSPGRPPAGDEPARLLEKYPEATWYE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e39744eb42887a031da5c644663c86c67aa39ca2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002283.fa
@@ -0,0 +1,10 @@
+>2_736
+MSSAKNSDQRRQDRAAVLQAHWAAEAKAARKQKVLWGAGGVTAVALVGALVTVAVVTDPP
+PPTRQDIEIAGLETFEDLDAMHVNSPVDYEQDPPVGGDHASTWLNCGVYTEKVPKENAVH
+SLEHGAVWAAYDPSALSEEEITALQEALPDTHAVVSPYEGLESPITLSAWGAQVAVETPD
+DERIEEFVAKYWQSPEAPEPGAACTGGLDGPGRVA
+>3_2138
+MSTKLMADPEAKAERRRKVLVGAGALTAIAVVGGLVTLAVIQNPPPQAREDIEIAGLQTF
+EGLSANHVSTPVDYEQSPPVGGDHASAWLNCGVYTEPVPNENAVHALEHGAAWVAYDSEA
+LSQEQVDALRTALPAAYVVLAPYEGLDSPIVLSAWQAQVAVDSPEDERIEQFVAEYWQSP
+DAPEPGAACTGGLDAPGRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5238614f6b37f2a150e3b661fad50ec441dbf054
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002284.fa
@@ -0,0 +1,8 @@
+>2_741
+MPVRLRPAVLDDAKALTALARSQREHLAPWEPERPARWFTEAGQREALEQADCDRAAGRS
+YAFVITDDAGHLLGRLTLASVVRGAGQFCSIGYWVALEATGRGVATAAVEQALQIAFGEL
+GLHRVQAEILPHNHASRRVLEHHRFQRYGLGHV
+>3_1935
+MEITLRPASPGDAEELAALTLAQREHLAPWEPERGPGWFTVDGQRHALRAADADRAADRA
+HAFVIVGASGAIVGRLTLASVVRGAAQFCSIGYWVAHEATGRGIAGEAVRRGVALAFGPL
+RLHRVQAEVLPHNHASIRVLEKAGFLSYGRAPEYLRIAGRWQDHLLYQRVNPDWRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aaae2c7ba991727acde80886d36fc639c3a66bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002288.fa
@@ -0,0 +1,11 @@
+>2_842
+MNDILTVGLVGVGRLGSAVGQLVAEAGHRLLVADRPGSRVFRSVVETLLPGADAVPLADV
+VERADVVILALPQPALADLDLARARGVLLDATNAWEYTDGPDSIHRMDPLAWTERVPGVP
+VVKSLNHAGYGELLMDARPAGAPGRRAFAVAGDDGAAVDLVASLVDSMGFDAVPTSAADA
+PLLEPDGAVFGRRFDEAGLREALPHAAARVG
+>3_782
+MNDTMTVGLIGLGKLGSAIGRLTAEAGHRILVADRPDDPVFGLVLESVLPEARAVPLAEL
+LQEADVVVLAVPQPALAGLDLTAARGIVVDATNAWEYTDGPDSEHRMDADVWAARAPGVR
+VVKSLNHAAYAELLADAREHGAAGRRALAVVGSDDDAVARASAYVDSLGFDPVPGPSAAA
+PLLEPDGPDSEHRMDADVWAARAPGVRVVKSLNHAAYAELLADAREHGAAGRRALAVVGS
+DDDAVARASAYVDSLGFDPVPGPSAAAPLLEPDGPVFGVRLDADGMRAALAEGLEADSAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f2fc97653d04b7e3597e55aa951990aa7aed3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002290.fa
@@ -0,0 +1,6 @@
+>2_877
+MTSTPTRAKRKQTARELAERFGVSPRTIRRTVAQERADYLADAAARHERIRALRAEGLSM
+RAIAAKEGVTVGTVHYAIHKDD
+>2_1290
+MTSTPTRAKRSQTARELAERFGVSPRTIQRTVAQSREDYLNEAAQRRARIRALRAEGLSM
+RAIAEREGVTVGTVHYALHKEDQQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44893a26309726dad562ce5089f2bd83dd2b5082
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002301.fa
@@ -0,0 +1,12 @@
+>2_991
+MKIPAAITGGVAAVLVLGLTSCGASEVRPDHGVTARLDRENGQVVLPIEDYAASQADEAV
+MTQARLAILRSCLQKSGHNGVKPPTSNAERAVEERPYGVWIVDRARAYGFDLPPAAETVE
+PAAPPGGWSDEADPAFNEAYEACSSEVMEQMLAVSSPATSPGTTSVIADVTARARGLAAQ
+DPVWDEARDEWQQCLRDNGLTPVAEEGAVLSAESENLSDTRDAQGQTHSVKAEEIRLATI
+EATCNEQTRLTQRLGDLEAGYQAALIKKHEAALVEEKLVTAEHLEAARAYLARHQ
+>3_935
+MRPDPRPFRLAVIAGIALSASACAQSGAPDVPPDTSATAHLDREHGQVVLPVDEYSLDHD
+SEQLIGQARHVIMRTCLNSKGVNGLAPTATSSPAEERPYGLWRTASAAQNGYTMPRPAST
+EAPPLGGQWSEESDPAFNTAYDACNEIVRDDLDSVTPPETERTTAIDIRDDAFTLASATP
+EWKEARKQWHDCLTSRGLTPRTDDNAWSSEQGFGILTTADPQNPSPAAKQEEIRIAVIEA
+TCNEQTQLTQRLGDLEAGYQAALFKGKEAQLAQEKADNQKFVDAARAYLASHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cea34ee9020cf3423a567b3929883d6dfa67804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002302.fa
@@ -0,0 +1,14 @@
+>2_1002
+MSPREPAPLPAAFSDLPFGAADLRRAGVSVERTRRADLRRVSQGLHRAREAERGEWADLG
+YPVDPLPWVPEEAAAVVPLTGGVVSHLSALLLHRLTVPPWVRPDGRLHVSRRHGRGVCDR
+SGVATHGRSVPQEDVVALHGIAVTSVERTWLDLASLMPRGPVDPLVIAGDALVNRPWIAG
+DGRRGEPVTSVESLRAALRRAGRFKGVRAARAALDLVRVGADSPPETELRLALVDAGLPE
+PELQVSGDPGDRFAPVADLGYRDWRLALQYDGGHHRSREQQARDARRDGWFHDRGWRSLR
+LTADDRLDGFRRAIAWVRRHRP
+>3_944
+MAPRAPLPLPAHLADRPFTRVDLTTAGWSIERARRGDLVRVVHGVHRSWEAETGDWADLG
+FPVDPVPWPPVDAAAVVRRARGVLSHQSAALVHGLVVPAWVRPDGRLHLSRPHDRGLSGL
+PRVQTHARSVPPVDVTSIHGIPCTSLERTWVDLASLMPRGPVDPLVIAGDALVNHPWAGE
+GQARGAARTTVVSLRAALERAGRFKGVRAARLALDLVRVGADSPPETELRLALLAAGLPE
+PELQARIDPADPWAPAVDLAYRPWRLSLQYDGAHHRTREQQGRDARRDGLVQDAGWRSLR
+LTAEDRHDGFRRAVEWVRRHGSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1750d07ccddc31f0ce164b53527015375ce5ec55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002304.fa
@@ -0,0 +1,6 @@
+>2_1114
+MTARRGPLTPFFDSVRTTGFRRTRPRLVGGVAAGIASGTGVNVWLVRLALVLAGLLPVLG
+VGAYLAVWALTPWEDGTVPAERALGGR
+>3_1044
+MTPVSRPRPGGARRTPLTPVFDGIRALGFRRTRPRLVGGIAAGLAANTGVDVWLMRLVLV
+LVGLLPVLGLGAYLVVWALTPWEDGVIPAERALSGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4ead2df9aee9d5ec1ccfb09fd0dc3c99bcc8b03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002308.fa
@@ -0,0 +1,11 @@
+>2_1259
+MGVTVVLSLGEPIDCGWLHGDARHLCDVLVSGLHTTPALIQSRGRQQGLELSLHPLSTRR
+LLGLPAGELAGSMVDVNDLSWPRHLLDQLRQSTWPRRFHLLAAFLTKRLEQHPHAPRADL
+VEALARIHRTRGTIPISGLAQDVGLSRRRLSSLFDLETGLSPKQVARIARFTHAKDLVQR
+GAQPSDVAAMAGYSDQPHLSREWKSMTGWTLRQSKDDFPLLQDTDMLPA
+>3_2422
+MAVTPAWRNATPEHMFGRVLRPDEFHTRARYASAAPAPELAPWVERYWSVCFDLDDGEAF
+RTATLDDPGVHLTVERGGVHRTAVPGPGVWVTGPQTARRFDVTLVGSGSTVGVAFAVGGT
+RAFSSGDPATVVDRSEPGAAWFPGASALGDVAESAVAAAAALDAFLAGLGPRSDPAYERF
+RAAYAAVDDPDVVRVEDVAARAGCDPRTVQRLFHRFAGVGPKWALRRARVIRAVGSLDRG
+FPGSLAELAAAHGWFDQAHFTRDFRRVTGETPAGYRARRRPDEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aed6fee39284581ff5744fdfbb4de4e9040cd808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002309.fa
@@ -0,0 +1,11 @@
+>2_1271
+MSADIDAYQDQLVAWRRHLHQHPEASFEEHETVRYIRAELEPRLPGATFENLTPTSLVVT
+LDTGRPGPTLGLRADIDGLAMTEDRPDLDFASTTPGRMHGCGHDGHTATIMSALVWAHDH
+RDELTGTVLGIFQHAEETPPGGAKEMVETGRFADVDYFFGFHYWSTLPTGTVDIKPGPAS
+ANSDRFEVHLRGEGAHASTPEDAVDVVTAASSLVQQLLLIPSRRVAGLDPCVVSTTWMDA
+GRQSALNVYPPEAHIGGVVRTHDDDVRDTVEAAMRDMVRGLETANPGLSCELDYLRGYDM
+VWNDPARTAVVHELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDA
+GHHNPRFGLDEDAFPIALRLVVEVLRNGPRLAAG
+>3_1181
+MVQELCEDLFPGSVITDPPMLGGEDFAAFSRTAPATYVFVGAGNAAKGFDAGHHNPRFGL
+DEDAFPIALRLAVEVLRNGPRLTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a1378e7dfeed8b5aa8ef309740ab1fea407a1ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002313.fa
@@ -0,0 +1,18 @@
+>2_1614
+MSAPHPRPLLLRGARLTTVETADVLVAEGRIAALGAEAAAQAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPKLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSQLHVC
+HVSTAGSVRLIRWAKEQGVRVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+EALADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQHAMVDTGLMDWAGVA
+RVMSVTPASIAGLEDQGQADERGVPRVGAVANLVLVDPEARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPAQPYRHPAVAEAGGRA
+>3_1511
+MSTTVPPALLFRGAALASGRVADVLVSDGRVAAVGEVPAVDAEGASVVEAAGTVLLPGLV
+DLHTHLRQPGKEDAETVETGTRAAARGGFTAVHAMANSTPTADTAGVVEQVWRLGREAGW
+CDVHPVGAVTVGLAGEALADIGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKSFGGF
+VAQHAQEPRLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVCHVST
+AGSVELIRWAKAQGVQVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVHALRAALA
+DGTIDTVGTDHAPHTAESKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWSGVARAMS
+TEPARIAGLQDQGQADESGEPLVGAVANLVLWDPAVRRAVDPETHATRSRNSPYRGMELP
+GAVVHTVYRGRRVVADGELTQPVVHADAPEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53454dadf20f48d1550287098139688dfbc25bfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002316.fa
@@ -0,0 +1,11 @@
+>2_1884
+MTDLAAEHPRTDAVDSVSTRTHDEPFAVVGPWKDDPAAAGTAEKVKVTDEMLELVEAVRP
+TLLADGMFLVGLDIVGDKLMEVNVFSPGGLGSCQSLYGVDFAPAIIEDLERKVSVRKHYK
+GQIGNANLATI
+>3_1834
+MKIGFVVNDVATEKPVYTTTRLAMAALQAGHEAYLVGAGDVAYEPDGSLSVLAHGTQKKH
+RSLERLLEEVQDPANAAQMPVDELDVVMLRNDPADDATERPWAPTAAVSFGQLIAAAGVL
+VVNDPHTLANALSKAYFQHFPELVRPTTLISRDEALISEFIDERGGKAVLKPLQGSGGSG
+VFLVDRKESPNLSQIVEAIARDGYVVAQEYLPEAKNGDVRMFVMNGRPLEVDGRIAAFRR
+RSSSDDVRSNMSAGGTAEKVDVTDEMLALVEAVRPKLLADGMFLVGLDIVGDKLMEVNVF
+SPGGLGSCQSLYGVDFAPAIIQDLERKVATKDHYLGRIDNTRLAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b264bd769099d6b0d3f4e70c5903e1ab16f1e81b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002321.fa
@@ -0,0 +1,8 @@
+>2_2294
+MRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLALEHALLSTGASRGREGLVHHS
+DRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWESVEEV
+ELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>3_294
+MYSRRIVGWAVSGSLHTAGLPLLALEHALVSTGASRGRQGLVHHSDRGSQYVSLAYSDAL
+ITAGVTASVGTVGDSYDNALAESVNGLYKAELIHSKRIWESVQAVELATMGWVHWWNTQR
+LHEALGYRPPAEVEAAYTHDQDPAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cbee4d10adfa915462cbb2e2230ccb19e747e76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002322.fa
@@ -0,0 +1,8 @@
+>2_2309
+MDENPSTAWTGTCGFRMLPTDDFAQGPSTARLTEVAGGAALALDYTWVHPEQGEQAGHLV
+LGRPDDGGRVTVAFTDSFHQSPEVRVLEGTAARTEGGGDAGRDRGAGAAPHPIDGDGVAV
+TMEYSGWGWTVAVRRQGGRLAMMMQNVVPAGVEGAEPGPYDVMRAAWTPAGA
+>3_2199
+MSLPSATDWTGTCGFRLYPTDEFSSGPSAARLTPVAGGAALALDYTWVHPDQGEQAGHLV
+IGRPDDAGRVTAALTDSFHQAPEIRVLEGASSSPEGDAHPVEGEGVAVSMEYSGWGWTVA
+VRLQGGTLAMVMQNVIPEGVEGAEPGAYDVMRAAWTRTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40e38be347a16ce106f87855d8f4dc6be545c389
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002323.fa
@@ -0,0 +1,7 @@
+>2_2498
+MFGGGMMRDLMVGSGWLGLLACMVLGGIARLPLAAAGTRRAEGRPWAVQGVLGFGLLGLA
+LLAALPADPSPAWYPREDGDERRG
+>3_2368
+MFGGDSMMQDLMVGSGWLGLLGCMILGVLASVVLGTAGRRRVQGRPWAVPGVVGGLLLAA
+AVASALSSFGTFFGFMGIAFAVFMGIGAWNAFTTPARAAERLREQEAHAERLGAAYARGA
+ATGPPAPHSPDAAEPGQAPAHDPDWYPATPGGGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f25a255cada33eeb338569ee7f17e989083f91d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002324.fa
@@ -0,0 +1,13 @@
+>2_2579
+MSDTLRVVASRRYGTLSPLRYPGGKAALAGFFGDIIDALRVERARYIEPYAGGVGAGIAL
+LREGIVEELVINDIDPAVYAFWKSAVGDNASFVEMVASVPLTIAEWQKQREIYRSRDERD
+ALRLGFAFFFLNRTNRSGILNAGVIGGQRQEGRYKIDARFNRETLIERLTAIGGLADQIT
+VSDLDGRTVIQRYAQDDRAFMYIDPPYVQAGSQLYLNAFDGRDHTALAAIVNTVEKAHWL
+MTYDTAPLIEKLYREHFQCRLELTYSARYPGQAEELLVASPAVAGVVKALQGQTVMADAT
+SA
+>3_1732
+MTALVMDSPLQVRASGRNAAFSPLRYPGGKAALANFFGDVIERLGISNARYVEPYAGGVG
+AGIALLRQDRVQELVINDIDPAVHSFWRAVVEYPDKFADLVVNTPLNVDEWRNQKHVYRE
+ANESNYLALGFAFFYLNRTNRSGILNAGPIGGMDQSGNYKIDARYNRQQLAERISRIGEL
+SSRITVISLDGASVARQYAGDPSSFTYIDPPYVEAGGSLYLNSFTYRDHAQLAKSLDRCP
+DGNWIVTYDPSDFIRRIYAKHDVREYELNYSANRTGKARELLIASRPVARVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de3b2cd2ac42be666fec7738887c4b04ce67610a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002325.fa
@@ -0,0 +1,6 @@
+>2_2580
+MLLAGVYFYAAAICTTIINDGGPGWLYLLVLVFVWNAFKFLWIGPVSLIQLISVRAGERR
+ERQPVPSSR
+>3_1733
+MLMFRLIWIASIHTRDLLHRYMPTNIVLGKLRTRRGLKWGVPAMLLTIPYLAVANILTIL
+IDRGAPGWFHLLVLLFIWNAFKFLVTGPVSVVLLVRARTVERRDRRLLSRSPAPTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc3aec6210b01c1822612cfccc6762f32bb62e6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002327.fa
@@ -0,0 +1,5 @@
+>2_2611
+MCRAVTCKTCGKTTWAGCGQHIAEVKRTVPAGQWCPGHDKEKEKAAATSGFFARLFGR
+>3_525
+MCRPATCDVCGKTTWAGCGQHVDSVKASVPAGQWCDGRHTPAEQAAARKDAPARGGLLAT
+LFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e823cd335d049702e5cb45fb424b312b4f1cbcbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002329.fa
@@ -0,0 +1,4 @@
+>3_0
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHATTNHMLSNPKAYSHPAGTTTGTIH
+>3_1353
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHVATNHMLSNPKAYSHPAGTTTGTIH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b570c687ecb1956406d1fa82760f6fe71cfd902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002333.fa
@@ -0,0 +1,10 @@
+>3_292
+MSDQNAVLVEYVDPDAVSLPLRVRARSEVWLPAFVVAVVLWVLFVMILLGLPPVLFEDPS
+AMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEAIWLNP
+THGLAPDKKTQVGFAVHERAWTDELRRGNRWDSGFPFGLGGMKPRDGMIMTQFATEPPIQ
+SLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
+>3_320
+MTVSDQNAVLVEYVDPDAVSLPLRVRARSEVWWPAFVVAVVLWVLFVMILLGLPPVLFED
+PSAMLVLFRWLAVVGFIPLSVYVAYTWMAWRRPRHLMVDEEAVWTDSWRVAWSDVEEIWL
+NPTHGEAPDKKTQVGFMVHERAWTDELRRGNRWDSGFPFGLGGMKPRHRVIQTQFATDPP
+IQSLLPLFERLRARAHGQPPEREKLWPGQEPWDGWVGPWS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42f0cdad12edee6e33b1e766f9ba6b6b68318128
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002338.fa
@@ -0,0 +1,6 @@
+>3_318
+MGAIDQSTDNDADYDVIEQTWLDAGQTVKELVDRARTLMEENDDIAAGAHQKAGNHMGLV
+HV
+>3_323
+MTIQYDSAAAAAYEDEVLRIASRIETILGDREQQKRFVADNYQSTDNDADYDVIEQTWLE
+AGQTVKELVDRARTLMEENDEIAAGAHQKAGNHIAGMRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcefbe9e727a133cb0903ec81dc0f2424ad38b5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002343.fa
@@ -0,0 +1,13 @@
+>3_616
+MSTLLPIRPRPAPEEALDSYLERVATANGVTTSGFVRQLTTEARAPLRFTNIAPPPPILD
+VLASWTGTDRGLLQDCLLTRYPVIPFIDSQNRHGTRSVVAHGWVLLNRSQACPWCLAETG
+VWKITWRLAWVTACLDHDRLLATDCPGCQKPLRTTHHGALRPAGPGARCGNPRPQGQGKR
+CPFDLSRISPLSAPPPVLQQQRRVERALRGAEVEVAAIALEGTTYLRQLQALTSAAMGLS
+APTTAVQPEYSEGVPAEISTLSGRARPAPRPADIRAAAYVRRDRTIFAPP
+>4_2155
+MITPLPVRVTPGPNEAMDSYIERVAAANVLAITPFTHHLKRLSGSTLRFLNAAPSPELVA
+TLARLTDTPESALHELTLSRYEVVPEIHNHHRYAARAASAKGWFSLIRTQACPACVGEGQ
+PWASYWRLPWVTACLKHGCLLITRCPGCRVKLRSTRLQGLRAGGFTPLCGNPRATGRVPQ
+CEDDLGTTALTLAGQPVLVQQQVVLAALRGSTVFCHGEPVTGTEYLRRVRSIAVLLFHTV
+AISTATGLPAWAQKLRAEAQARTKERGPRWGVSAPDCPQSRAAVFLIAHQILTGPVGAGR
+GSLDVWLDLVPPSNEGTRAWAEDHTTTPDAISYLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..883cfdf57cebda6cb1f267d013d945de86da5d62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002344.fa
@@ -0,0 +1,20 @@
+>3_617
+MTDQEHPPSALAPIVGESLSGYVRRFNATGLTPPLALPPRYADADLPPGLTDAVHRSTGL
+DAGQIRRMTMAGWPLILRGRGLHHRRGWALHRHDVWLCPSCTPLTGYRALRWRLALAPVC
+LRCHTLLTHERTFTPTRAATTEELARLRRLDELTTRALQGSKASRSHLSVLRRICAAGDA
+HEPDGDVLPRPPLGGTSRPAGNQRGTHPPGEPGIVMKQLATLDPALLNESRARAHLQQLQ
+HQDSLPSSFVVAPAPFQPESPTALALARARRRALLRQLTDLCAATGLRPQHIPTVVDPWR
+STRWSRLRDLEDQAFEALALHTLLLEALGEDATGSAVFVAHGIPAVVNQHDLLTRVRTRG
+TLTPGECDRLLARAQALVDDGLVDYAYRRGTLLAVPSLPRIPAVHLPRHPFWPARTLVPA
+WAWVEYARGLPDSGPAPDLSLESVDRFHADLDPEARLRLLEAFDTHVRGEDWAAIASAAG
+SSFPTFASAHQRSA
+>4_2156
+MSRPVHMPPLPGESLTGYLQRYRQSGMAPIRLDVTGVFDNASAPASVVVPVHTATGLAPE
+QIKAMTMDRWVPSIRGYRVQRRHGWKLHPHQWWICPQCTVKTGYQSLRWRLALQPVCLRC
+HTYLVDPENPQIPRPVPEATLKIVQSYDRILDDALSGSLSARQRLSGLRKTCKGMAQAMA
+HDQQPASAGAQPSTLTWWGAYPCGDPVTVGHLMTLTRAMVTRGPARRRTVPRRDRPLQSK
+RAVSGATVTAMSRARLRATVSKLAEWSQSTGLSPRHVPTIAQPSLYGTARRPSMVAQAGT
+TLALHMLLDEATGIPVSSARTRAAHGLSGEPLEHRLLHSVITRGGLEEDQQRLLLRTAED
+LITDGLIDFRLRRTVFRSQPHLPRLPTPAHWIPAGEEFSAETMTRAWIWMHVARGHPQHG
+PVASVRLDEIDDFDHLLDPETRMHLHESAAAQIDGPDLADILTTTTTHNRRARQQDLREH
+AG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c8b0ac8e23632f4ecb8dff6c7add9afb5373e2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002352.fa
@@ -0,0 +1,13 @@
+>3_656
+MTRMSVLEAWTWINEYGSAIGAVAGVVAALVAIIALISAALDSKARSQPMIAAEFRPAVD
+SDSSIDFIITNLGPTPARDITVTFNPPIVIPDDSDRLLAPYLVKRYERPIPVLNPGQILS
+NTWWAGRAGTGNELTNHEPTPDEVNVTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDM
+IRTERCIEEHLVLHGGHVDHAHGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMI
+LIGMPGIEKQFTHYPQLYSRLGFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQA
+IAAVERITRGNFRLLERLLPQIQRVLKINELDVITNDVVEAARSTLVIGTT
+>3_660
+MTSQFIVTKEHRRFAEFADAVRKQNTIGVCFGPAGVGKTLSARRYAHWDSIGPFIARWAA
+RSEDDTKIYAAAHRARTVFYTPEVSATMRALQEDLRHDMIRTERCIEEHLVLHGGHVDHA
+HGPNPSLLELIIIDESERLTGNAIEWLRDQYDRTGIAMILIGMPGIEKQFTHYPQLYSRL
+GFAHQYRPLGHDELLFVLERQWRKLGKTLDPDDFTDAQAIAAVERITRGNFRLLERLLPQ
+IQRVLKINELDVITNDVVEAARSTLVIGTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee7ca3fbb43cba169cb236f321550945bcea0f40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002357.fa
@@ -0,0 +1,8 @@
+>3_1170
+MQPPSPGGPAGAPPWQVDLDWLWGTPPGNDGSPATLRLDVVGPGAARAAAAWLGSLPGDE
+DGGRGRGGWRADPGEQPDADDHAVLLLTSAGEDVADGLEDAADDAHAALAAVEGLTLRWT
+PLPRDPSR
+>4_1481
+MQPPSPGGPAGAPPWQVDLDWLWGTPPGNDGSPATLRLDVVGPGAARAAAAWLSSLPGDE
+DGVRGTGGWRADPGEQPGEDDHAVLLLTSAGEDVADGLEDAADDAHAALAAVGGLTLRWT
+PLPRDPSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7440f82f6be6230ded175c91ee73f868a6db8d41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002365.fa
@@ -0,0 +1,16 @@
+>3_1845
+MWALVELGKRATSEPAAQLRLETLDDIEFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALEELLKAARTSTSKAT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST
+>4_863
+MWALVELGKRATSEPAAQLRLETLDDIVFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR
+TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALDELLNAARTSTSKTT
+DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG
+WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP
+FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS
+RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW
+HPDFESKLEEMLSHVSST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1f857f4ff6a44a735104c967bbe48cbacbb3b34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002366.fa
@@ -0,0 +1,12 @@
+>3_1846
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRPLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAIPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
+>4_862
+MVTHDDLEITGKRSYYISHQCELSPDCFPVCVLIVSSIYDLFGEECLRRLIEHEEPRNRS
+IVRGEPVVESEVSDEVVADPVLSASHAAERDAASRSLNGYGQLNWVKSDVMLGTLKPKVA
+RIVRHQFRHRVDGGTKSGGGIVALAKVFQPRELSAMPAFSVSQFSEISSDVDTSFEFLAD
+PALEECDSLASLTARCDRRFLLGNGIEFNNVFSECLHERFAARLQTFNRCLAPRGDPLRR
+FEASFQSVQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002369.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b4b26c1ab857b81db4c1d006d5a81a64d5225dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002369.fa
@@ -0,0 +1,8 @@
+>3_2264
+MEIAFASTRHFGQGEVLRHVSADYVLKDFMEMNKVPSAAMFRRSRWAEVGGYLESMRWGM
+EDYEFWVRVLRDGGIARPVPTAYYHYRSRENSRLSTLGTHAARDTHQAIVEANPEHHAIL
+LQAAFLRLEEMHDLHLEYRSYVHKWQDRFRPLIRARDFAKRAVRKMS
+>4_496
+MDMNKVPSAAMFRRNRWEAVDGFQEGLDGQEDYAFWVRMLRDGGMARPVPAAQLHYRLRA
+TSRAATAGSEYWEATRKAIISGNADHHEALLRAAFERLDELRADLAEQKRYVQNWQRRAR
+PLIAVRNRIRSLLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ade45c0fcb6bbc9f526e3d9ef9961af0e6a1ef8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002371.fa
@@ -0,0 +1,9 @@
+>0_32
+MTGQWEWTTLREVLVPQPNKKPLQQGWSPKCIPSPSPDSETWGVLKTTAIQPGRFDETQN
+KELPATLAPRPAIEVQQGDLLMTCAGPRSRCGIPALVRSTRPRLMMSGKMYRFRPVEGVD
+SAFLEKWLLSAEAQARIDAMKTGISDSGLNLTQDRFLALPVPMPGMEEQRRIVDIVEEHF
+ARLDVAEGSLDVADKRLEGLVESAIQLCLDWGSVRQVELRSLLAEPLANGRSVPTREDGF
+PVIRLTAIRDGWVDPLQRKGGDWSRNDAKKWLIRPGDFLLSRGNGSLGLVGRGGLVLDDP
+GEVAFPDTIVRLRPNREKIDLDYLSMLWNSRLVRRQIESRVRTTAGIYKINQEALKSIEI
+PVPSLEVQGRLASSIGGVRLAGRRIAGVVEAERRRTAALRRAILTAAFAGRLSGRSTDTE
+VIEELVASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f8b6972efed41c79b01b199f9c13b9675915be4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002375.fa
@@ -0,0 +1,11 @@
+>0_386
+MEVEGWTHVSPSLGEYRYLSGGEGQRVTAFDVTVPDSAAHLVLQGHAWKPEFPVRVNGAP
+MVLRHVHPLDTPVAPFSPDTRVRVWDFVQHVPVSPGTASIEGVVHASLPTEKSTALLTVG
+FLDEAGRPLPGPSDLPQNPTFGPFVQLRGAAEGPLETQFQIAVPSQARWVRIQGRRGWGN
+SDVMMQAEVDVTEVRSSAAEIDAFLAEIPEGDTLLVIDTTAPPLGHETLSLRPNNLARAF
+ERAGVWVVFLPFSSLQEFPARVSDRILQVARKDFGRLVRGLTTRRRSMGDTYICSSFPSI
+GAVALGTQLKTLGWQVVYECRDDMEEFNRVGYSKWYSPALERQMLIVADKVVSVSTALDA
+KLVSMWPALRDHAVIPNAVNRHVIDQSEGLRTEESFDRREHLRVAGYVGHLTPSWFDWPL
+IAEAARRMPETVFEIIGHGAPQGMSLPSNVHLLGPRSHEQLADIVTGWKAGLIPFLDIPL
+TRSVDPNKIYEYFAWGLRCVTAPMGSVETYPSTWVHRGVDEFVEKLDEALSTPWAPGERE
+AMESFVQSSDWDDRAERLLSYYGITTEGRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71462cd49d9106c8e1ee03a8c7a814a449a3ee36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002379.fa
@@ -0,0 +1,8 @@
+>0_495
+MKILVYGAVHQQPNIGVSALAAGAEAVLSRAFPDADIRFRSTGPLGDGPMNLSHTAPLLK
+EMVVNRRGLRGWTRSFDLLCDIRGGDSFTDIYTSKMFFKLSAFPLYAQALRVPVVMLPQT
+IGPFENRASRILAKRFMRGCRLVMARDPRSSDFAAELGRPVDLTATDVVFAIERPEPSLK
+HRDVVLNTSGLLWHAGNRHVDSDAYRAGIRGVIDILLAEGRQITLLAHVVGRTDTGADND
+RAALAALREDYGDRLEYVVPSGLDEVRSLMASANVVVGARMHACLNALSIGVPAVPMAYS
+RKFAPLLDQLGWHHTVDLNASGEQIATAVLEEIHAVEGEDLTPVLRTARARIDAAVEALR
+QLSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e93882f81a6de538329a0e55665a5bb31da05892
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002381.fa
@@ -0,0 +1,3 @@
+>0_497
+MPNLNDFHRPALDDVTTVDPRTPLLPFLRQLARAELVVGSSLHGVILAERLGVPARVIRS
+DAEPSFKYEDYYEGTGRANVRLAADIHHALDLGGVDSGSTVDATLAAAFPRDLWER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34409172b1f6cdcb8851935b321ba2cb4e37d514
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002383.fa
@@ -0,0 +1,7 @@
+>0_565
+MSIEAMKWAQKVAETGQLNTGQAFVLLLLGDHADEAWSCHPSQELLARRSAQTVRSVERH
+IARLRDLGLVDTESRYGDGRGRIGLRYYLREEALNDLVQDAETRMNTRPDNLSGKSETRT
+KTRPDNLSGKSETRTKTRPDNLSGKSETRMNTRPDNLSGESTHPTISADSPDNHDFADYK
+DRARTNPQEPSSVRPSVRQSGAVRAETTTDDGRRTDQVIDGGEGVGLVHRGVVLADLVQR
+VPAAADLGDGQLRSIVDVVLARASGPVRKPTAFVARSLASEFEELVTVTRPRPVAVTQAP
+AASGQVRELRTGEPCQDPDVHIPAYGQAVLADCPHCRLERRAMPRALMEAVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eec845e718446b659460166c7d094a1ccbadab51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002384.fa
@@ -0,0 +1,6 @@
+>0_566
+MTGQADRVAPAGMVLVTGDELAEAVASVRGTVVAVLGPSGNGDVVEDVLQSTWESAWHSR
+ERFDPDRGSLRTWVGTIARNRAVDHLRAVGRSRAGQEALEASAVAREKTAVSTVMEDPAE
+AVVEALAAHREVAEVMRVVESVMESSEMTARALAVVLAFGDDVVAASEAMGVSVTALRQA
+RRELVRCARVVRAAQEVARSGQAVTMRVLISCLPDDGDAGDWARQVALACAQAGGRMEAV
+TVEDVMQATGFSHSTSRQYLAETRHLLRVATTVIRNERAEK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2128bd4e2f215319f71ec88049bb6847b2b56c4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002387.fa
@@ -0,0 +1,9 @@
+>0_580
+MTESRLWLLCDARAAHRQGRAGLDRRRHERLVEMVSFARARSPFYRRLYQHLPEQLTDPV
+LLPVTGKAELMRHFDDWVTDRAVTLSAARAFVEDPALVGEKFLGRYTVGTTSGTTGTRGI
+FLWDERSLAVTTALLARLLGTWLTPADVLRMLARGGRIAMVNATGGHYASAAAAAALRKN
+RWGSDRIGVFGVHTPMAQLVAGLNDFRPAILAPYATMGALLAAEQRAGRLHINPALVVLS
+AEALPEGEYDRIAATFNAKVRQGYAATECPFLTYSCQHGWLHVNSDWVLLESVDADHRPV
+PPGQPSHTTLLSNLANKVQPILRYDLGDAVFVRPDPCPCGDPLPAIRVRGRTADLLTFHT
+PAGEPVVLTSLTVTAWVDRVPGVELVQLVHTAPTHLEVRMQFSAGTDPERLWQAVHTEIR
+RLLVDHGLGHVTVARGDGPPQPTPGGKFRAVIPLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a719d7dfd24d31452804cdc7722ef94f2a89268
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002388.fa
@@ -0,0 +1,9 @@
+>0_581
+MPGATPIGDEAEVPTLGAVDHLRVLTRVLLGPVVKGPIVRRPAAVGLAERLDADAAGVAE
+MQRLRSRYGAGPVQLRIPGRRIALLLDPADVRRVLNDSPTPFSPATLEKRGALNHFEPAG
+SLVSTPQQRLSRRPFNEQILETPRPVHSHAEAMKAVITEEVSTLGGHVDFTGTLDWESFA
+VMWARMVRRIVLGASARDDDQVTDDLRRLRARGNFSYLMPQNRRLRERFLRRLQHYIELA
+EPGSLAALVAQTPAPDEAVPHQQVPQWLFAFDAEAWATFRALALLTNHPGATGTARSEVA
+HAPDLPFLRATVLESLRLWPTTPLILRDSTATTHWRNGTLPPDTALVIYAPFFHRDDQTL
+PQAHRFSPELWLQERDDNAWPLVPFSAGPGMCPGRNVVLLTSSLVLGELLRQHDFTAQEP
+LDTGQLPGTLSPFSSHFTVRHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b436e928882956d28588d2f18b1dfa7c289963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002389.fa
@@ -0,0 +1,2 @@
+>0_590
+MTATTAALALALYLAGLAAAFGARSWIPLRACDLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c386f3e392ecbecf2ee7c54927d5018706d5d952
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002394.fa
@@ -0,0 +1,9 @@
+>0_675
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+LVIDVGANIGNHTLNLACVADARVVAIEPDSHLADALRRSVELNGAVDRVEVYECAAGAQ
+PGFGRLILHDPANLGTQSLSFEEGDAGQDVAFYTLDDLIQRQSVRMVKIDVEGFELEVLQ
+GGMEMITRDRPLIWVECLDYEAYEAVSSLLSPLGYRVVDVVNASPTLLFSPGGKQNDAGE
+RTGINAVMHRLYTERRIAESLRSKFQTITNDLEDPEARKLVTHLGALAELEIGQSAAEAE
+LKGALTDARRRIAELEARERLHLEDFRAIRGFVETVEDRLWSTRTVQAENEAAAERLRYL
+EDALELVTTEKEMALAEAGEMRATLRRIRSSRTFRAGRALSEAQSVSGASRALPRLLAII
+REEKKGRDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1cbb10d93ffbbf4277b4aeffb91ebfa7d1b4527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002397.fa
@@ -0,0 +1,6 @@
+>0_810
+MKRPERPISSDWLDLRRPADERARAGSAPLLDALAEHFTETGADSPVDVIDVGAGTGANP
+AWLAPRLRFSQQWTLLDHDADLLELVPSQLQDARVRHVRRVTAGIEDLGSLDEAEQDRCL
+ITCSAVLDLLTMDQLAGFCDFLAERRMPALLSLSVTGDVVLDPGHWADAQITRAFNQHQR
+RGSLAGPDAVGYAAGRLRADGMRVEVAESPWKLGPADDVLLRRYLHDRAQAVIEGAPDMG
+DVVDSWLAEHLGQSDEGRLHVEVRHRELLCLPPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c25f9f7a9a8480090c48c2d1a0cb2850f19b969
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002402.fa
@@ -0,0 +1,4 @@
+>0_866
+MADALSLSEKVSQRALFGAMARIWPEVMAVPLGNNSWAFEHDGPDPDWSGPHHAARTAPL
+PTVEPVPRTGPRRVGEFSGRTLLALCRGLMDSPHPDVLQDHLSEPILTAVVESALHGTVS
+PPEGMERRVFARHLWRIALADQWYGWEWMPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52e6fcac8cd56e2c922563c28e7c389772e29dea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002404.fa
@@ -0,0 +1,5 @@
+>0_918
+MAKTTKYTAEVSEGRDELLDGKTIARLRTIAVKNQRGETVRELKAADNDEDVRAKLRAAG
+YTLKDWAGGTTPATLERGRNPLVAGCLWPLVAVMALLAWAIFSAFNNASPDEPEEWDAKI
+ACQTLVKEKLRAPSTAKFSRETASGGPKAWTVTGAVEAENALGGTVGHRYSCSVTFTGDD
+EYRGTATITDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..634d265bb6200dcf1107b220ac68bc5182ee5c91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002407.fa
@@ -0,0 +1,3 @@
+>0_1439
+MTVAYTLGDQTFATKKAVLAHASEVLNRASLGEVLRGHDEAFALDLLAQHPEVGRKHGAG
+IAGVAVVVMPEWGTRNFVVLREDGSIDNWSVKKCVANLRPDGTRRSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48ea581ad516cffee77a48a16c7600e1d88027b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002410.fa
@@ -0,0 +1,9 @@
+>0_1447
+MPAEFWKAAGCRLTKSAGESSWMLEAGDLVGVSRVSTALGDVTLQVLPKLATADVFFLAD
+YAYDQRHEPLRLLPFEQVELDALRRDPAACLLVWHARAIHRFATRWLRRDYRRVDQVLNG
+KIKGKPLISRYVSQHLAVGDPARIPCRVKERTQDTPNNRLLKAGLHYILSRSHELELPAA
+RRVAVREAKAALPLFSQVSDIRTEPVSQRDLTATTHRGAMSHYRSILLSTEALLRGEIMG
+PEVGAGVSTASFMWDMPTLFQEALRGVIDSAPGLALSVEGIGRARVHAHDGKQVRSSKVD
+PDLVLETAAGGQLVIDTKYKDVLPSDHGVDDEDVTLVADRRRIKVTRADIYQVVAYTAHD
+KWRGATGALLYPVVLAEGDTLPRPMQIRGFGPPVWMLFVDVGQQAKGNLPAFLDSVRELA
+DRSAAGAVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87fd8e24b4f7a2dc0c2c2eb532f669289e78296b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002412.fa
@@ -0,0 +1,3 @@
+>0_1455
+MSTIYRTQEWSGHGKQNYFWNEYRLEGDTVVKYRCNRFKFFDGDENVWEHTEDAQESWAK
+GDPNMPDWLLQYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e03ed5b1938393f410a2a301fad996db6c13145d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002413.fa
@@ -0,0 +1,6 @@
+>0_1457
+MGTLGNPHGTFRLDDPDHWIGSYLRRQDLPEILGVGDDALADLPFVKTEEGEVVDENKVH
+RALGEGRIPGALPPGSRKISLNELVLTAVLRRTFPDCEIQRQVKVKNPRTGRANTVDLRL
+DVPGQEPILIEYDGPSHFIRQYRAEIPHPLARKTELEPSAGMEIVIWPYWMHICSASAQA
+LFDPTVHGVPALWSSNKFFGDFATPDAACVIEEITGRFNAVGEEGYGTVYEAGVDGMHKP
+AHPIIESILDGRAAKETLVPNGAENPNRWLPISVRDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc41c0483cccc2344a7783fbf78025883691d8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002422.fa
@@ -0,0 +1,12 @@
+>0_1900
+MTDHNPGYTLERLPFRGALPPEQEKNARMRDWPAVYVIDNEKQVYVGETTNVVARRGQHH
+MDPRKARLTTMRVVLHDEFNKSAALDLERYLIQMLSGDGAREVLNRNAGLTESDYYDRTR
+YQEMFADIFERLRAEKVFSRSREQILNSTLFKLSPFKVLTPEQEASLRHIVQLLVADDDV
+DRGPLVIEGGPGTGKTVVGVFLAKLLVDLANLTEEDVEVDLSSDHDFFDLFTHANRNALL
+RGTKGRGLRIGIVVPQQSLRQSLKRVFRRTPGLHPSMVLSVWNVGDAEERYDILIVDEAH
+RLGLRSAQSNGALNTKYTAINQRLFGDDDVSHTQLDWITQQARDVVLLVDPRQTVRPADL
+DAATMDALLARAHAEHRHHALVSQLRVKASDSYVDFFGKLLRGEHPPAPDLGEYDLRMFT
+DFGAMREAIRARDTEFTLARLAAGFAWKWQSKGFRKDPSKPDWDIELDGVRMPWNVADTD
+WVDSPGSLDEIGSIHTLQGYDLNYAGVVIGRDLQWDDTAQRVVFSRADYADTGGKKNNGY
+LSRTYSDEDLREYVINIYNVLLTRGIRGTYLYVVDAGLREQFARWFPGISGPDVTSAPFG
+VPPGGRPGEVLRTVDVGHTAEAEFILSTDDLEQARRRAEELRRSRKRTRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..614d67349e8b4a5275d85648343ff4ac4412c86b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002423.fa
@@ -0,0 +1,6 @@
+>0_1954
+MDHDRRVLVERYEALAKKLDSATNYEQPSRRFILDQCRRLDLNGVLLTNIRFPTPTDDGR
+YFLHQVDHLLLTERSVTLIENKHWTGLIFDGTLPRGEHRSWKLLFPDLDLGDDFAIQLQR
+KAETPGQIDVRIVAEDHNARSPRRQAINQAADLRTYLQSLSDCRAPDFIHPAVFYSHSDS
+YVVATDERLGRRKVDVPVLTTVGNSVHDLLLLRSREPGPSVDVRCIVDALAPQTTDITGF
+GTFAGSWTSTFT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a33f263064ab6164f0126c83996aaef66743bc92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002425.fa
@@ -0,0 +1,3 @@
+>0_2006
+MRRTTYLRILAGLLLMVLLVWFWGRYALFPMEMTTGNARFIGWGLALLAGYGSYRLWMKA
+AELSEDGHDTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4a2b29a862c26512816f2bac1bc45cb6aa098c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002427.fa
@@ -0,0 +1,3 @@
+>0_2162
+MNLNASLGRVVEWDRDGGWGVIDSEATPGGCWVHFSHLPMLDSVPSSLTVGEEVEFLFEA
+LEAHNDQDGFLYRAIAVHPPHGGLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3b529866012dc5a4c9f155e8936490b1a815d35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002428.fa
@@ -0,0 +1,4 @@
+>0_2172
+MTEHDTGEPYADSLPFSLVAHWSFCPRRAWLEAMDEKAPKVAQIQQGVADHARVDVPTTR
+EAQTMRGIDVRDPSLGVHGRVDRVERLPSGRLRVVEHKATPVKRAARISDANRLQLVLQT
+MALESQGNTVEDAEVYFTTHHRRVPVELSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f257ecf54e7725da96ac236e118d2e2deb7cca74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002434.fa
@@ -0,0 +1,3 @@
+>1_77
+MRTRGHGTQHPRHDHVDEFMRPVRFSLMAALAGVTSLDFPTVKEQLDVSDSVLSRQASAL
+ESAGHLVVKKGYVGKRPRTWYSLSAEGAQAWKGHLAALRAIASD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ec004bc2805d475e322086ec6b3de63a5ec5179
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002442.fa
@@ -0,0 +1,3 @@
+>1_340
+MEISRRSVATGLAWAVPAVAASTAAPAMAASSCAGYTAGKPLPASAFTLTYLRITNETLG
+RLSNKQVALDFDFRLSDEAAACGRVNLSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af1d0d8067bf1b9b595df697d450d9deab73871f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002451.fa
@@ -0,0 +1,3 @@
+>1_1069
+MTTPTQFLRSKYRAIEGGCVTCAGDLAVVESLPGVKEVDALASGLVLVTHDGTVSDDAVV
+AAAKKSGLPLVAAGPARPVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe873e4c1922dc7431ea7fb7bc4346dca4bf0e98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002453.fa
@@ -0,0 +1,8 @@
+>1_1257
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+VVDQPATIGALPVAVAQACDGVEVAYLPGLAMRRIADLHPGSAKTDAKDAAIIAEAARTM
+PHTLRSIRVDEEQIAELAMLAGFDDDLAAQITATSNRLRGLLTQIHPALERVLGPRITHP
+AVADLLGRYPTPAQLRTAGPGHVRARLRKHAPRLAASLTEQIFQALDEQSVVVAGTQAAA
+TVVPILAEQLAGLTRQRAGLASQVEAAVEAHPLHPVLISMPGVGIRTAARILTEVVGKDF
+VDAGHLASYAGIAPVTRRSGTSIRGEHVARGGNKRLKRALFLSAFASLSHPPSRAYYDRK
+RAQGKRHNQALIALARRRTDVLYAMLRDGTLYQDPTAPPAPSSVALAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eaf0151cd1a440fa427b82dbba2c818b8d65fd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002463.fa
@@ -0,0 +1,2 @@
+>1_1886
+MKDRKNPTSIAKAHQKRATGQFTRNFPPRDFFTFPFFDADPGAPPGWKPCPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5bd83278795f6720377a8f991cc36c14e41b8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002466.fa
@@ -0,0 +1,3 @@
+>1_1966
+MLLLARISPERFVRQMRVKADQKGWERIDWSALVSKQRFVKTLAVRQGEAEALLPQVEAW
+LEEGAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44cd8872e8bedab7a45b1c7c99c9795d1bf1ca29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002471.fa
@@ -0,0 +1,4 @@
+>1_2157
+MPPDGCRRRGGFICGERRHSDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDL
+TGVDDLSDGCGGYAAVRIEEPTGRAEYARRQREFAARGQALRVRLLAVLDEAVGAAPGTG
+PDAEWTSSARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f743e35111d51ab0d808d4a93d68a3e8195f5aaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002476.fa
@@ -0,0 +1,3 @@
+>1_2163
+MPVSPCPECGRDVIPAGIGQAPRFCSTSCRQRRHRKVTRVRGELAAAETERMPLRAAYYR
+EWLARLMGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf010b98937f3e46367290ad5ab699eb9b8c1541
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002483.fa
@@ -0,0 +1,2 @@
+>1_2174
+MAPTLYSPREIAEMFGVSTRRINSLIREGALPVYVLGPRTRRIDVQAAREALALERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3234f709b9630362cc709f93296fe16339184dbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002488.fa
@@ -0,0 +1,7 @@
+>2_36
+MTDTMTTPTVHDLAAQLTRERARAVALVNKLENIGVKSSKRLTAAREAQAAHSRLLAEKR
+RDAATVEHEITEAAATANGDALTDALARRQSLAGAVDALNSPAVLERLVQAEVSAAYAAA
+HDARESVAAYFNRAAEEFVDVHREHFSAGPLLAHHVLGTTAAGHWGELVDAAERMSLAAA
+VLDVVDGVEDEAPASRYGRNLLHPAAADHSPIVGGPSMLRADGDLVRVGENITAFAGGWE
+WLGSPEVAPLRPWIDLATADARPGERVAIAYDPDAERADAATFAAMAADHGNVQSSQYDV
+STRAGYAAAWWQKRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70af13009507b472822b3fdec5229a8c448eac96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002489.fa
@@ -0,0 +1,3 @@
+>2_38
+MTRERIPEGLRERGTRLWKETTDVLDLEAHEELTLLEACRTADRLDALADALEDAPLTVT
+NARGDEVAQPLMVEARQQSIVLARLIAALRIPDAEDNRPQRRGVRGAYGVQMRSVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..320051ac2788a094cbc0cbafd23c1d2e73622e60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002494.fa
@@ -0,0 +1,3 @@
+>2_68
+MERKDDRRAFLTWTLISAVGLALVIASFTWPAWLVVPGALLALVGVSQSHEYRGYSHWFG
+LLVAAVAIGGGPFHLLSLAGDLGSFLGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e789ee303aaf6d317807e24fa38a1e4ce0726c1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002496.fa
@@ -0,0 +1,7 @@
+>2_92
+MTTTALTGLDLRIATALQVDPRAPWRRIARVLDEPERSVARRGAALIETGAVVVAGMRVR
+AETALLRVEAAPGIARVTTEALAQRADTTFAYAVTGGADCVAELIFDPGRMRPVLVNELP
+ATVGVVRANTYPVLRYFRTIRKWTTGALSAEQVAALSGEDGPELSAMHPTLDPLTGTDLR
+LAEALEADGRATMDVLARAADVSESTAARRVAALLGSARLQVRALVEPAAVGLPVEALLW
+MRAAPGSVEELGRRLARDPRVRYAVAVAGEHQVVADVTCRTNQELYALMTSSDWAPLADS
+VDTTLVLHARKRGGRHRAWEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc5991e58951c93aeb8c4b6b86a53e1af1a4f4f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002507.fa
@@ -0,0 +1,6 @@
+>2_166
+MRKALPTAVTAAIGLALVAPLAAAAQEGDTAALSVLHGVPDLTVDVYVDGELTLDDFTPG
+SLAGPLELPAGDYEVAITAGDAEDDSAPVLGPVDLTLAGGGDYTAAAHLDAQGNPTVTAF
+ETDTTPVAAGEGRLTVRHIAAAPAVDVWADGAVAVPGLANPDEAALELPAATLEAAVSVA
+GTTDPVIGPADVEVAEGVNTVVYAWGSATDETLALATQTVEGLQSAPENVNAGMAPAAQD
+DTALYAGAGVAALALLAGGAMAVRRKAAVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62cf18c1399beb91bb59de67986cb86832e162ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002508.fa
@@ -0,0 +1,5 @@
+>2_167
+MPDRLSAATRRTTARATAAVALAVGLAAVTTGCTAPGAAISAESAGPSATSRPSDAATAV
+SDEGEVGARDVSGRRPVPVRQATPRPVQAPIPPTRLNYPALGVDMAVESVGMADGGEMQI
+PDDADVAGWYRFGSVPDRGVGSTLLAAHVNTVHQDRGALYHLDEARIGDELQVVDAAGTA
+HPYRVARVEHLQKATLDWLPYVTRQGPEQLVLVTCGGEWIEELGAYDENVVVVARPAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31cbff73da03b2645e0317b8409dae2ce292a48d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002512.fa
@@ -0,0 +1,4 @@
+>2_182
+MDSDSAHAARPHDDGADLGDLMHVVFRRLRRRWSAQLEPLGVTPHQVRALRGVAEGAGGG
+IGSGAGTRAAAGSVADDDGGVRLRDLAERLRIAPRSATDVVDQLESRGLVERAADPADRR
+AVRIRLTDGGRGLLRRVHEARRTEAADFFAVLAPADRAELARLLARVAADPAEGAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d346f25320e027f915058560c30851ff9d04a1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002517.fa
@@ -0,0 +1,2 @@
+>2_293
+MGAPDEVPDRTDPGTTTASRPWAAVVGLAAFAVQVPLARRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d394699a03ccdeba0b82f0cb5763a2ecafd3e0cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002518.fa
@@ -0,0 +1,7 @@
+>2_295
+MGWSRRSATAASEPRGSAPDRAPTGPFVREMGGSVALTGRTGRRIRDDGTPVFTKARADA
+PAHLFEREAAGLRALAAAGARVPRVLAWSETGLEIEWIDDGGRRTRQTEAAFGRELAGFH
+AGSRPEAGAPDRFGSPDDVAAGWLGACPVDYTPADTWAESWVGRRILPLARRAERAGVVP
+ASARADAERLAELTDGFGADAPADHPGAAVLGSAEPSSLVHGDLWAGNRLVDADGRSWLV
+DPSAHRGHREADLAMMRLFGGFGEEAFAAYREAFPLADGWRERVLPYQAVPLLVHAVLFG
+GGYGEQAAASLRAAVRLAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9083af972afe5c95aca52540450635ca66b257be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002519.fa
@@ -0,0 +1,4 @@
+>2_309
+MSPVSDEHLEQQRTLYGAPLAERFTGVREAYGLSQRALAQTLGLSAPMLSQLASGQRIKI
+GSPAVYARLVMLEERAGEPDPAAVLAEVRDSEPVLTSQSFAASPEADLPARLARLAGPAG
+LRAAESAARAAGAARLADVLGAAAEAGARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c0f72932e16fdee1862daaf3a6810e4447fa21d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002522.fa
@@ -0,0 +1,4 @@
+>2_326
+MGPTMDARTAPQDPAGSPPASAAPALLLLAPLAGDVLSTGPLATSLSSEATIAGRALTTV
+LALVGAVLLLRGGRDASRSLRAIGGLAVAAALARGAGVVIGAIDRSDSSLSWFATIWLFL
+FGGAVLAGLGVAALLRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2adebae889e4c26a0dc96e05d1769ca2ad64938d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002523.fa
@@ -0,0 +1,6 @@
+>2_344
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+VGMTLVLLLPLRRTAQPALVEEPRAFRRSTWFLLGTAVLMIVLGPLGVDSTDFVLVKALT
+FLILPAIVLRFMWQGGVGVRIARGAWRWWAPLVVVAVWTWLAQAAPWVEPADFSGTDVEF
+LIVAAVVTAVTAGVGEELFYRRWLQTRLEAGLGPAAGILATSILFALMHTGTHGIADLPM
+DLAVLVAVQGTMGLFLGLLWWRYRNIAANIVLHLIVNGWPVVAYLLSLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19301f2a5e9723c51ae23dd6e473d9b63276c732
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002524.fa
@@ -0,0 +1,5 @@
+>2_348
+MPHRPPPSSPSPRWGRPLRGLRGLVAAGGVVLLLGSAVQPAAAQPADTAAQSAAVAHAPS
+TTATAASTPRLPRVAAVRELDARIAEAGAYLSRGSDGVLRFDAAAAAADGASADVLDLGA
+VMNQMAGPASSGPHAQAKLSLPIWGNWCGPGHGGGTPIDVLDSICRTHDRCYGARGYFAC
+SCDREIVKNIRANVHRMGSRESLVAAAVATYFAYCLCNPLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5560984d01faf7c743994cc8a1c1821bff31533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002525.fa
@@ -0,0 +1,3 @@
+>2_349
+MTSATSSSPASPAPAAACLVLTLAATAALPDWSGSGVARPLWALLLPAALGLAGAGLALR
+ARRPGGGGGGAAGGLGAGPALIVVTTIVSGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68be0950760b0a0f9dc99dcdad6fa15eb1c78060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002526.fa
@@ -0,0 +1,2 @@
+>2_352
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f1894556c3e731c2d5a4429d863766536998690
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002530.fa
@@ -0,0 +1,6 @@
+>2_413
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+ESRGRGSGRGGIGQRGCPARARPTGCRTDGWHAAYARPPRPLQARGRGVAQTARPPTGGV
+DGPTAPLMITGPCMLSAVIRQRRRGPSVVSVTTMSARSLASSGVGSQRRVAFHVKHSYGH
+ASRRIACSSAWMSTAGRVTVLGGVHNGPHTQRPHARPQPPHPRTEPAGGIAPTDGLRRRA
+RAQWPPQAACAGPQPFAAGAPRPAISAAASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7dee230c01df6372eaf947cdb8caaa15116ba4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002535.fa
@@ -0,0 +1,5 @@
+>2_448
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+DATTPPRELLTFDVHAERIVDLRDSEALAALGVDLADAMAPWKPAVEVGEEPSSWAVRRR
+LEEAGAHGLIDPSRTAPGLWHLTLFRWNEGGAPRVTRAPGGVTAGSGASPRRTRWTGRGG
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd1f18197f9f532818a1cc217705106f9b532980
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002536.fa
@@ -0,0 +1,3 @@
+>2_449
+MITGSETPRETIAFFALIIGCYALPALCFAAAKRVLLALLSGALAVVSFPLALSIGYVVE
+MLQSQQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f46ea3be52603fe1d08388a20e02a985b30fa652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002538.fa
@@ -0,0 +1,9 @@
+>2_460
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+ATLPAGIRVEWAERSWRSVGRQQVPVRVHAVTPDALVAWVGGCEAREQRVFAERVAAMRR
+LAEAWGGSGPSAAGGAGSAPQTQDDDDEAAADPRELTLAAALRRHAQRLTDLSEPDFLRV
+VAVLEWLRTTPVQGLRPRQLPIRGVDSKWFGAHRTLLEALHAPQEGGLGIVDAHPTVRVR
+ILDPALRPEGLRDLEVPLEQAAAWPIAPARVLVVENSETLLCLPDAPGAVAVWGRGFDTA
+ATVLPWLRGAELHYWGDLDSHGFAILHRYRTRLPQLRSVLMDVRTLEAFRDLCVPDPTPF
+RGALATLTSDEARALERLRAEGDVRLEQERVGWDHALSALDAHFVFCDAGDRAAGGEDAD
+GRRIAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fccfa46284dca555c36e3c8fffde4c7ee64b4023
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002542.fa
@@ -0,0 +1,4 @@
+>2_464
+MTTTLTLLDPAGPDREALTDPTPLFDLRVAERFRGRGLGVEILTALTRHVFETMPDVDRF
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+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..153361b7258a206ba29b2df7ba1d3bd41bdb25d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002544.fa
@@ -0,0 +1,7 @@
+>2_467
+MTRVHVLATGGTIASRSGEGSGATAGDSAEVLLEGMDATADVEVTSEDVMTVGSYRLGLP
+ELATIARVSRERAEEPGIDGVVVTHGTDTMEETAFLTDLLNGTDTPVVFTGAQRAADHPD
+SDGPRNLRQAVLAAAHPNARGLGALVAFDGVLLSARGTRKGHTMVSQPFTGGTLVGATHG
+DEFRLHARPHRPGTLDLPDSGLDGVRVDLITAYPGADPAVLPAAVDRGAHGIVLAGTGLG
+NAGPGHAEAVADLVARGVPVVLATRTLAGPVLGVYGHGGGADILAAGAVAAGELTPFQAR
+ILAAALLAHRPDPHEFAARFTRLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9efcbb79b520df3a0a36d29a9277f9d1d53d1431
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002545.fa
@@ -0,0 +1,6 @@
+>2_468
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+VGYVAPWWEFSTVTNEILLERGFLYDHSLMHDDHTPYYVRVGDSWTKIDYEAASAHEWMK
+PLVRGEETDLIEIPASWYLDDLPPMMFIKSSPNSHGFVSPRDIEQLWKDQFDWVHREMDY
+AVFPITIHPDVSGRPQNLLMLERLFDHIQGHDGVEFGFMKDVAADFARRFPRERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea1a4f1e76e76ca0dc7c3524c66b6cddd19a868b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002547.fa
@@ -0,0 +1,4 @@
+>2_472
+MPTPITSQASTAWDGDLFTGSGTTTLVTSGSGTFDVNWKARAEEAGSTTNPEELLAAAHA
+TCFTMQFSNMLKKNRTAPTHLDTTADVTFVAGEGITKIVLKVTGQVPEISAEDFERIAGE
+AKEQCPVSQALAGVKDVSVEASLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d2d78b2efd703e6209e5e55320f658f529c812d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002548.fa
@@ -0,0 +1,7 @@
+>2_474
+MTTLTHRYIDQVVGRVAADQRHDVAAELEGLLADMVEERTAAGVPEAEAERSALTELGDP
+ARLARRYRGAEEVLIGPELYPGFVLALRWLLPFVAVVALVTSAVDYAASTPVPHLGQAIG
+AVAGPLIQALFGSVGALVLLFWVLDRVLPVESREAVRRDVAPEWTVDALDDDPGSDRGAC
+SEAWASLVFLAVAAVLPVLPTSFLYVGHLNDGAPFVNQALWDFWIPAYYVLLAVGVVQAV
+WVLIRRRQTPGSLVLQAALTLVTAVFFTALVLTQQVIDPAIAAGPVQTGVHPLDWVDGLY
+VAVIWLVALWELWTLSRQWRTRRRSGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f2f89bdf3f2d81486571ee01f33e56e50d74c45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002553.fa
@@ -0,0 +1,4 @@
+>2_485
+MADLMGLLYRSDDHGTVELRRILPVAPADLWPELTDPERLAAWFAPVTGDLREGGDYRIA
+FEEDDDEPGSASWGRIEQCERGRGLRLTWQSAEDEPAPSTVQVSLRAVDGGTRLVLVHSG
+LTHGEDVGHAAGWEVYLRDLAAHIEGTPAEEGDWFERWERHRAAYEATL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eafa547439893de11e3e6b754be98ef00a457fff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002560.fa
@@ -0,0 +1,4 @@
+>2_518
+MDTADLPDLPAPEDRTATASRRVEAPAGVVFELIADPSRQPEWDGNDNLAQSEAGQRVTA
+VGDVFVTTLRKGVDRANHVVEYEEGRRIAWKPAEVGGEPFGQLWRWQVEGDDDGGCRVAH
+TYEWAQLTDPQRIRRALRTGPEQLRASIDRLAALAEAEAREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eec02961243c13a761f0df224a292207229f7d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002563.fa
@@ -0,0 +1,8 @@
+>2_569
+MSTASTHPTTAGRRPGGAAVAPGTAGPGRPEPRRTEPRRTPFWTAVGTVAAREMKVKGTS
+KPFIITTLLLVAAALAATLLVPRLGDLFAGDGTSVGVVEQTAPAVAALGEDYDARTLGSA
+EEARAAVERGDVEAAVLPSADAPGGLEVLAMTDVPTSLVQALSVSPAVELLDPSAPNPML
+RYFIAFGFGLVFFMAALTFGQQIAVSVIEEKQSRIVEILLAAVPARAMMAGKVLGNAAMA
+ILQVALIAGALLLGLQINGDVLPLDGLGVPILWFVLLFSIGFVMIAALYAAAASMVSRQE
+DIGSTSMPVMMMIMLPYFGVIFFNDNPDALRIMSFIPFSAPVAVPLRIYLQQGQMWEHVL
+ALGILVVSTALAIWLAAAIYERSILRTGKALTWRQALQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1e0f403441a0c804f1cb8bc8f11662f712f04a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002566.fa
@@ -0,0 +1,2 @@
+>2_587
+MLGAAGLRGLEESLRTRVDAYGGECAVRADADRLRLEVLLPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7fe073d42f1e55a00d89c17b182a16ee1cd5c8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002570.fa
@@ -0,0 +1,6 @@
+>2_601
+MTVGEVAALTGVTVRTLHHYDAIGLVRPAARSAAGYRLYGPDDVARLQEVVAYRRLGFGL
+EDIPDASADRRAALVRQRELVAARIDELTRLGRALDAALGRPGDETEEDTMQNEDTRRRP
+GTRPDLDLTDADLRELFGDEYAEEFDGYQAEAEQRWGETDAWAESARRTKRYSKQDWERI
+KADQEAATGLAAAALRAGEPASSVAAMDAAEAARAHITRWFYEVSPGMHRGLGDMYAADP
+RFAKTYDDVEPGLAAYLRDAIHANADRLERDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..100c11b90f63e967606d47e8e605d54b9b1f34e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002571.fa
@@ -0,0 +1,3 @@
+>2_605
+MPKKFSPELRERAVRMVLERQATQGGPRSHSIRAVAPQLDVSEETLRMWCQRHGHEIAQA
+PVSETPAEEIRRLKRELAEARRANEILKAASAFFAAELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a503654a88a418f41b516ca3f65b2cae45ed6e70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002572.fa
@@ -0,0 +1,2 @@
+>2_606
+MIAFIDEHLDQFGVEAICRTLRATECGFITST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd83862d2cee442e4055302dad005e9f29284ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002580.fa
@@ -0,0 +1,3 @@
+>2_691
+MAGFTLSRGGSTFLRMELFPGNNTYRAGTGKARGWSLHKDTAGHANKAWKLKDRSGSIRA
+SIYADGKFACDRYSQCAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..995d0fb8afe733a9288372c2d6d8aa0221e01734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002584.fa
@@ -0,0 +1,3 @@
+>2_714
+MPKKYTPELRERAVRMGLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002585.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a575fef9e9cb56571891981db8cec353e567547f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002585.fa
@@ -0,0 +1,4 @@
+>2_720
+MADTTGADTDGLPVVVIGAGPVGLAAAAHLAERGLTPLVLEAGPVVGAAIREWGHTRLFS
+PWRYNVDAAAARLLETRGWTAPDPEALSTGAELVEQYLQPLAATEALAPGSAPGPGSSRC
+PGPGWTRPAPPAGPRPRFWSESPTRTAPWRTFTPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef9fa39da43fdeecc043057a40664763fd572de1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002587.fa
@@ -0,0 +1,4 @@
+>2_730
+MGITPKNMWPAVKAMLHSVYDQPDAQAVDAQFDRLLDYVSEKLPAVAEHLDAARADILAF
+TTFPKDVWTQVWSNNPAERLNREIRRRTDAVGIFPNRAAIVRLVGAVLAEQTDEWAEGRR
+YLGLEVLHRCRLTPVSNTGDEVDTDTALELSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f8d623498b0ea5fd05e218eed62578c5ab822e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002588.fa
@@ -0,0 +1,3 @@
+>2_733
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..126b0b8d10ecb336ead73dd68e40cffbecb113e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002594.fa
@@ -0,0 +1,12 @@
+>2_772
+MPRRPPSSSASGAPRPARLAPLDARQRLQRGGEGRVLLLERRRGLDQRFVPGRGVVDGTV
+RDGGLLGLDLRQQPVPQPRRGDAVVPVVVLDVGADRPRDLGVPGLHRGDVPVVLGDAVRR
+RRDAVLRPVLRPHVERLQLLDGVARHTGPQGGADRGVEVHEQARAEPVVQLALAHPVAHR
+EPLERRDLVRGVVVDPHPRVGRAPRLHERHELLERRPLLAAGVRPQPREPEVPEGRAGGV
+PARGLHPAPQVLQPLHLTGGGGPQRVALEVEEHVPLAGLGQPEDRHRVHDGERRGPVRPP
+GRQLGRGLVPQRPPRALRHPRGGRGGVRQLLDGLDPGLPQPRALQAGGPGGEQHVPVRLH
+RLRTGLARPADRQGVVAPAGGLPGGHVCPQQALQPGPLVPIHRDDLGEVRPVPGAVAQPE
+AAVPGARHAHPVQQVRVGGDLQQRRHAGVPGQLGVHHLVGALGVLLVPAQHQEVGEAAER
+AVVQHRLEDDGGPPRQRLRGPLARGRHGGRGVRARPLQPHHLLLAMLGHQAPEGALLVGV
+AEPGHALQHGVLDGEPRRPPQRRIHLHAQPPVGARGGGRDVRGAEGDERAVGRDADHGHT
+LGVTPDTARPHRSAPAVVIRCHEVGGAPVRLDAGHIDGVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a4cc773bcf8aa5067bc80a18d84116e067b0a10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002595.fa
@@ -0,0 +1,3 @@
+>2_782
+MRAVEHWRSAVANFNMTDIRTQLDFNLFTEFDADGLAPRERRAEEFTGLMEQLIIAARRI
+AAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8df50185ebf6a8920514e189fa6df090bc69d366
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002603.fa
@@ -0,0 +1,5 @@
+>2_802
+MPKVVDHDSRRSELVEAAWRVIARRGLTGATMRQIAEQAGYAHGALKPYFPAKTDLLDAT
+YAHVFGRTQARIDDALVGVRGLEALRRLCLEVLPVDEDLLVEARLVISFWDQAARHEAEA
+RVSAATLEAWRTRLDAALGEADDDGTLRPDLDRRALVDLILTWLFGAQVTAVVDADRHDR
+AALEAQLALLTAAIRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcc8712d5c6e17cc992b3ba6fbed8f1b4f201176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002605.fa
@@ -0,0 +1,4 @@
+>2_809
+MGGVRDVAPALTYGEVGATLGELPPGYRHLDERRTVGHGRADFDRLAAQLLAWRLQRAAG
+FAVHPSTPTLDVGTQVRLAPGPGLVPGGGLLGRLVGGWQCRVVAVVAEPDRAGFAYGTLP
+GHPESGEELFLLTLEPRTGEVVLRIRAFSRPGTWWSRALDPLARAAQRRITRRYLRALE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aab4294c3798a77fb1fcb9e75382d03103755d0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002608.fa
@@ -0,0 +1,4 @@
+>2_866
+MTDAAAVLGAFFVAENARDWETYRSFLHPDVEWVLGDRVIRGIDRYVEAMQAAYGDDVRF
+RCEWSHVSESGSLVAALLVDDAGRRSLDVFEFKDGLVWKEHEFLLGRTASEAEPRSLPTQ
+GEPRSTEATEHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e98147007878ef4906edf2ecc990a9754853c322
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002612.fa
@@ -0,0 +1,6 @@
+>2_944
+MGGVHVRAGREGRGGEHLAGGLAQGEQHVRGGVLVRGAGRRQHGVHEPLDAAAGGGALGR
+ALPRVRLHEGRVQQGLDRHGGALAGVGHAGGEPAAGGVEVADRPARLAQRARDAHRGGPG
+LRRRGGLRRGVGAADGGRGGQRTAVGADGRAQGLEVGGGGRRGGGGGGPADQEGALRLAE
+GEVAVDRRVVGAGGGLAGGRVGRGLAHGASFRDGGCGARPTAAGRGLDSTSGPRRDTVGA
+GVRRPRRGGLSGPAGGAGVWWCPRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cfc17195e9b2e58ac88ecb69c6afb1822e8b8b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002617.fa
@@ -0,0 +1,3 @@
+>2_1034
+MNRYQQSRYFQDQEKTRANTASNIEFTGIGGAYSANVKAQNRQSGDQYAEQKGLGRNKIY
+NIPNATPTGQMTRLIVTNDTWTTVTVSINGWYRTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40ce226b15bcf5c68e09d27c72b889d9d8d3dc0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002618.fa
@@ -0,0 +1,4 @@
+>2_1035
+MVDGSYPLYAAAGRSSAGFVVLSALWAGLHAGLIALMSALTALLIRNRVLALLAPAVLLV
+GASIGLELTVGPAAAPLITWVHPGGLLPSNLIAAAIPGLTLGLACGAMAVVLLRRAPQMD
+RFS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6238f8b045c5df3d990f9a7641a682e1e5430ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002623.fa
@@ -0,0 +1,9 @@
+>2_1192
+MTFLQRVRRKAVGDGRLLRQVLTVLSGTTMAQLITIVGMIPLARLYSPTDFGLFAIAQSI
+VLAGTMVAALRYDIAIVLPESQSAARTVHRLASRIILLTCVVLAVILLLAHRVVSEHYGN
+PSFGIWLTVTALIVYAMAQIMNTQNWLIRMKQFGLISQNRVLAAALMLTAQLVCAPLVGG
+FEGLLIGMLVGQVLTLIVLNRRVPELRTSHPVDAPAIREMAVRYKKMPLLNAPNVLVDAV
+RDAGINILIGNIALGSLGQYSLANKATNAPVYLIRGAIAQVFLPLMARARPGELTPLVTR
+LLIRIGLVATPVFLVFYWLAPWLFPLLLGDQWGQAGLIAQALMPWLFMNTFTSPLANVYV
+TTERQGWLFGFAVVYAAAPLIFLTTSTLPLLPRVQVMAWIMAAALMCMLVMTLIITRQFD
+RRGQPAEVTPDMARPTKEPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19c3905a255f9bac811ac855f0d4c132e841f73d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002625.fa
@@ -0,0 +1,8 @@
+>2_1244
+MLAVLRNPTYARLFSAQIIALLGTGLLTVALGLLAYDIAGSDAGAVMGTVMAIKMVAYVL
+VSPVTTALVSRLPARRVLIGADLVRAGVAVSLPFVTEAWQTYVLIFLLQSASATFTPTFQ
+AVIPSVLPDEREYTRALSLSRLAYDLESLVSPLLAAALLTVMAYNNLFFGTVIGFLVSAA
+LVALARFPAIQAPEPAPFLDRLTRGTRAYWARLELRGLLGVNLVVATTTSMVIVNTVVLV
+QADLGRPQQDVALLLAAYGGGSMVVALGLPRVLDAVPDRRVMLAGAAALPVLLLAAVGAM
+SGLDAGAQWAGLLVLWALMGAATAAVLTPSARLLRRNSTERTRPSVFAAQFSLSHACFLL
+TYPLAGLLGARIGLPAVGVVLVGIGAAGLALTVLAWRRAEGQPPVDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e75ebe35c61e7e701fc745bedd6ac3f4fd5ce0e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002626.fa
@@ -0,0 +1,4 @@
+>2_1245
+MPYYLRMHADTKISGTPEPFPDHVEMAAEVLRLLSDATRIRLVLALHRDEELPVNALAEA
+VDRKPAAVSQHLAKMRMARMVTTRHEGTRVLYRLTDEHAVTLVLEAIRQAEHSAGPGQPL
+RHTHAPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1c7b047a45cad3eb86e27620478b61110cbc4ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002632.fa
@@ -0,0 +1,8 @@
+>2_1277
+MSDFPATPRSPSEEKSEDSLDKAPPTTAPAAFDGPAESEDSTLGAMAAEQDEEAVRYAVE
+FLKTVLRLRGVRIDRAQFLTSELQKRGIAITDIARAVEDNPASAGVHMEVLDDIVSSSIA
+LETRKSSALSFAAGLPGGLAMFGTVPADVTQYYVHAFRVMQKIAYVYGWQEFLHDVKSVD
+DETLAKLASFLGVMMGVGGASASVTSFAAQVARPALQKNIAGKALTKTAWYGPLKQTLKL
+VGVKVTKDSFAKAATKVVPVAGGVISGGMTFVSLKTQSARLARHLREIPPPGVDAAEYVS
+RLVHEEPEAKGKTMRAKVGGSILAAADSLRRSDAESGTGPDASTAASAVKDAAASGRRAL
+SGAAQRLRRPKKDSPASTTDAEIGDAGAEAPDAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6d2080b28cd91dc69007bb99cdedfc0c26cbd49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002641.fa
@@ -0,0 +1,3 @@
+>2_1304
+MDPDRSGQRGPKDFHRRIVRAEDPAHPATEVLRTITEPGSRGSRIRAVEGRAGEQAGPTL
+EH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8efde79e00c4c58ede91ba633dee6788d98d391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002644.fa
@@ -0,0 +1,2 @@
+>2_1322
+MLDAVVAALSAAWAAGGAARGPAPGRQRELAAAEGWIWLPETDGAGRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002657.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cda5a8fc76b344d21f6bc2c0e920aed31e53c431
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002657.fa
@@ -0,0 +1,8 @@
+>2_1479
+MHLPIRAQGTTLADEQAKILDDEFFLSNPLSHFSSRVSMLLETARSSYEASPENEPEFFN
+ALGLDSADTALKFDTQHRSVQVAIDALSLRHQAAEALTRFIYARVAATPRKGDAKSTYLA
+IADCPNPMIKVIEANKAAHDADPHRFLQLLFPPGIVVEGPVVGAAETAVEWANHAVWLLT
+SDELSINAAHNKLKHGLATSARGDVRIELITTPPNEDGTIPTSAFGEGKSLPLFDRPMLT
+YLSRPPKDLRQGLEAVSLRVDLPVVLAQTWMMANVYAAMFHIAAREHYGKSLPEGVAPFP
+TRVVGRLPEHVIGGRPLGYRSAATLPPDGTTAPRPSGVAFFKQFWPMTVDFESKTQGVVV
+DA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64e8cdacf1be0ec6a4f8276c1314cb2af708806d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002661.fa
@@ -0,0 +1,5 @@
+>2_1595
+MRPVSDPGGRTRPPAVLLGLLAAGLLALTGCADPAPTAPSPGAAASVGPAHESEAAPGVD
+EPDDRPVVPFAALDDDARRALLRLPASDAGGEGACGPADVRAALVFEDAALGHRYGTITI
+TNAGAEPCSLRGYPGLGARGAYGHRFTPEVQQLPFTEGFQHGDEGAVATDLRVPAGGAAQ
+VRIEWSGALGGAESEPLGDLVLQLHADQPPLRVEDAEREAADIGAFTSLRVGPFSLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54435065befc102a390a2ebe3971d2e942f58e06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002662.fa
@@ -0,0 +1,9 @@
+>2_1601
+MSTGSTPSDPSEQRDQSNRTAPSDHPSSRGGGPHAAAAALARLAESPARVGLVRDVRPWG
+GPRVDLRLQDGRVAAVVPHDPAAHAAPIAPHASETDDGLVVEGHGALCVPTLADAHAHLD
+SVRLGLPFRPHTGRPGVWGMMSNDRENWRHAEAPIGERVETALGMMIARGTTHVRTYAQV
+DVDAGLERLEAVLAARERFADAADVEVVAFPQAGLLLEAGSADVLAAAMDAGADVVGGID
+PCQLDRDPVRHLDAVFGLAERYGAPVDVHLHEQGSLGAFSLELIAERVRALGMQGRVTVA
+HAFALGTLPDARRDALLATLAELDVALTTIAPAGAGTLPLDRILQAGVRLGLGEDGQRDY
+WSPYGNADLLDRAWQLAFTQGFRADDDVARCLEVAAVGGRSVRDPAAPRVSADRPASART
+IAAGDAADLLLVPAETLASAVMDRPAERTVIHRGRLVAAGEPHAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002664.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ace98e7dafdfbb2d2af5250ad1511968f528704c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002664.fa
@@ -0,0 +1,4 @@
+>2_1704
+MTGPAVTVTGPDEPAPGMTAAQEEDAHWEHLAALAQAAGVMIRAGALRALPLETEASASL
+EALAARGRDRAEALTVLLGLPEESLGTGPPEDALSAEAVVGLQWALAERVGVDPDAWSTP
+RPWARAWAARSSRSRSGGTSPPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49b040831ce2e1efea22e380bf5e14d769930bac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002667.fa
@@ -0,0 +1,11 @@
+>2_1771
+MLLTSLLLTLLPVAAAVPISRRLGRDAGWVLALPLLVAAGVLAAAWRGGVEAEHHPWIPA
+IGVDLDLRLNGLALVFSMIVLVIGAAILAYSSRYLGRDPAVHRHGTFYLLMTAFAASMLL
+LVLADNLVVLFVAWEFTSFASFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVATMVAT
+TGTASLSGVLDSGIWQDPTLSTVLAVLLAVAAFTKSAQFPFQSWLPDSMVAISPVSAYLH
+AAAMVKAGVFLLLVFSPVLAGHAVWSALLLISGLTTAVFGAVAAVRRHDLKGLLAYSTMS
+QLGLLTAVIGIGTPAALTAAIVHTVAHALFKSSLFMLIGVVDHEAGTRDLRVLAGRRVRL
+PVTGAALAVAALSMAGIPPLLGFVSKEGLLAAALGTPGPAWAGPAVTAAIALASVFTVAY
+SGRLVLGALGLWGAEPRRRARALGVRPRRGGPRGAGVVLGDARAGRGGRRRAGPGPARAR
+RPCLRRRPRGRRRGAPRPPGPVARGESGPAGLRRRDRHGGRAGAAAPARRAGRRPSGPAR
+LGPRRGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2be15bd97fdbd85cb878dd21fda2da625af3f164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002669.fa
@@ -0,0 +1,4 @@
+>2_1802
+MAEDPAAAMAAAWRELTPAAGRLAVLMDNPRSDTSMPRCLEQHRDDPAACAYGKAEGIEE
+SGAPALQAAAASAAADPQWGLVDVNHLVCPGEDACAPVIGEALVLFDTNHFTATFARTLA
+PELGEQIEALLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91ec42f88b8aa2ec3ef557f21e3cf76fc65b3ef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002672.fa
@@ -0,0 +1,2 @@
+>2_1820
+MMMSFRSTGKGRRGACGAVAGFVLVVAAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ebbc64e11a5666438b51e616458b3831fac34d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002673.fa
@@ -0,0 +1,2 @@
+>2_1821
+MPCPTWLDVVEARLPAAKDMLKKLDEGVDFIGVMPEAMKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1877988586fdce92a8e9bea8cafdea0d2a34550a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002676.fa
@@ -0,0 +1,2 @@
+>2_1843
+MAHGGVIRAAVGLLLRHEGEAFAALERIDNARAAVLQGAFATDTGAEGWGDWTLEGYGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..223d3a468145b5b8d68aa79109c53985b3f7bac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002677.fa
@@ -0,0 +1,3 @@
+>2_1871
+MGAVFAAAMLAVGGTALATPPPAEAVTTVVITNGNFHNCTSRMNSEMKLFRMEGYTVRIA
+YKCKWFADARRWEGTFYASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fa3a4791f163de35b1f0fab88aa3cafc8899452
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002685.fa
@@ -0,0 +1,3 @@
+>2_1902
+MSVHPIRLQIPFADTSLVFGFDADAERDVRLLLRFARARASHGAGGFWLEYGWDTGESQM
+VWIDPAHMPTARFDVTATPVADQGREDDMSRHLARTHHVYLTAKGWQSDTHELAVDN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3ddb11bb7442999b0f07d40f5475e1240b1a280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002686.fa
@@ -0,0 +1,3 @@
+>2_1903
+MAPPVIRFPENAAFTGRVKSEDLSSGVWSIPADDMGVSFAGTTVADEDACRRVDDVDQDG
+PDCEGPDGGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13900d08352e57cd4ee5fc8fd93722f92e84b037
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002687.fa
@@ -0,0 +1,3 @@
+>2_1904
+MSARIAEWPPIEAWITAPDPNGRGRIVESVVLRDGRVVPAETDPADLYPWWAPAAGTRAH
+AVQRVARAVTAALVPVLAGLVFAAVVLLAPAGEWAAEQLIRGWGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfa5d9737f4019f9613e72da30fd7b12994133f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002690.fa
@@ -0,0 +1,3 @@
+>2_1908
+MNDPKAKAAYHGVPCDGRCCRQNRHLGVCPHGRVCAYHLNEDARQAREERERDQIADLER
+AARMTRRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4040fcf0e3c7373ab955f1ad080a11482ea6d46f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002692.fa
@@ -0,0 +1,3 @@
+>2_1910
+MSYHHINEDGTAVVCTAQESAWCRSRPNCDTEEWNEHGCAEHDREHALTPGHECWQARNV
+NAWGGPYPDDQPDLRPGAPVTLTYEGEGIVTWDYVNGARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a9c39d9ee97409a06ce82e0b2808c18e13eb6fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002695.fa
@@ -0,0 +1,6 @@
+>2_1913
+MKLFVEIADLRRALQALTPHMDPKDELGVFGRIRGHATDGNLFLMATDRYTAAMAVVSLW
+DKDDLTGSIRDDALEFSAQDVKEVLTLFRAPRRKDEPEGDLLIETSPGSSDPARRLVDVS
+GLFPGKEFRLPGADVDEKFPNLARVMSRRPAPTRTVRSNLTFAGEHLKKFLAASKAYEEP
+ITLQPVAEGSNMMLVAVGESFRGMIAGWRWPEDKTPDFEGWDMQWRLWSEELLGMAPDLR
+RPEGHEEAPADGEERDWSAALEQWAKDLADRLAKEQDDSEDEGDAPEQEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cf47638fb206c5e84a8a719f8c20b1c252626b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002697.fa
@@ -0,0 +1,3 @@
+>2_1915
+MRQDEYVRMMAAGMSEDQLQRGVERLARSLGWLAYHTHDSRRSSPGFPDLVLVRGDRVLF
+RELKTEKGRATPAQKTWLAALTAAGMDAGLWRPVQWFDRTIERELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..990746c53302cad87ec3a7b3c208efdde07a0883
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002699.fa
@@ -0,0 +1,5 @@
+>2_1917
+MSELMELVDRLTVETRQILHTDAGPAVVRAAPLLEQLQDAVHPSGEGGGGSSGSVGSGAP
+LDVTALALLCQVKDEAIHLSWLARSTPGVLTLRPGLGGFTLAERIRWTASALDGRAAEAE
+MLATVRGWTASIERLFDPPRVVALRGAECPACGIARTPVLNRDLDEFVDVPALTIVQGQT
+PRASCAECGAQWHGPEVVDLAVQLGAPPSVAHLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1e22648d2ff66defaf84f0878eba099b818d389
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002705.fa
@@ -0,0 +1,9 @@
+>2_1923
+MAVLNTQEETLFLRMRDQVRRHQPTNRHRENLFNARKQLQKIGFSVPESMRSFAATVGWP
+EKAVMVPARRLKPTGFVSSREEELADELNAHLDSGYAAAVEQYAIEASVRHGCSFVFATP
+GDQTAGDPDVVLSARSALEASAIVDRRTLRTIAGLEATDEAGVWLMHVPGEVLLVDTRTG
+EHVVRERYRAAPGEVGVVPYVWDRSLDRPFGRSRITNPVIDLSGQAVRIMLRQEVQAEHF
+SSPQRVLSGAREEAFTDETGQRRPMWQVATGAIWGIPDFFDEEIGEWRRAELTQMAAASM
+QPHTDHLRTVAMMFAGETSIPISQLGIVHDNPSSADAIRQHESAMVDLVQAQIPSYMASR
+KALGRLVLAVAHRGLSPATNTALAHVHARFADPGTITRAALADRAQKFAAAYPELRGSSV
+ALRAWGFDDVEVRELQDHLQRAESAGLVRQLLEAGPGVGMSGHAEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e672378e1e69dd4721ffd4a0ee4dd1390acfbac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002706.fa
@@ -0,0 +1,6 @@
+>2_1924
+MPSREQLEAFNRDQALLHDLVMGALDGMARRLGRFATPDQVLTALLEAMPELVGQFGHAS
+ATLAAEWLEEVYGIRAVLGETYPLEAVTQTLRRHAGQLWQGAGPEAVVAAMRDDVARWVK
+AAGRGTLRDSATANGLRWARVPSGPITCAFCLMLASRDAVYLTRNRALRTKSGEDRYHND
+CDCIPTPIRGPQDYPTGYDPDELYSVYSEATSAVGSRANTTAILENIRRAHPGRVRDGVH
+TTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbd148e4f667b57a14d122d057a93016a5218717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002709.fa
@@ -0,0 +1,7 @@
+>2_1927
+MENLNDLISAVELTAEARMAAEAYEGEGQSFARYLPSVTTDGISIELTQTGSGGLVEEAA
+YRAFSAEPEIAGGELGDIVTLRLPALGQKRPLTEWAQLMDRNAGEEVQRAAFRRTARLAG
+AAIAATAERQRVSVAVTGAATIAGRRFQSTDDFGRAASHTQTAPQLWTDAAVSRTDYLRS
+LVDVYVGTNGVPPGAIVMGSKVYRALLRGSEFTETLANGATRPMGRDAVFAVLDDLDIPV
+IERYDLRTSAGPILPENVVLLMPPAGPTVAEEPTALGAMYWGRTLTSGMEQYGILEAEQP
+GIIVGAFRETGIPHTAWVESDAIALPALANPNLTLAATVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e297952516cdcf308caf9de238d88d8e84fca3a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002712.fa
@@ -0,0 +1,3 @@
+>2_1930
+MRWPRLTGPPRPPLTFFVDDYVAIAVYSGGGRDRFGEPLPESRVEIPECLIAPRSTTEPQ
+ERSDLDGSRGVIYVQSEHTFHGSDRVEVLTGSHRGLWEVDGVPTLWPDGWEIPIRRGDRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2710d511913918413c86566097301df24fc277ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002719.fa
@@ -0,0 +1,19 @@
+>2_1937
+MAVVGVAEVLVRPSFKSFQSEVGKAVDQATPESGPASPGSRMGKRIATGLKVAGGAAITG
+AGVVLGTALTKGFGRLTAIENAQAKLTGLGHDAGTVEGIMRNATAAVKGTAFGLGDAATA
+SAAAVAAGVQPGEELEGVLKLMGDAATIAGTDFTSMATIFNKVKASGKLQGDEILQLSEA
+GIPILQLLAQELGVTASEVSDMASEGEIDFETFRSAMEAGMGGAALKSGETLQGAFANSM
+AAIGRFGANLMSGVYPQVKGFFASFIEWMGPVEAMGKTIGEWLATALGGFVNFLTGTAVP
+GLRSFGETVAAYVGPAFSDFAAFLTGTVLPAASNLATFVSGLLTPVFAALADYITGTVLP
+AVGGLLNWFRESPQWVGLLTTGLAAAIAAVAGIGVALKGWAVATTILTGAKALLTGVLGK
+LWAVMAANPVTIVLGVLAGLAAAAVYAYQNFEQFRVIVDAAWAGIVSAAQAAWTGFLQPT
+FQSIGDWLTNVLAPAFTSFWQNGVVPAWNGIVAAVQGAWTGVILPVLSGMVQWVGTFLAP
+LFVQLWQGHVAPAFLGIASAVQSAWAVIGPALAELARVVGPVLAGAFNFLAPIVARVAQV
+LGTVLGGAVTLAVKFIFMLVGAFVDHLGGAIQGAIRFLQGLVQFISGVFTGNWAAAWEGL
+KSIVVGAFKFIWHTINVVLTVQVLGVVRGALSGLLGLFRGGLSSVTGVFSAAWNGIVSLM
+RGAWSNITGIARSGASGLTSIVNGLVNAVLGFFRSLGSGMGSIVRNAWSVARSTFGGATA
+ALRTMVSQMVQGILGFFRSMRAGITSLSKSTMTNAKNAFIKGIAALEQSVSTGLLRVQAF
+FRDLPGRIMNALGNLGGLLKDSGRALLAGFTDGITNGFSRAKDAVADGLGAIRRLFPFSP
+AKEGPFSGRGYTTYSGRALSRDFADAIADEAGYLRKQAAGFMDAADFSASSRITAGVDLV
+PLSTRDLLLDGAGRLPAALQVAHSVAGPPRSSLERLKLAAPEGRQPLTLVLEDGTAFPAY
+LDRRTDTRLAGHVAGLAQPLRQYAGAMQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9ed09ca1e6d7ccee244d45cc6919fabbdd2ea1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002725.fa
@@ -0,0 +1,4 @@
+>2_1943
+MPDRILRTSAGVLGGLIIILGLTYAWLGITWLISPTPTRLAGIEWAPIGAHTVGIWWIAG
+GLVALIGGAWSARPVAAGVGAFAAILTPAVVAGLFLVSVWHGNDRGLITAGSYLPYALLA
+AWVTWRSGRGSEDTARDMAATRHDSQEGRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18e31dca7757498acf74ad4b42724811c5158312
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002727.fa
@@ -0,0 +1,7 @@
+>2_1945
+MPTPFLTGLGRVLTTAGVTWEGVPGWETRTGFASGYRDVYGATVHTTETHDATFAKGGDA
+PTLEWVVDADGSRRGAHTYALLIGRSGKVYLIAAGPGWQAGHGSWPSKLGPNPGIPDDQA
+NFHTVGVSMDANESQYPPTEAQLVSLVKVLAALRAEWAPDRFDVMMHGEWSPARRTDPTR
+VPGGWDAIRKAVAAGAWPVQPKPTPPTPAATSSRPAPATGTYTVRPGDTLGGIAKAHGTT
+WQALAKLNALADPHLIEVGQRLRVPALPTHTVAKGEGLWGIARQHGLTVDQLANLNGLTR
+TSTIHPGQTLRLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec752c39bd3ddcdbf93a3242fa6e687fe07e38de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002734.fa
@@ -0,0 +1,4 @@
+>2_2005
+MKPGPSLEKALYVGCLAAMSIIGVAVAVLGLLGQFRLVVILLGLGAVVASVLIPVHARRM
+RRFMGVAIRRAGGRGRAAAPTSSPGPAASVEVGRETMAALTRINRQLVSLREETMGGQLR
+PVSGAGSTDAADDRSDSSMAVAEALVGVRHELSVLRAEVAHLAEAPRGGRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49ae023cfcd3e61353456a1f74ef6c28f5c869ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002736.fa
@@ -0,0 +1,4 @@
+>2_2037
+MASHCPFCAVVRGVGPAHLVAESPLALAFLDQSPAADGHTLVVPRRHVESFSEVTPEEGA
+EVFALAARVAAVLRRVVSPGVTLHLAEGWEAGQDVPHTHLHVIPRRMDDAVTIDLPALRT
+PRDLAGSAAALRAVLEGPAAPGGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8fb955624b4357376a9c76142522e44f952b008
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002738.fa
@@ -0,0 +1,9 @@
+>2_2054
+MADRGHYELPHSGHNGIELVGTFAYEDAILRALPRLPADGASVEAQFTVDLVPEPDNPHD
+RRAVSVRHRGEVLGYLSRDLAADYHLPVKRILASGARLQTGARVFAYLSWDDKPEVRVYV
+GLPAPDALTPLNDGYPATTAVLPYGRTYQVTKEDQHFEHLFDYVPRSGQGPVILTLHKSE
+AMLRNGTVRRTVEVRLDAEKAGELTAATSAHYLPVIEHAEALGRVVGVWGTITGSGLAAE
+LTIKGAKSSELTDEWLREMPIFPHLVPEAHSYEVPDAYQGEPKTKGRSRAMGGHSAARLR
+EQLDQRFVSTSPAELDTTPSPSTPSPEKKPGKPQPPANPTPVPLNRDVTRLGIGTGPRTP
+IYYTVKGKEVFVDDRDRSSAGKHPRRTAWLLIAGLAVLGLILSGVPGIGPFLTLLTLLLV
+LISGPDQLRKAKVLDIDPHGTGHPSRDWRDRERGDVGEENQDHDTEDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e098043030d2f6ea5c452fb52bc70cf7e64310c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002739.fa
@@ -0,0 +1,4 @@
+>2_2057
+MFHPWRALRALTHVVVVWVRPHPAAPAATNGIDVVWLDPRLTQVERRWVLAHELVHLEHS
+HRGCQPAAVEHAVRAEAARRLITLDALLASIPWSEHLAVLADELWVTEQVLLDRIAGLTP
+TERQAIAARAEVHHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51341af8d625c02139db174e6d6144681e60ee15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002741.fa
@@ -0,0 +1,4 @@
+>2_2117
+MHSESLDPSPVPDRHGSDPDRPDPLVVVDGAEGRVVPAPTAAPSSTHDAGGDPASGGEGV
+DPAAAEPPTLVSVGVLADWLGLSPTEPLPEVPEAPAYAQPGRCRPRRLVLLDVRFRATGG
+GADHEAYLRGHLPGAVYVSPAQPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d482e15767da0771c7e6690f1d0f282c1c5a043e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002748.fa
@@ -0,0 +1,6 @@
+>2_2163
+MAQLNWTYEEVVLAADLVARNGWKGLRSADPRVAELSRLLRAATIHPLEGRPHNFRSPSS
+VQRKTFDIATRHPDYQGTPTRGGKHEAAVIGAFLDRPEQMHDLARYLHASLGGADPAAGV
+AEPAGVVADPEEEALAAWEGMTRAVRHLRRERDPKLRAAKITSMVAAGGRIACEICGFDF
+EQTYGAVGQGYIEVHHVRPLHDSGPVLTRLEDLALLCSNCHRMIHRARPWLTPGELAARI
+ADRGLVRGSRPDHAARLCDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef855adc4cce360013e778cfee511243dc1887a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002750.fa
@@ -0,0 +1,6 @@
+>2_2166
+MPVLPGFIADPLWEQFQALLPERNINHPLGCHRPRIPDRVVFDKLLARLVLGGTYQQHAD
+ETCSATTMRARRDEWIRADVFEQLHHLALEAYDQAVGLDLNNLVVDGCIVKAPCGGDNTG
+HSPVDRGKSGLKRSVLVDGGGIPVGWVLAGANRNDSPLLRPTLETLAVLGFRLPEVITVH
+LDAGYDSARTRDLLSELGCTPNITPKGAFLPISHTRRWVVERTNSWHNRGFSALARVTDR
+QGCVQNAWVALASAIIIIRRLVRQSWKRYRWDSRPARCP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d190a796c22e889e976cc7dbd30849e4a2925770
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002752.fa
@@ -0,0 +1,4 @@
+>2_2174
+MKIRHKLAAATAAFGLAVAAAAPAQASSIPRTYDARTNTYYSYSDSANQVCYQKGTNRTA
+QARLSVQIKINGRWYTRISALYSDTRLHCFTLRSQNGFYEGRSVRLIVSDNRGSSTTRYF
+YR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45d86dbaca34fe8253835cf5ae645a51104e8ffd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002755.fa
@@ -0,0 +1,4 @@
+>2_2178
+MSQAWTTKRTAAAGPGRPSPVAGAASGRAPFAAIGRFYAGYVRFGGRTGRLAFFQVMAWL
+LLASCLMQFVFYQLGATGHLGGAGWLGAPLFSAEPAFSRHPDVPAATAAFQWVSNALALA
+HVLPTLALTARRLRDAGFHVAWTLLAFVPGLGSLVLFCLLIQPTGRRFP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b21b580f25a1235c6f25f144c3c8bdd12b4d2d44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002759.fa
@@ -0,0 +1,3 @@
+>2_2248
+MATGDTVAVGQELAVVEAMKMEHPVTAAVAGVVTVHVAEGDSVAAQALIAAVAPAGADES
+AEPAPHEASAQNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac501f55285953573ee9a1844ae9bc60eacec819
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002760.fa
@@ -0,0 +1,3 @@
+>2_2274
+MWFLIALAVMAVIGFILRPISSLLAMAKFIAFAVAAVAGFAWYMGGPADMYAGPTILGAL
+AWIGLMFVPQPRFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e99f063e1d72f458ed2b15709ac3cdd46e5a8fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002766.fa
@@ -0,0 +1,3 @@
+>2_2319
+MSVVIDAPRASALDRPGLDQDLIPVSQADGLDPVIAVALAAGRRAGERLTSTPLTPRQRA
+AVAAVMGGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52e464ba832a35d35e956e7e3f0b1490ec7ae65a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002768.fa
@@ -0,0 +1,8 @@
+>2_2353
+MTTPSQDRLTIGATGAFERDNFGDLLYPMMLRDAWAAWAHTALLSRFPVSTEDLLGQAVL
+DYDDAVSTQHFDALVLTGGASVPISMTRAVQLQDHEPPVLHEDPHGLPYVPEVNPRGVNA
+DTPVFINSAGVWPTGSMRVRHRRRLLRTLQGAQLITVRDRESAELLDSWNLSAHLAPDAV
+HALSQYWPLSAHDRAPARVAIQLSDEFLDEHGDAAVRQGLLEAGRVAVERGLDEIVLFAA
+GVAPGHDDLGRMESLARTLGEDLGMVARISQERSPRDIVALIAGSGLVIGHSLHVRVVAA
+SYDVPRVSLRRAKTEAYSRSWDPAMPSGTAPARLATAVSEALSDDRRSTASADARSLVRH
+ATGMVEHLGSDIRWWSGRRAEVGRIRRGVNRRNDALKVADTVVSAGRRARASVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b46fd0e8ae997bb888d1a187d7e5c2ab6bb837d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002778.fa
@@ -0,0 +1,3 @@
+>2_2523
+MSTIAQFADAAALPYGAKADMAAEPTLATIATTATTALTCITAAFGHHDSERLDVMSTVE
+ADASVDTMVAARRDALQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2507d498990a8ded5e7248d7927f202d18ef136b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002785.fa
@@ -0,0 +1,8 @@
+>2_2562
+MSSGRVSVSREEELKVYVRAGGRCCFCQAYLVEGQIAGAPMKIGEMAHIVGAKISKRSPR
+GEDPLPQQERDKAENLMLVCRGEHKEIDRVGASDWATVDKLRRIKADHEGWIRRVTGLDR
+SRHTTVLRFVGDVRGNAVDITKAAAAGAVLLSGDRYPKFPLSADDFGFEIDIRAFDETSP
+DYWQRAAAHIDRIIDHKLRDEVTAGRVDHVSVFAFALLPLLVHLGSKLDDTFATDVYDNH
+RVTRSWEWPDSEAAARFETSFPADPSSADEAVFVLNVSGSISDAEVPAALADLPQWTLAL
+AGATPGPGPLRSAADLAAFSAASRGLLAEVERRAKHTRRLHVLAALPLSAAIELGRVHDA
+HVHPRLAVYHRADGGYKQALELS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00f71987ba398db08ac761145aadd16ee0cbbe68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002789.fa
@@ -0,0 +1,6 @@
+>2_2589
+MNQTTAVPTAGPVLALEGTYNFRSTAGYPAAAGRLRENALFRSDALHRLSEDDQRVFSAQ
+GISRVIDLRDSEELRHSPNAIPAGPTETVHHPIFGSGAGLPAIAGSFSIDSVYRYMIEHR
+ADRVAGAVRLIADAPEGGVLVHCTAGKDRTGVVVAFALTAVGVPRDQVIADYAASAANLA
+GEWAERMLAASAERFGEFDGDARELIVGSPAEAIDRTLDLIEDGYGGVERMLLQHGLDDD
+ALDRLQRRLVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cd6c57a5edb21a52094b3b539e9fd6d4614b612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002793.fa
@@ -0,0 +1,11 @@
+>2_2597
+MPVAGVAGLAMDAAFPALGWWPLAFVSVTLSLVTLIGRRSWGALLVGTVFGAAFWFPHVS
+WSAQFLGEHPLSWVPWVALAGALTIYTAVLTVPIALAYRWLPRRRNAFAMRLLALPLLVA
+GAWTIRELIMGSWPYGGFPWGRVAMSQSESPIAPVASWVGVSGLGFLMVAVCAAAIEAVR
+WIVRAQPARGNATEHPRTPLASWAASIPVLGLAAVMVLVPQFPTSHAGTIRVGAVQGNGP
+AAYVDEHEPGAVLESQLAASAPLEDEQVDIVLWPEGGVDSDPLADEATAHALDDAAARYD
+APILLNAAAADGHLVYNTSFLWTSNGPTAAHAKRHPVPFGEYVPDRWFYGALVPSLVDLL
+EREYAAGVDTPAIEVDGVEVGLAICFDVAFDDVIHEGAHSGAQVLMFQTNNADFRDTDEH
+LQQLAFARMRAIETGRSVVNLSTTGTSQVLAPNGATLAALAADEPGLMIADLELRDGLTA
+AVMLAQSINTLIVSGTLAGFLVLAFLLLRDRASSRHHRVLDSSQRSSIGLHECADAHRRE
+RL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ebb83bbcda90c2574432f8f2b725e1d8d658593
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002794.fa
@@ -0,0 +1,4 @@
+>2_2598
+MTTIDLTEDAFSAAITDHPIVLVDFWAAWCGPCRSFAPVFEAASTEHPDILFAKVDTEAQ
+ASLAAAAQITSIPTLMGFKDGVLVYSQPGALPAKALHDLIGKIRDLDMDHVRAQMQASDP
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3205be8fa99fad03898f2a22dbf2a7713fb50300
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002796.fa
@@ -0,0 +1,8 @@
+>2_2602
+MTPRRGRSSLALAAVAALLVTGCGASEPEPVRDPYPVDGSLPVVDTSGLQLPTPFEELEV
+VDPGWDITPQYADGVYLAAGERDGVLEFTAVDVYGDVLWAAQRPASCTGFVVTTDAHGRA
+LAILGDLQITADALAATTATAYDLTTGEQVWGPVEVPGPYQGPGLVFAAPPDGFMGETGP
+RVALDPTTGDVAADESSPEGIRIIGEYHGIVLLTHEDALIARDTADDHELWRIPLAEHGW
+TAASISASLRPEPGDGLALIATSETTGALLNLDQGSIVSSTARDAAVDPTTGTLVTLDDT
+GLHGYDADDRPLWSLPVAAETTIAAIGGVFLYLREDGAIRVHNVLTGDVAQAYEPDGQGP
+IIVPTHITINGAALLLQERRHLVATIAESPLNESFPTSSHAGMSIVGARVADST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7f0ec012bfee0edcae190c6760ecccd53feac5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002797.fa
@@ -0,0 +1,6 @@
+>2_2603
+MDIGLLAAFAGGTLALLSPCAALLMPAFFASTIGSGPRLLLHGAVFYVGLLTVLVPVGVG
+AGALGTLFVTHRQAIVLVASLVLVVLGAAQALGFGFDPARLLPAGADLHAQAASKTGLVK
+TVLLGAASGIAGFCAGPILGAVLTLAAARGDTLAAGVMLAVYGAGMVLPLLLIAALWQRL
+GARGRRFLRGRSFTVLGRELHTTSVVTGLLIVGVGVLFWTTNGLVGAPELVPLDAQAWLQ
+ENTAILANPILDILAVVLIAGIVLVLWARRRRTHARADAQAGEHRAEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a83ffbcf158ccec6672e28a676c5cbabd194d61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002798.fa
@@ -0,0 +1,6 @@
+>2_2604
+MPTETTNRPKPSNRSRSSLIVPVAVLTLAAVLIAVIVAVKWSGTTAEEGGSPSDSGAPTE
+VQNPEQPDLSAAETRDEADLLAAGPVDAPVVLVVFSDYQCPFCARWSEQTLPSMMEHVDA
+GDLRIEWRDINVFGPASERAARASYAAALQGALWEYHDALFEDGERRSESELSEEALVAL
+AGELGLDTEQFAADLGSEETAQVIAANQQFGFDLGATSTPIFILGGQPIVGAQPTEVFQE
+AFQSALDAAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68167a0625fbe2687719982bdd44504e4640a507
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002800.fa
@@ -0,0 +1,4 @@
+>2_2606
+MKAADGRSGDLLRLGALEAQVMDVLWDHGPATVREVIEHLPSDPAYTTIATVLTNLDRKR
+LVTITRQNRSTRYGAKITRHEHAAGLMEQVLEASRDRAASILQFVDSMPENDLDLLRDYL
+ERRDRGDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002805.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c6c0cad5f0a3488d9a14c8296a2ee2d4dc88fea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002805.fa
@@ -0,0 +1,4 @@
+>2_2619
+MRHRLATWVLQGLLVLAVLLILFLQVIGLPWLGGEVARDLPAEAFMRWPVTALAIVGLAF
+VQVGLVGTIRLLALTRTDRIFTARALPWVDAIIAAFVGGGLTCAATIAYQATAVSGPPLW
+SLMLLVGTAAGLGLALLMGVMRSLLTRATALRDEMDAVI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1722682f77c126307dfc32e554560ed8650c416a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002806.fa
@@ -0,0 +1,8 @@
+>2_2622
+MSSQHTWSDEGLRLLPRHLLAGPVAVLHPPLPAPDRVGAQHRVNEEQERQPRGVKSAGGG
+PAHGAAAKHVGDERDEAEPGRDPDSGDARDPRSMRSLGLEAPPDDVWAGSRLTCRPRSGA
+ADGRAWRLAGGRETPCASFQGREAAGAGFWWQGELPPSPRQGVVECFGEAPRVPPVHPAL
+AAPPRPRLHGCPKPPGRDDLGLLAADRALGRISVRTAAHRARLVRRHGNGERVRVRHGRH
+AGCRRRRGASGPPGHGWHRRARGRVPVRAHECALQASRRQSCRAERGVDTTHHDHAGGHV
+DNGPDAVEATQDLTWMRSATSSWCAAELGACVRRHPVWCVADPRDAWPRACGHT
+
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4533739d3057f6788d4dc23abb5dc710ecd5f7dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002807.fa
@@ -0,0 +1,8 @@
+>3_43
+MMSRMSENSEPGSEADARDSGSGSVGNLELFFDLVFVYAMAQLTELVRDDVSWRGFGHGV
+LGLLAVWWAWVCYTWLTNTFTTHRVVFRCLVIAAMAAMLLAASALPTAFSTGALVFGLAL
+LAIRVIHLVMFVVDASHDDEHLRAGLLRLVPSLLIAPVLIAVAAAFPAPYRELLWIGAAI
+IDFGGPLVAGVEVFRVVPSYFVERHGLIIIIALGEAVVGLGTGASEHLQQPVVLAAAVLG
+VLIAASLWWTYFGLTAGAEQRLEDADGPERARLARDAYSYLHLPLVAGVTFFGFGASVAL
+EHVSDPLPLLPAIALSGGVGLFYAADVAYRWRDHHQLVPDRLLAAAACLLIIPPALSMPA
+WSVLAALTAVGALRLTWELVRRPRIGPATAGQVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2784dba85be071cf35e547ed7a9aca58766bdd65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002808.fa
@@ -0,0 +1,4 @@
+>3_45
+MLIVLRGNAASGKSTVALLLQDRLDRPAAILSQDHFRRSIYAECEQDSLAHADLLEAAAL
+HCLGRGHHVILDGIFHAGRYGPMLERVAAASDDARFYAFDLTFAETVRRHAMRPRAAEFS
+ADEMASWYHGWQALPFVDEHRITATEAPEQIVTRILHGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dda6ddd69950cc6cc1357eb8d0a7bc0c4b292084
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002809.fa
@@ -0,0 +1,7 @@
+>3_46
+MDFHRPSLEELRAAAALPSHTAAGLTHEVILTEIAAGRMKPEWSCIATNDDGDVIGRAMW
+WGRDSQEPIALDLWDVAPGTSEPGEVLTGLLTHGGVLVEAPDRRALLPHTLRVPVGWGDQ
+PEVAENVRLKMQVASANGLGRVNERLQFQWDWGETVPPNPARLRFTPASDEVFMRLFADA
+AAGSLDVMTARELEQTTAADLARDEIAYYLSCPGDRSWWRVAQTHDGEIIGLAIPSATPT
+NRNVGYLAVLPQHRGHGYVDEILAYITRFQIEDRARRITATTDAVNTPMVAAFTRAGYTL
+VEVRIDLEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6600839c850df6d4a16eaa31420e3e6b8d80a7bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002811.fa
@@ -0,0 +1,3 @@
+>3_69
+MKRLNVTARLAAAVLLAAGLSATPASAASPLPVSDGVVAEAGLAPVRDGGVDSGVRDGFC
+TVFPFMCDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002813.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbf680af215699d74129d47e2365562d80f816d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002813.fa
@@ -0,0 +1,3 @@
+>3_77
+MSALITLLALSLTTGLCCGVPYATMTEPMPAHVHSTGIAIGYDVSVAVFGGSAPPASPVP
+TSSCERASALSGAAAARRSGRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6a4b7f8e1980262b32e806c2bf24dba22ee529d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002815.fa
@@ -0,0 +1,4 @@
+>3_157
+MDIPTRRSAVALAAAGAALLAGCAAPTPEITVVDDAGTRLFLAASPWEQREGESRGLLTG
+TLEVSEGGCLVVDDGAVGVPDHTSLPLAFPSGSTLVRESDRVTGVRAPDGATVLLGDSRG
+WTGGRVLVDDLERDARDALTQCTTEQAVFVPLAEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a4e44492c7280a04f96f39109fe7b642a1c0c5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002826.fa
@@ -0,0 +1,3 @@
+>3_201
+MSATPTPAAALSLTHLTPQDLAARVGVPVATVYNWRTTGYGPRGFRVGKYLRYRLADVEA
+WEAEQIAAEDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002829.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c452ccc909c54a678e85cd28d14934af7a856fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002829.fa
@@ -0,0 +1,4 @@
+>3_215
+MRAVEELRYLILAAQREGNRLLAQGLRALGLTPSQAEVLRILSDHQPLTLSALGGLLVCD
+SGQSPSRLVDRLVGKGYIERTPSKQDRRSVELALTAEGSAASAKVAEIEEDVYALIGEAL
+GGTDPQPLTEFLWKVVGGTVAGEALAQRRASQQEQTNV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caa625fce1df3414621e464ea9048a9d55790002
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002831.fa
@@ -0,0 +1,9 @@
+>3_255
+MERLPAWLLETPLLAPWTVPVCVAVGVLLVLGLWVGRTRRRPWWVQALVVGVPAALALAS
+WWWVNVVWAPIPDGVAGPVFAWAALPVVVLAQAAVGPWRPRPLRWGLGGVVAVLAAVLCA
+TLGVNAHYSAYESLAVMTGRNVTWTDWDAVDTAPARQVVPVDRWTAPAGLPEHGTVSRVG
+IPATDARLAPRDAVVYLPPAYFAEERPALPVMILMAGVPGEPPDWFSAGHAAETMDAYAA
+AHHGLAPIVLSVDANGGGALTNRLCWDGPDARVETYLTQDVPAWIGRELQTDRDRTHWAI
+GGLSNGATCALQTVARTPDGFGTVLVFSGELHPSLGTEERTIAEGFGGVRAAYAANDPLS
+LFAAAQRGEGPGADGAYRGVAGVVSVGRSDAYVGMPVPQELVDAGRAAGMDLTLREYPGG
+HTWTVWSRAFADQLPWAAGRMGLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002834.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18d9180db3a96d7e20318dd0f5ded46b4b8ded4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002834.fa
@@ -0,0 +1,11 @@
+>3_275
+MSSPERAGAGTANGTADALLDRLLHEWEHETAEFKTAETKYDRDKLGKYVSALSNEARLR
+DCSAGWFVLGVDNTRTVVGTAAFSREGQLLELSRRVAEGIDQNLTVRQIHEVERAGKRVL
+ILEIPPAPRGMPVSWQGHFYARNGESLGSLSLDKLDEIREASHQPDWTNTLIPSARLEDL
+DPDAVARARQGFHERHSRIPVEEVESWSDHEFLERARLMRLGQLTRAAVLLLGGPTAASL
+LEDHPGQLTWQLKGEQEAYEHFYPPLLLSVGDLATRIRNVKLRLMPPDELIYREVGKYED
+TSILEALYNAVAHQDYRRHSRILVVEHPDRLEITSVGEFFAGAPEDYLVDAQPPRAYRNP
+ALVQAMQTLNLVDQMGYGIHRMVSAQMRRFMPLPDYDLTRIGEVTLTLHGAVIDERFSQL
+LMARRDLPFESVLALDRVQKGLAITAEAASHLRRQGLVEGKRPRLRISPSVAAETQDMAA
+YVRTRPQSDAHYTRLLIDYLTANGGSDRKGIDALLSPLLNQALDENQTRNKISNLLAKLR
+RQGRIKNIGSRPQPHWTVVGEAGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a7dd1d2da0ed514b58ee42bc110056ba787396c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002836.fa
@@ -0,0 +1,5 @@
+>3_291
+MHTDDPQQSLDTQQELLEEQMPETAATLGASRVKTLRQTTCTGQYDPETMGESVQWSVNI
+TRDIADLDAAKDAASPVQQYLEQHGWNLDVGPGKYPGPITTIFTGTHEGSGLQLIAEYRT
+GGNESLLVIRGGGSCVDMPKGNQMVRSHLDNGFGIPQAEYDWEAERRSPDYQEYSLPPGE
+KPGPVTEEPGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f86b57283001f2a6a44000cd434cf1431a936127
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002838.fa
@@ -0,0 +1,3 @@
+>3_299
+MHASGQSPYWQNGVEMLIRHSNGQCTHYAHLDRALYRAGASVPQGRVVAWSGNTGASSGP
+HLHYQAIDCNTRVGIASTLQGTKPGTGSLPVSTNVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..691f7a4945c12f3215d71af951db70b151a48dc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002844.fa
@@ -0,0 +1,3 @@
+>3_322
+MTFALNEPEYVAVIDSVDGDLGTVELKARAVTTEVDELLGICLDSDVTSALTQFRDDALD
+KALRALTESARAVVDSGRAVATSYREFDAEVAKRATAAELGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c753d02c16cd6ec6c4fdfdca0b28bec7065f0dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002849.fa
@@ -0,0 +1,4 @@
+>3_334
+MAEKFGWRPNDYLENPRAFGKEDTSPAWRETWFDGTVIQDDPRHHDRQIAAKIQHLVAIE
+VTRAARLRDETLADVSKHTRMGADQFRRLMRGEGPMQVVDFATFRRVYHVDFGINPDPGL
+ANIRETKF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002851.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7233736f1e8a95bf678a10b45aa4ef03bcda696
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002851.fa
@@ -0,0 +1,7 @@
+>3_336
+MPCGCYRNNDSLSSHTRSAALDITDYRPATIPAPAWNRIADFTRAVAADTQAHHGNRFNT
+RDLMGAIAHHVHWVTDAACLPLDRSVVFHRDVIEDYIAHGTPTLGPGSRSTRRSFLLRAA
+EAVLPDDERVTRLYPHHKDAPARPYSEFEQRALRSWAVGQTTAQRRLDCHTILALGLGAG
+LGTADMMSLRVEQIDADDKGVVIHVTRPGVERDVPVLAAWEQPLINVLAARGLDDWVVGV
+RRAGVYKNWMTQFLRRALPERGVTVEVARLRNTWLVHHITAGTPLGPLAFAAGLETFRTI
+EKVLRYVPQPSHDEARAHLRHAMAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002856.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bed5fa8caa20b6e44fa8dc8424795fc22d9ec24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002856.fa
@@ -0,0 +1,6 @@
+>3_394
+MTVDAGVLVGENGRVRGIRASSWTPERQRRVERLLRVVEAAALLLFGVCAAVLLLTEPRL
+SGTIRSVSVEGVGARLSRYGLLFAAAVITYVPRRWKWALPGYAVSALFVVGMVKMLEGAP
+SEGFPGLQVFRTDLPWLIGLLLVPQVAGVARRAGLSVRRRYASALAWTAFVEGAGAGRND
+CGCVKNRVVQNGAQETRVLLQRFDGTRRSGQVWGVVEPSECIEVDAARAVVARTDWRNAL
+SWAALDRWGRRLPGREEAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2138e10dbe4dfbdd667ea6abc2e4e262c00f70d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002863.fa
@@ -0,0 +1,6 @@
+>3_430
+MTSSDDDTVLLALSHPGRRALLDALHERDGQSVTDLGQALPELGRHAVLKHLGVLEDTGL
+VTSHKAGRTRLCYLNAAPLVALAQRWLDDYALGWGQALNRLKSTSERRPEAMTTAAPLHR
+QAIVIDATPERVWTALTQECSSWFFATTLNSSLEPGSDYTYTYPDGRRAAEGTIIAADPG
+QRLEMTFSPTWDDAVTPEAPFRLVWSLAAQGGATLLTVEHYELDPSTETARQVGPGSLFL
+ISNIKTWIETGKPMHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1176477c846043f29aa750f7b9fb4fd55d220da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002865.fa
@@ -0,0 +1,3 @@
+>3_443
+MAAAEGAGLIRSRVGGAWAPAPGPHDPRLPLRKAGFRHAGDAARWVRSLTPLGAPVPQGA
+ELTRRILQARPELPVDAAQALTLLAEGAGPGEDAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4ec2adbfbe48d8d59f99387819c13c28f80f27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002869.fa
@@ -0,0 +1,3 @@
+>3_508
+MTTTTAPRPAARLRSTLVAVAVLPALMIGAPAASAAPAVSPLGHDMRISDPGTASPDFYR
+YICRRVPIIPC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be468380de14b4c56775f45ea22ffef9f48eee79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002871.fa
@@ -0,0 +1,5 @@
+>3_512
+MTAALERGRPLEGAPARPATPHRRARCTPPWPRPGVLALAAVLAALLALAGAAVGHSAAG
+SLPAGLLGGPHTSDADWTLTGILGRNLGAALLVFGGVVTGGALTAVTLPLVGVWVGATLR
+LALDAAGWEGAVGATVLYAPLEFAGVLLAAVAGLVPLAAALLRPRDADVVPGPLSRYLGA
+LPSACLLIGCALLLITAAGVVEHLVVSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c8ffd54ede13a4efe5ad8af04f0d57eabb3feb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002873.fa
@@ -0,0 +1,4 @@
+>3_514
+MRLTTTHLRIALGAVGLLGLGVLATLLWGGVLPAALSSTQRGIVLTAAAVAAVAPLLGAV
+LPVTRIERPSSAVLPSLGLFGFGVLFTDALDVFPVRIIVILGGLLALAAVVAALFGGPER
+AEAAEVPERTAHRFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002874.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f1d17c0e89a33dc58774f2e72cf17c5e3ad8d8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002874.fa
@@ -0,0 +1,11 @@
+>3_515
+MSPTLAAPVGTGHHAVPRPVPAPDAGWSRAAPAPTPRRRLSLLADLRCAELLTSLGLRMS
+LRSARLLLTVAAVAGPVLLVLAAFAGARFTALVLPPGGTLEALSVTVLPLLCGLSLGGVI
+LAEAVGRQRETVSGHPNIPYFRALDVPATLVHAVYALPRLLTAGTVWTCVGAGVLVACLS
+TTSDASPWWAAGTALLVLLPVALTAVASAVSLAVASRPPRAGGPGVLAVGVGAAALGAFA
+GAGLGRLAAGAASRPGRRPGEVSPVTAVPGQEHGVVLLAGGVLLLVLALVGVAAGRRRLR
+ARSFPLAAADPVRLRRRSAPGGGALSWAWMLWRQRRGSTRWAAERRVLWGLALVAGAAAG
+ARAVGVGRLDASLAGLPHSPLLEGDPVGAVHTVLVLGLTMVGVALGETAHGDLGRHRFGR
+HLRQAVELGAPLGVTVRGWMLALLGPALLGGVCAGVAAVLVWPPVGVLAPALVLGGVGAT
+VLADHLLPPPRTADGGVGEGMLTALLALVLASGPAALLLAGAGPLATAAGVALLLVGAAA
+CLARRLCVLTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d5a8a89f4297d7efb29899118a9cd73f58293fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002875.fa
@@ -0,0 +1,5 @@
+>3_531
+MTPVRGDAGTQALAAVVAATRDHRMTFPIQARVSLTSPHQPEPEVYEVRARGDGGFAAWS
+ARHDLFYDPRTGQERLVVHASPGREGFTREWVWPWLSPSHRVLAMFAPAELGIWGGNHDQ
+HRVCAARWLGECAVRVDLVRREEPAGSEATGYAEVDLGNAVVTRMLLDGEAYVLEAARVV
+DDGDVTGPVVGPHLPGWPRSFVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea4ab257ed413bd7d313457cc9c9ca0bb46287c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002879.fa
@@ -0,0 +1,7 @@
+>3_601
+MTEARRPTSARSPVLRILARILTAALLLALAVLAVAVFTPHSELGQRLTTRLFLAQALAF
+AEPAGAGLTLLGLGVLALHRGAGTRRRTAVGGVAAMLLGLGVGLLAWPDAPPWAAGPATA
+TGNTGRHVRVTVFNSLDTLTAADARRLIDETDPDVLVLPEAAPSRVREALAGTGLAGGVH
+EGADSGFSRGRPAGVAPTTIAMHPRLGAYHQTAPTPTTFGAIRLEPADGADGPVVVGVHT
+GPPLPRLMDDWRGDLDRLSAVDHAAAQGPMVVAGDLNATLRHGPLADRVHLADTALRCPD
+DVGGTWPSDAPGRLRSPIDHVLVTGDVEVLSCTTLRVGASDHLAYAAELRLPGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e23b05f819916cc42551ec70710b666ed1b4a5d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002883.fa
@@ -0,0 +1,13 @@
+>3_612
+MAHTTTPPSPRGGKRLTIADVPHMRERYAASNPLPPEEVAAGSNKKFTWSCKAGPDHTWE
+AQANSIRMSKRGGCPFCAGKRPSVTNRLDVLFPDLAAEWDQELNEGPPAVVAGSEKKVWW
+RCRAADHAWQANIRNRTVLRAGCPRCAAEKSSKTRSVPLPGRELTAVAPDVAASWHPTRN
+GTLQPDEVAAFSNVPRWWQCPAGHEWEISPAGRLSKGGAGCPYCSGRLATAETSLEVQRP
+DLTLEWHPTKNAPRTPRDVKPGTSATVWWICSAGHEYESRIANRAYLGRGCPYCSGQKIG
+YGNDLATKAPLVAAEWDHERNGSLTPADVTTGVQRRFWWSCTQGHSWRTTVASRVALGTG
+CPECGAGWRRSRPEIALQFELAHLLPAAVVGDGHVQTADKDFRVDVLCPELKIAVEYDGN
+HWHMDTFERDLAKTQALVEAGWVTVRVRQNPLPLTGRHDVPCENGDPAVYPMTVRLMTSL
+LEEAAAAPTDHPIHAHLDELRLRLETYVDGGTARAVEEAERETRAHHVDRPKRDPFAPPP
+RPKPGRSLAELNPAIAAEWHPSKNGGLTPADVANARNASAWWLCSLCGAEWEAVVGQRTR
+RQTLGCPDCGKARAGAARSRPQPGLSLADLRPDLAAQWHPTRNAPLTPHDVRPGSHKRVW
+WRSPGGQEWESSVYNRTSKRPSSEVHGDAGPDSPDSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20f7ce35c3cae93f004d0c1ada1374e79a49835f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002888.fa
@@ -0,0 +1,4 @@
+>3_636
+MSTRTTQQTVEDFFSAFGAGDLDTVKNLFAPTINFTVHGSPAVPWAGTRHTRDELDTFFP
+AFAALGPATEYTIHQIVVDGDHAVALGHNEFPVLATGKSFSNDFALHFTVQDGQITGYQM
+YEDTYAVDQAFTPTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..718db80e5d2912c2556e192cefbb5d539a1f52fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002890.fa
@@ -0,0 +1,4 @@
+>3_641
+MAVGDKNALLVQVFDTMVADEHAQRAGATPQSTGDAPDTCVKRLGVLVQPFVAMFTGSPE
+LARSYASILVSGTHSSSLFTELHARLVEEFATAITKQGCTPAADAPAKAQALYAAYVGTL
+FTWSARGLVDPSAITNGLRTSFAAISICKE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be1007b0725ed8a8fd5d0e80dfa859a0f148db4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002891.fa
@@ -0,0 +1,6 @@
+>3_643
+MSLQRVPLAAGRRHSLVVVDGGRVLAAGPPGAGECAVTGWSDVVAVAAGNVHAARNTGRS
+HSVGLRADGTVLAVGWNAHGQCDVTGWSQVVGFAAGWRRTLGVRADGTVLAAGRRDDGAC
+DVGGWSGIVAVSAGDWHSVGLRSDGTVVATGMDTRGQGDVAGWSDVVGIAAGYLHTLGVR
+EDGTVLACGDTAAGLAGARRWRGVAAVVAGSYHSLGLTQDGRVLAAGDDGHGQCSTQTWR
+DVVAIAAGSTHSLGLRSDGVILAAGNNADGQCHWALSAPGQYN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5632573e097567cbd966c35716616d0dffaad16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002892.fa
@@ -0,0 +1,5 @@
+>3_663
+MSTPDELADEVADVRSLNALAEAWRTAPDGSRRFVPNFDPRSGGTSSRVLVLMQSPGPQT
+IAAAHTAICSEDNPGPTAAAFRAARIESGLARNDYLRWNLIPWEILGRVRPVDIDEGRHA
+LETLLKVLPVLDAIVTYGTAALNGVMRHLTLDEHPRLVPVIAAPHPSPANGRHRAEQQRR
+SVQALRLAALTHRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfcfd78ca5a612e839cef7eec0a7761377bf4c39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002895.fa
@@ -0,0 +1,4 @@
+>3_671
+MVESNTAGVVVVGVQSGQGHDVVGVAAAVAERFSARLVCVVVDPALLSAGVRADGSEIIE
+PIDPDTADSDPQQLPDEDMRVIRDLAAARSVDVDFVSRVGDPSHALAAVAEERDAVMIVV
+GSQAGRRRIAELLTGSVAAHLTHQQHRPILVVPHDPVGATVLLPSEAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002896.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1700b5529e41bf16e66db59833d4c2c1c8ec7f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002896.fa
@@ -0,0 +1,6 @@
+>3_673
+MSLRKLRPYAVTGGLTYQRPAVSDLARTAILHEGINLLEHAATVTIRHEDSPMYGEFAVR
+VAGELVGYLDSSTRGYLEPDPRFRHPARYQVMVVREGDVLTIGPAYAWIGKDEPAWIYTD
+DSATHPEKRSGKKFAPATVEASKVKGAFPVAGTNTSRADSMLKVVKRLELTEGETVEIPA
+VIERRPHEFGQNEAIGVRVGDDVIGKLWGIHAPAFGDLRGDRTVPVVLRLEVRNLWDNGV
+RVVGAIWSGGGTTNWTNIAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d361b9f9347d479ace308e77614512a3b8b11e04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002897.fa
@@ -0,0 +1,4 @@
+>3_674
+MAVFYSFHYDRDVHRVQLIEQMGALEGQPILNHQEWETVKSGGDTAIKEWISDKMKWKSA
+VIVLIGKETASREWVHYEIQKAWDDKKPLLGIRIHGLSSMGSVDSSGPNPFDKISSVSGV
+PIFDPTQTDWTGKIDSKATYNHLKDHLTTWATQGKTRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d081d80bb75efbb7140be73f4deb271c6769684d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002900.fa
@@ -0,0 +1,3 @@
+>3_687
+MPRTISVANTGEWLTRIAVGDAIGITAEATTHNHRAPEVVYLPIEDAPPVTVALTWPGQR
+RSHPQVGVVATCAQDYFTRLIDIGSPPRLLSTGADGQLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc9e1563068ad3d987a886ef8c334af0fc72a76c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002903.fa
@@ -0,0 +1,3 @@
+>3_695
+MTYVIALPCVDVKDRACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+LPDEWSDYSKANVEFFDELGSPGGAAKTGPTGFDHPLIAALPIQHEQTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002907.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6843213befe5c54cb5503cf5ae330133d90d63e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002907.fa
@@ -0,0 +1,3 @@
+>3_702
+MASNDYQVTGMTCGHCEMSIREEVSEIPGVQDIQVSAQTGKLNVTAEGEIDDAKVLAAVE
+EAGYSAVRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4229fc6527ddcbb500f2fc61d53b86a54edb13e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002908.fa
@@ -0,0 +1,5 @@
+>3_719
+MGQTRRMPDPHELIAAALREQAAAERRLHGAVQAARDAGWSWTQVAEVLGVTRQAAHRRF
+HVAPAVALDDGGARGDGVPADVAAENGPGGASDPWAEARAAAEATVEAWLRGDVAAVHAR
+MTSAARAGLPQSALRGVLLEIEDLSGGLRAVRVTGVHDLDGELLSGEPASGGPSPAGGAG
+RAGRRRAVVVRCVVAGEDADPVVHVLIGPGGRVSGLSVRISDELEQWPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79acf1908cda33c813c53e8b9d0396f42f24f0fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002909.fa
@@ -0,0 +1,6 @@
+>3_721
+MRRPSAPASRPSPAPEGSWLSRLWAAHAAFLVTGGVLLAVVVAFTSLAEEVYDSVTEGDG
+VPAVDHPALQAAISLRGPVLTGLAQFLAYAGDTPGAVAVGLVLLGLLTLARREATPAVVL
+LGGMAGAVLITVVGKSHVGRLRPPVDVALPPIVTSPSFPSGHTLNATVLMALTVYLVAIT
+PRLSLCGTHRRAVTAAAVVAGCYAVLMGLSRVYLAAHWLTDVAAGWTVGLAWAAAVVLAH
+RVWLTVQDVRRSRAGTPAAPAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002912.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90a3107bac22d22edb14763d0efda409147b5fdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002912.fa
@@ -0,0 +1,5 @@
+>3_764
+MTGAERGGAVAAHPVPTHPEAVPGDRATLRWAVPAGLLGMVGPVGDGPAPLEALRADGTL
+RALVAEPAALRLTVGEGRTWRAEGARVRAALQEALALLAAGEATCAPEAPASVVGGPGGG
+GKARAVARAGASADSDAVLRAAVEQVLAGPAGEYLRSHGGTARILGVEDGEVELALGGTC
+HACPARGFTLQMRLEAEIRRLCPDVRAVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002915.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f30bda5d619bf353427ecc8c869a57d4e4eadb98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002915.fa
@@ -0,0 +1,13 @@
+>3_806
+MSTHPHPGDGAGIAASAAPQPAPGSPSSPAPTAPSSADRSGGHAAPGHRPATAERARTGM
+LMLAIGALGVVFGDIGTSPLYALQTLFSADHNAVTPSFAHVTGAISLVLWSLILIVTLTY
+VLNVLRADHHGEGGVLSLATLVRRHYDEATTPDSDTDVAQDAAAPGPERRRRGQWAFTAG
+LIGCSFFFGDSVITPAISVMSAVEGVAVAVPSLEHWIIPASLLILIVLYGLQRFGTGGVG
+MLFGPVMAAWFATLAVLGVGPLLDRPDILVALSPLPGLMFALQQPMVALVAMGAVVLAVT
+GAEALYADIGHFGRLPISRDWLFFVLPALALNYLGQGALILDDPGAVANPFFRLAPDWFA
+LPLTILAIAATVIASQAVITGAYSVTRQAMRLGYLPPLAVRHTSGKEAGQVYLPLVNWIL
+LAAVVLVVLMFRSSVALATAYGLAVTVTMIITTTLVLVHMATTWRRPLWQPVLLGTLVLP
+LELSFLAGNLVKVFEGGWLPLTIGGLVLGTMTVWHRGRVAVSHRWSRTEADLETFMAKAA
+HHVETGDLRRVPGHAVYLAPSARLAPAALRINLRANRGVHEKITLVHVVTEEQPYVAEAE
+RCTVREVGPLSGVHQAVIRVGFFDALDIPGTLRAHAAALGLTNRDLVQAVYVLSRSRYLT
+PRGHGPKTWGTRAFVSLSRLADQPVWQYGLPVDHTLEVGSRVRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ad904a3aacd4f3a25b5b134976daa5948778a1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002917.fa
@@ -0,0 +1,17 @@
+>3_850
+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_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3aa49bcd26c58eeab8cc4b906697c60156b60dd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002923.fa
@@ -0,0 +1,4 @@
+>3_898
+MASQEELTRIIDNINADVNGFIGASIVDMETGMPLASRSTRADFDLEVASAYNSEMVKSK
+LKTIQVLNIRTTLEDMLLTLGDQLHLIKMLDERTFLYVAADRSATNLALLRSAVNRHTVN
+FR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59519b9e68555a4f0970bdd3ced9861ad2e722e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002925.fa
@@ -0,0 +1,8 @@
+>3_914
+MAQDPAGWRRTAVLLSGAWREALRVSAPRVEPEHLFLGVLASGGPAARVSARQGLSLTAA
+RRGAAVRANRQLRAVGEDVARAGRIPRTPLAAVDRGGAATLPLSAASEGMLPARRLAMTE
+AAWALDLLQEPAGAVSALVAAAGVDVDALRHALRAADRDEPRLPGAALDVMPAPCPVPPD
+ALTPPDGIRPSGSRASRAGRLSAIGAEWFVAAPREHVMRLLRDPEPIRAITAQPADAEVD
+DAFGVVTTVRSRGARGGEHRSTSQLFPSETSTPDGAARIRWAEVLDEHRPPHQDSDGTLV
+PDGRDYSGDLAGAYVFTLVDDSGPDPDQPVDYPGHQPLSGAGTRVRLERTRRTVRRRDAL
+ASRATRWPQAWAVAQHLQSLASLAADRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e530dcea5cf8197edcdeee897283e5fb202c8893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002926.fa
@@ -0,0 +1,3 @@
+>3_920
+MSVRQPRIYTIPCDRRGDFLDRWQSTAQPLMETLGFRFVRTWEGTPDPVHRPHCRGCWAP
+RSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e093d3830155620858f16bbdbe87c3043239e6a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002933.fa
@@ -0,0 +1,7 @@
+>3_994
+MSIDQNTADTTTPLATTGVRGRSRRRRTAVGALGAAGALAAVGMASAPAQAATVDASVLQ
+SIQACESGGDYTAVNPASGASGAYQFLDSTWATLAAAQGYASAADAPASVQDAAAQELYA
+QEGTTPWEASQSCWSDAASVAAMSTSTSSTTVSDAAVAQADVATPVETVAQVEPAAGAAD
+EAEADTAAGADAAAEEAAGEETDAGGTAPTAAPDAAASGEQAPAPSEPAPEPAPQGDQTG
+RQPAERPAEQGRGTAEQAEQGRGTADQREQRGQDVEQREGRTGGERQGAAPETGGDAGHQ
+EADAAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..220442039315f03e87cc616a709b8bd25fb1b9ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002937.fa
@@ -0,0 +1,7 @@
+>3_1033
+MALFTVLLPVLTVLSVLAIVIGTALSVRPTTTSAALLARVRSHGAATAVTALLLGSISGF
+AGLAAEARPEGPEWTWDAGEWHGVPVFLDAVWLALALALLPAILVAAVTVGAQRSVPAPQ
+GRVRRAVLTPRTAASLVPRGPALPGVGIGLALGATLVLLWAEPSVPRLFPSDGAQEPEGY
+TPLAAGAQLAPWILGALVADLGAAAIGLRAIAHRPPIIGLTAAQDRAARTVAAHRLVRTV
+AWMLWLLTLGAWGSVLLSRTQRDLLHAVFPGHPAALDARPGLGWIGTVDAWTGLATLAVA
+LVLLLWRPPALGELRTGPGIDRARTAETVRTETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ec9d5a343580e934fbd56b90a629dd307ad2d61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002938.fa
@@ -0,0 +1,8 @@
+>3_1057
+MGAVTEQTPDAPHPSPAPPSATGGPAPAAPPVGPLTVRPITEAEHVEVLRRHPGASFLQN
+PRWARVKTDWSGQSLGFEADGRLVGAALVLGRRLPVPGRTPLLGRSFLAYVAEGPVLDAG
+VDVVEALAALVAELHAQGAFLVRVAPPGVVRRWDADTVRKALPDPAHRMLTDLEPAEEHA
+DALELERRLREAGWRAPEVLPGFSAGQPMFQARIPLEGLDEEGVLARMSGSSRKRTRRSL
+RNDLDVVVGGPERLDEWEALQDETAERDGFTGRRKEYFARLMDELGGSELADVTYYLAEY
+QGDPVAAAFHFRQGHVCWRPYSASSQKERKRDAPRLLEFEQIRQGIADGCHWLDLGGVPG
+SVDSEDRITGLTEFKTTQGADIVQTHGEWDFPLHKTLAHAFGLYMSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..216a0077cab62f95f0befc6e85f85971e5637e86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002940.fa
@@ -0,0 +1,12 @@
+>3_1159
+MGFVSIQDGLISLSPAGQKFSRDPSRDRLADQFANRIRLFAEALAVLSEGPKTINEINEH
+LVQSYSLSTWKTVANTRTRMTWLEVLGYVEWLSGNKLQVTGEGIDALARWELVTPEAIQL
+REEEPAVANIPPAPASIEALLDKLTRDPRAHESRNTYNIWVPSPASSPNKIANMRICIEA
+TAEPIEKEDLLSFIADTFGLKRSSVESMMPFMRAAGLIQEIRRGVYSATPAARAWLETGS
+DLDYVRIIHAHMRYVGEILRVAAPEALRSEVYAQGSQYGMNRDKVRWILNFLVEAGLIVD
+ISWSTIASTALGKAFAASLPLAPPNADEPLNPASQSSFAGLEDDSAEGITDSNSESLLIA
+QHLRRYAVDPFAEGVASGAAFENAIEAAFGALGFRSQRISGSGDTDVLVQWYDEDGQLCT
+AIIDAKSSASGSISHTNVSDVAIASHKEKHSADRVAIVAPGFSGETIRATGAKRGWALLT
+ADDLAGVLETAVDLGLTPVETSIMFDSSDGFSRLTELIDGRKRQLDLISLVVARLWSESE
+NDEPFSPRDISLVERKSDLEPTVDELVGVVSRLNALDSRVLRTVEASSDPKHETYRVGDV
+QAVARQLRAIARALEFGLDPKRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002943.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fe16050201200e21dbebfc4159a970495d70390
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002943.fa
@@ -0,0 +1,8 @@
+>3_1189
+MTNPFLGRDDQAIDVSDTPRGELEVVHTFTDGPMPTGVSVSHTGRIFVNFPKWGDEVPAT
+VVELVDGAVKPYPSAEANQAKSKADQDAFVSVQSIVIDPADRLWVLDTGSPLFEETQRGG
+PKLVCIDLTTDEITQTILFEPDVALPTTYLNDVRFDLRQGEAGFAYITDSSDQGPNGIIV
+VDLASGAAWRRLHDHPTTKALPPGEMVPVAEGRVFAERSAGEAPQPVKMGADGIAISHDG
+ERLWYCPLISRRWYSVDTAALRDRALSDEDVAATVVDHGDKGGGADGLESDDQGRLYATN
+WEHNAVLRRLPDGEMQTLVHDERLLWPDTMSVARDGHLYVTANQLHRQAKYQDGQDLRVY
+PYHLFRFAIDAGPVLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7933743727bb5032cfb7c35bed13700bbc6eede
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002944.fa
@@ -0,0 +1,3 @@
+>3_1192
+MLEIADGMVTFTPDSPSAAPGWSVPARQLTLGRAGVRFPGSFVVRGAEAEDIMLEVSTSE
+GARWREAGDARDLPDRSTHREVQQILVGWGARSVRPRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1aade719da470ff0f8fd7b8db34f12574dc6f42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002948.fa
@@ -0,0 +1,8 @@
+>3_1208
+MTENQHPDDPRRPEDTGGGAVPGESARHGVEEGAPEAGAAGWPDKPPSAGWPDHTPVTGT
+GHGSSAYTPGGDGAVPGPYEQPSYGQPAYGQDAGTQQAGAHGQPQGAYGADAYGAGAQHP
+GSYEQQGPYGQPTGAYGQQQPGAYGAYGQPLGGYGAYGQQPGVYVTGAGAPRPASNGLAI
+AALVCGVIALLLSFLPFIGLVSVLIGAAAVITGVLGLRRGQSKGMSIAGIVTGALGLLIS
+IAVTALTAAAVSAAVQEGGPALSSIGASLSSEANAPHEVELRATVDQGDATVNYSIGGSS
+SDQDITAEQISVTDSVTGSETLSISVTEDVTDTGSQNVTCEILVDGRSVAKETGTSSAYC
+NAGYGDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65829cb51be9c55aaa030df74ea08ccf02cd464a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002949.fa
@@ -0,0 +1,3 @@
+>3_1269
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELLGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDPTSRTPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1151fd6d6fcde29da85b850caf0e72a40d5b809c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002957.fa
@@ -0,0 +1,8 @@
+>3_1557
+MTPHRRTAAATLLAMALLTGCAPTANAPDGAASGTSQDASSSDSASDLRADTPGTSSTMP
+PASPATASGEPRTVTINTSGDLLWNEPLFDAARTGGGFDFRPMLASVRPFVAAADLAVCH
+QEVPLAAPGGPYTGWPRFRAPQQTVAAVVDAGFDVCTTASNHTVDDGWDGMVRTHDALRA
+AGVGVAGTSTTPGEDQAPDLFTTADGVVVGIVSQTFSTNLIPVPEGREWSVDLLDPDRAI
+ADAHAAREAGADVVVFHMHAGDEYVRIPNEDQRWMANQVTASGEVDLVIGQHPHWVQPVE
+KVNGVWVVYSTGNLIASMKGERPGTHDGAIVEVAFREGDDGRFDATGVTWAPTLITDADT
+DPTGRPRVLLIPDELPQAGPELRGRLEESAARTRVAIGSDNTPGLSERTSPGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00dd9a4a85acd17b3da7a7896affff658bdea413
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002958.fa
@@ -0,0 +1,3 @@
+>3_1562
+MRAGRRSRSLTSETEAKAGSCTTKDGKSYKAFGRFADEGAWWDAERGGFVFDASFDKAFH
+DGQIWFFDVKAGTITIDAYYPLTAPNFSEERRSAPAADRAAPGGPQLTNKLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d10b1370a1df5f92f447c25bf173203c7b06dd5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002960.fa
@@ -0,0 +1,11 @@
+>3_1676
+MNPSERTASPDPVADLLPTLRALPLVRRPTTPDRTARTVGALGWVLLVAAMVVLVVVGFH
+AARLGRDPAFLFDCDDFNQCEDLWLDARTHYRMVTLIAALAAAAGWFLAGTGRTAPVPST
+PPMDARHPRSPRRRGVDAPAVLAALGGGLLTATAAGFATSMMRSGHPGLPGADALAGVVA
+TALVSATLLLIVVPRCQAGWVLLVAIPLLDMLALLLGVLALPQSLNLVGAVLVGSATAAA
+VLGRRFLDVHGRGARDAHRLAGTVAATTAAVGLLGVLPLLVAWTFAWPIGVILTCAALVW
+RGLWFRSLARTSDGATSSAPVEAEAPPRVLWSVLAPGAVAIALLAVWAAWPVPAPPADAR
+PPDNVVPPPTPAPAPVPGTASADPTRNPQARPTPVAVPPDMPACAPEQLTLQVTGFDSAM
+GKSGAGIRAANTGSQPCALRGRPVITIIQGGDPIDLRPVPMDDRTGEVPAADLAREDPDS
+GAVLAPGGTATAGLFWPGYRNAADQTTPQSVSVALTVGGPSIPAPITGDGTVSGSPGPAP
+FDLKDGVPGGAELRVGAWTPST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ec7f1c37012863af43069e26371b4562aed22e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002961.fa
@@ -0,0 +1,8 @@
+>3_1696
+MSETHSTSTAPSRRGVLAGGALAAAGVIAGTAAQAVPAEARGGRHPQGASMPLAFGATRR
+MKIVQFNDTQGGHAADRRTIEFMGKVLDQEKPDFALINGDVIDGSPTTDVQVKQGLNNFV
+SPMESRGVKWAVTFGNHDEDSVEEHGTSMTEDRLLEFVRQYKHNVNPPKMDGVPGHTNAQ
+ILVRGSRGAAPAFAIWLLDSGRYASEADTHGQSTDGLKSYDWIRPAQIRWYEDASAATEA
+RFGRRTPGLMFCHIPTFEHEMMWHASQAAEEASDHAEAVRRHRITGVKHEDVYHGLVNSG
+VYASVKERGEVKGIYCGHDHINTYTGDYYGVELGYAPGTGFDPYGLNDGTWDQHTLRGAR
+VFELDERNASVYAGATRIVWARDLGIDMNPEGQPLATPVPFPPYVKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f821bf178ddc07b300d728e241ff5a04f6dddcd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002970.fa
@@ -0,0 +1,7 @@
+>3_1742
+MSPNLYHLARLLAPGSDRSLGRVAGDLASAHVPVFPCVPGQKRPLTARGFHDASTDLAQI
+EHWWARWPEANLGLPTGASGVVVVDVDVREHVDGRESMRCALNAGRVGMPVFTVVSPSGG
+RHGYYPATPDVVQRSWQVARAGVDFRGDGGYILIPPSHTTAGSYRLATVRQGAASGIDSD
+TLRDFLDPRPALKPRAADRGMAQSEPGVVVWRLAAWVAGLGEGERNRGLFWAACRAAEHD
+ITPATAVETLGAAAAEAGLGPREIAATVRSAYRTTHPTTSTARRATEPAAASPVRVPVGA
+GWGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ac92f1ec1ac83ddd33ff20e5eb4eaa9bb47298e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002971.fa
@@ -0,0 +1,5 @@
+>3_1744
+MSTHEHEHHPVEPPVHDDYGPPDPEELALTTPSPLAENLDQETVSERGDLVPPKAPVEEL
+NEQLAPDIDGPDAGFPELDEGAEGVPEAVKARTARTTSRPVGRQVGRGVEWVRPTDLLAR
+RGATVAGRGIHFQTALSQKTRHGITVSTRRIGDRAAWLAPLSAFGRGRAQSVPGRSAVGM
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f52bccd4ea7b20994c3acfa8325ffd1ef57f10fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002974.fa
@@ -0,0 +1,5 @@
+>3_1749
+MFWWVHLLGMDTSDRSSRRRLVLIAAGSVTALVCGVGIYGLATGPRTPTSTPGTSPTITT
+SPSPSATSTAKPSASGAPLVPPVASSADPEQFARNVATTLFAWDTTTGLLPLDYTSAILA
+VGDPSGTEQAGLATDVAAYLPSRTAWQDLREYGTSQHLTIARAYIPDQWGEAVAQAPEGQ
+LAPGTVAYTIEGTRHRTGTWNGEPVASAHKVEFTVFVVCAPTYDTCHLLRLSQLDNPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002980.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1416a3945ae824b4acdd5baea1ee8aa94e4f3c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002980.fa
@@ -0,0 +1,11 @@
+>3_1763
+MSASQRQSGSMGEELTNAALIGLIALFLLTLVLRAAGSVAAFLTGAPQPTASWAAGAGVL
+FNPGNPAVALGAPGLSPVAYWVTTIVALGGLVALAGWGWVVWRRRSHAQVVDPHRLAGIA
+TRHEVAQVASEKALLKRASTLRPSLKDPALGEVGYRLGTSKGQGVWASVEDSILLIGPPR
+SGKGLHIVIPAILDAPGPVVTTSTRPDNLTATLRARQRRGPVAVFDPQHLAEGLPAGMRW
+SPVRGCEDSLTAMIRATGLASATGLSAGGVESGGFWEGKTRTALQALLHAAALDSRKPAD
+LFRWTLDPAAAAEAVAILANHPDAAAGWADSLGAMIDADPKTRDSIWQGVALALGALADP
+RVLDAVTPRDNETPFDPETFLRESGTLYLLATGAGAGASAALVAAFIEDLIETARRLAAR
+SPGARLDPPLLLALDEIGNLAPLPSLPTLMAEGGGTGITTLPVLQSLAQARDKWSDHQAG
+AIWDAAIVKLILGGASNSRDLQDLTTLIGERDEYTDSVTLGDHGTRSNQRSVRRVPILPP
+DRIRTLPFGTGVALLRSAPPIITDLTAWPTRPDAEALKRDRARLEQLLQNPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38743ae8a82be07e93361646f59407e2de5d403b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002983.fa
@@ -0,0 +1,10 @@
+>3_1767
+MAGQFCFCGDVGRGIDAGVYEDAGGGLLGCVGGVLFVVDGDAGEQGAVEDASFGWVALVV
+ELVEVDEEFGELVQACSGVGVGVGEVVEPSGDLIEAGADAVLFAFEEVEGDRVGVVSLDE
+FEAFGFELVALGGQELAFVLARSFELIEHVVEDLPDVLRLGLGQGIALVGAFDLRFGAFG
+KDRGAGAVGGLAASSGAGEVLVAVPGLVAGAFDHELGSAGAVQRAFEVVVVLLGSFAAGV
+VGVEVGLDAQPGLGVDEGLVGAVVGDAAEGDGALVVGVGQDLVQSGGGDWFGRLRGGGPG
+GQATGCEFLGQARQGPVPGGVGGERETDEVGAFGVDLDLAGLASSGVGGADVEVAQRRFG
+GGATDRGLLGHAFEDFLGQVQRVELGHGGQDAVHQHPRGGLVDVLSDRHQTDVRIPQRGV
+DHGVIEPVAGEAVDLVDDAVPHRMRGRVVEHLLERASLGGLGGLAGLDELLDDDRTELFG
+LALRGFALGRDRQTLFQPVAGGLILGRDPQVADRRHLPLSPGRCGVWAWCGAGEASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95dc50bef9b56c5b5aad79b9592907ad061f335e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002987.fa
@@ -0,0 +1,3 @@
+>3_1791
+MLFVDAIVVKVRDGQVRNTPFYVVMGVTVHGERDILGIWAGDGAEGARFWLQVFSELKMN
+RPGFVRGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002991.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2b4e9b62d5865aff8665ffbd33845d8e65778f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002991.fa
@@ -0,0 +1,6 @@
+>3_1832
+MTEQTPAPGPGVDSVSTGVHREPFSAVGPWKDDPAAAGQVVFTSVHSGHALRPEVAERMV
+LAEADRFREEDPFTDAIGAGVGSGLVMHRSRFEVDLNRPRATSVYTSPEQSWGLDVWRGG
+RLDEDVAERSRQVHDAWYAELGRRLDVLAGRGPYVVFDVHSYNHRRDGAKAAPAPQEQNP
+DVNVGTGSVDREPWAPVVDGFMDSMARPLVAGLGRRLDVRENVKFWGQNEARWAHRRHPD
+QACVLALEFKKEFMDEWTGQPDAAVVRELSAALADAADAVAQALADVKVPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8783ac8df886793269f38babc3af8d1fbd64f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002995.fa
@@ -0,0 +1,8 @@
+>3_1869
+MEHISGRPLTRRGTLLGLGGAGVAGALGLTGCSSAQTTSAPQTSASPSSSPVAATGIEDL
+AVGQDAVVRASLTTAWLKPDVDRGWTDEPVTQADPRPDEWLPRMDDTLQRGLLGRSDTQA
+ALGSRVTVRELSGDWARVSFLDQAAPNDFGHQTSWVPRAHVVRDLGFLSAQQADGAPIMR
+VTAHSTGVYEGEDMEKTLVVVPLGTRLPLLEEGDEASKVLLPDEREGWIAAADTAVGEPA
+LGTAEQVFETARSFEGTPYLWGGMSRFGIDCSGFTYTVLRAHGILLPRDSGPQLYDSGLP
+RVAADDLTPGDLLFYSHVPGGRRIRHVALYLGKGRGINAPFVGRPVTVETLEQLNAKHDY
+AGAVRPRYAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..281bef7a22b410c203f418ed4ff2ac8aa125cf12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002998.fa
@@ -0,0 +1,13 @@
+>3_1932
+MALTIMSRVPDAQPYRDEDLDGRIGAAGLAGATLEHGLLRFHTHESGSEAARLLAFHFPP
+GFTEGWVPFAVDWRGRQYCRVRQDGVDSAVRADPGLFAASSVVDFEVFMDTVLTDPGAAR
+VLGAEDCAAALAARGISDLPFDQCLGYMLPPFAGGEDHSSNILDVPVNPYWAAMADMKNQ
+WQHRQPGAHAIAVAARDGGLTLVFDTDQDPEHSPGAGTRAERLVVTSPHGPAVYNHGLAR
+ELTDEQAREAAEAVREAFGTPDAAAPFLMDWRARCYAVERVDGRDVVVRSCPVTMTRTPV
+AEADGFRDRLAGNPALLDLFGEAEKSLLCARLRLTEIPAGDVLVPPAPPSVAGPEADDPA
+TFRLQSASVAWWLAGNLARLAREAGPERRLQGYVLTPEGRLGLQTAPADGPTPPPRPSED
+TAGLPPVRFAPRFAALAETGVVQTAQDDDAAPDKDAGDAQMAIAWYGLAGRVYNAGLFRF
+LGAEGVAQAAGHLRESFGGQAAEAVPVIVDWLGRYAVREVVEGQSMLVSYDAASGQREEL
+SRFEDGLEQILVTPVARELFDEAGFRRALDTLGLVRIGQGRCVGVKRPLFLGGDESPENW
+EDDSLDVHWSWHGRVFAQARAMPEGARIQRVEPLEDGRPLIHYTLPDGRTGDGLSGLHDG
+GAPGVSEAAAARQDGSGPKQEKGFFGRMFKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6da60f0128beb189007789281165709ef748c20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002999.fa
@@ -0,0 +1,6 @@
+>3_1933
+MEIYKSHLPVDEGLLVAAGREWKRFPKLLSKDTPKGVKKFLGRRPGVELGENEFSDAHFQ
+FALLLALAGEREALVPLFRGDLLMEEAVKPARSTKMESRRVVNRWCAQRVGLSGWAEVFD
+APPNSEPGPEAHIPRVSFNFGSDKEYAGIAFDEKGDLEGAMKVTPSNYVVAVRMILDGLT
+WLLVARDVPWMNDYGWERERIEREVAWHVGVVRARLGLPLEQAPLTEDPRVDLPVEFTGF
+VSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e1fe5973157b37f5e0a120e216a720a9ed2691a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003006.fa
@@ -0,0 +1,5 @@
+>3_2121
+MDPATISGRALGAVLAVVANAPAMLPRRQPLHPRGRTRRATWRVHAAWPESGIAAFAAAG
+DTPVLARTSRAVGLPEPLPDFTGLALRFADGGALLFASTGTGPFTRRLLAPRVPGAVDPL
+TTLLPLHCRLGAVDVGAQVRGDEVGILTSLDGGPWVDRARVVLGGPADVVVRFDPLRPPV
+GLWWSDFWAAARSPAYALARRLTPGAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dda43b878ad489f224c34681d308f486990227bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003007.fa
@@ -0,0 +1,2 @@
+>3_2122
+MSDQQSPEAKNSDAPGDQDEAMQRQAPAQVDCLAEKAEEEAEQDKGGYDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87d8104d2856d89070be22accfa8a641f2fd2672
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003022.fa
@@ -0,0 +1,4 @@
+>3_2205
+MTDTFPTPLLRRRASRTLALGGTLALAAAMTGCGPDPDYRQTSEDYAQVCRDETTQERVP
+DEDCDDSAGTSHAHAGHRTGWYFIPLAGGRTVPAVGQRAGGGLTTRPGTGTTTKVPSSGG
+EFAKSGTVSRGGFGSKGGGAGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535073b27b4da3814d1cc7aaf0e642c8e174661f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003024.fa
@@ -0,0 +1,4 @@
+>3_2221
+MDHRTAAAASPLPSEPAVAAPVGGSDTPLTRFLRAGEAGDAAAARGALHPDVRLVSPMAG
+GAVMRGPDDVALLLGEVYAVLRGLEWVEHYADGRVHTVLGRARALGVALTDAMLVTVAED
+GRVLEIRPHLRPWAGLTAFSAALLPRLLRHPGLLARSTRPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..209d59caf4b5f2ef1c8a82206b1fecde5647aebd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003025.fa
@@ -0,0 +1,15 @@
+>3_2226
+MSTAQTPREPEHGGLEPTPDQVPERDLREQHAELVERIRAARTAYYQDDAPEISDAEYDR
+LYRALEDLEALHPELASNDSPTQEVGGEASEAFAPVRHGSRMYSLEDLFSLEELETWFLR
+AAGSLAEVRPGRAPRWLVEVKIDGLAVALRYRRGRLVQAATRGDGVTGEDVTRNVMTIAD
+VPQTLTGEGWPEEFEVRGEVFMPSRAFAELNERRAEEGQAPFANPRNAAAGALRQKDPAV
+TAQRPLSMFVHGIGTVEAFGADGQEEVYGMLAGWGLPVSPYTRVVEGADEAALTRVVDVI
+EEYGRRRHELVHEIDGIVLKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTRLLDIAVN
+VGRTGRVTPFAVMEPAQVAGSTVSMATLHNQDVVKAKGVLIGDMVVLRKAGDVIPEVVGP
+VLPVRERLLAQGEDLREFVMPADCPSCGTPLAPAKEGDVDLRCPNARSCPAQVAGRVEHL
+AGRGAFDVEALGEEAARWLVIGHGPDPAEHEGMVLPEGAGPITAEAQLFDLASGTPEEVT
+GPRGEDGLTDLQRSLGDVRVWREGRTKVDGRMVPSGVFSLKPYFFTAGTAKKPAAPTANT
+LRLFDELEKAKTAPLWRVLVGLSIRHVGPAAARSLATAFGSMTALRAAAEAGERDRLAEI
+DGVGPIIADALIEWFAQDWHREIVDRWAAAGVVMEDEQDADTPRTLEGVTVVVTGSLEGF
+SRDSAKEAILVRGGKASGSVSKKTHFLVAGEAAGSKLEKAEQLGVPVLDEAGFVRLLAEG
+PAAFPSEDADAETVDAAAEGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67ff38f9c4c09ef2b9a399361169fc3582446d93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003026.fa
@@ -0,0 +1,2 @@
+>3_2252
+MDRPRRPGLTPTPSPDGAAAEEHGVTGLASHVPSQMTPAILGAADLILAATG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47873785c2f16d571042d13146215f308015d691
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003029.fa
@@ -0,0 +1,4 @@
+>3_2365
+MSDCEPCDLQSVPAMTDTAPALDVDALAADPVEQFHRWIRQVVGSGVPEATTVTFATVDA
+REQPDARTVLRAVRVRGGVRDAPLPEGARMRTVRPERVEFWQGSPEDHRHVRIVYTADDV
+GGFRGEVTRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c660034591423e6299e75b49cb6f960840f3a1c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003030.fa
@@ -0,0 +1,4 @@
+>3_2367
+MTQPAPGPPAPWPASGGPGLAPAPWPGPDWQRAHDQAIVFGILAVTTGMLGLVFGPLALN
+QANRARAIGPDVGVARVLAWIGIGLAALSLLFLLGYFLFFGVMMAEMLRQLSQLSSGGTF
+AALGAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f4726aff4a5ee3620eeccb67346fc6c90a33c0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003031.fa
@@ -0,0 +1,3 @@
+>3_2372
+MTAPYRPQPQHQPQTVVVQQSRNTLIAYLLWFFLGNLGVHRMYTKRWVSGVVQLLLAWGG
+AATAWLLIGWIPLAIWAVWWIVDLFLVPGMVRDANAREAVDSWRTVGVRRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bec3372ebdc66f82568cb79db08d8cbd066db44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003032.fa
@@ -0,0 +1,8 @@
+>3_2423
+MRLRHLSAAMAAAALAASGAAVAHAAPSAHVSASPGARATAVADAHDVRVATYNASLNRG
+TEGELVRDLTTPDDQQAKNIAEVIQTARPEILLVNEFDHDAAGEGARLFQENYLSVGQNG
+HAPIEYRYRYTAPVNTGVPSGLDLDQNGTVGGPNDAWGFGLFPGQYGMVIYSQHPILEDR
+IRTFQDFRWADMPGNVMPEGYYTAKQERQLRLSSKSHWDVPVRIGGTSVHILAAHPTPPS
+FDGPEKRNQRRNHDEIRLWADYITGGKTAEYLYDDAGVHGGLPRGERFVILGDYNADPLD
+GDSWDGAIDQLLQNRRVRDPQPRSAGAAEASVLQGGANRTHRGDPSLDTADFNDVPAPGN
+LRVDMALPSRNLPLRGAGVFWPKQGEPGSELTGTYPFPTSDHRLTWVDVKVPGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0867e3b82bfe7a54048995a6ef29ab11c56bba2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003033.fa
@@ -0,0 +1,2 @@
+>3_2429
+MTVNLVKLHVSQLNGCAPCLRLHPREAAAGGWESGCVSAEAGAALALAEDVTHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a0fc1071899a8088466d9ba5046058fd14c90de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003034.fa
@@ -0,0 +1,3 @@
+>4_74
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9046575fd9fd8d9db3fd063f758d520788293236
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003039.fa
@@ -0,0 +1,5 @@
+>4_154
+MMVFPAKFSELNALELSDEARLILTRIIRVAFPHPDFPDGPYERMAQKIIDASEESRWFR
+MALTQGLVTLDSMSDGHFLELPEDRALAVLKRVADLEFFGFIRRTTVLNLYDDPEVQATL
+GYEGESFSKGGYLHRGFNDLAWLPDPRIEESEEQVTEIGPLPYTVAPATPEGGVKPVPDL
+FKGTGTVDEGSKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc6a1a41bd09e4ca09c3a0fcf3a6e4b2515a77a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003040.fa
@@ -0,0 +1,10 @@
+>4_155
+MSTQEISASIDHEDDSAVVIVGSGAGGGTLAHELVEKGIKVVLLEAGPYLKNEDYEQDEW
+AAFNQMAWLDPRTTSGSFRLARDFPNLPAWIVKAVGGTTTHWSGATPRFKAHEFKARSTY
+GRIDGANLLDWPITLSDLEPYYERAEMKMGSTHRQGRPPLPANNNYKVLANGAERLGYRH
+YATGPYATNAEPYDGRPASIQDGFNFQGDKHGSKWSIMVSEIPKSLRTGLLDLRPESQAV
+QITHSPEGRVDGVLYSDAEGNLHRQKARIVAVAGNAIETPRLLLLSASPLFPDGLANSSG
+QLGRNYMRHTTGSVYAQFDEPVNMYRGETMAGLIADESRHDVDRGFAGGYYMETISLGPA
+FLASFADPGAWGPDFTALLDGYRNTAGLWIVGEDMPQETNRVSLNTTVTDRLGLPVPNVH
+FDDHPNDVAMREHGYQQGSLLYEAVGSVSAHHAPPYPSTHNLGTARMSERPEDGVVNQFG
+QAHDVPNLFISDGSQFTTGAAANPTLTIVALAIRQAEYIADQMAASEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ef3278511115736595630d8a753200a189b9142
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003045.fa
@@ -0,0 +1,7 @@
+>4_490
+MTGVESAHSKVPVRSRKSILLANSDMTYRGGTQAWIRQMASTLQSHHDVDVFSLEGAPLE
+FTAFRPEKYYDIALVNHWTTAQALRGARIHTRITTVHGVIPFEEVPVLGSDAYVSVSEAV
+QNHIPYRSMVIRNPIDFAHFSPDPARLMSPVPRRVAFVSNRQGDALPILREACDRAGLEL
+RVVGRETSVEDPREVYLWADVVVGIARVAMEALACGRNVLCFDYQGCHGMATRERLPTLW
+QSNFGGHRPGVWPTADEVARALLEGYDPRRTLRSALLAEHDPERVARSYLRLAETVGSQR
+VARLVRAAPRQVMSPKITRMVAAIRRRPSEVRLAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..902df559df3de70f0aa7cfc99207bb11f5756a3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003046.fa
@@ -0,0 +1,7 @@
+>4_747
+MSIVIGSLGGIFLWLIYQAIGTRWPEVYATARDSLDLMPRRSSVKYLLIYRGIPTFSVTV
+LALNLAVESGGDPYWTSAFVFWTYSTLAEIRSTFSPKGALRQLSTVNTVYLSASVVVTTI
+YCSVAVLVYPHFSVLVPSVRELVIALWTALFASVLAISFQRFNTRSGPDVQMEIDYSIKD
+IGQKTWSQIDSICMRENIDPCLIKALAAAEAQQRPRWIRQAERVAGRLFGGGTFGVGQWP
+SSRPIDDLTSIEFRAKQLAPVGLTPHECDIAEVYDFLDIDYFIYSWNSDESFADSARGFY
+SAFRRAKMVEHVAESDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c93f7a508adbe2da9c98dbe9b3964dda262ae528
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003049.fa
@@ -0,0 +1,2 @@
+>4_1014
+MDVLSPVFEITTLVVLGVILLLDLLYVARRPHEPSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb1d591d33b483596b192c0d5b9a7b9824d17c0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003052.fa
@@ -0,0 +1,3 @@
+>4_1299
+MCDAHRHPTIIRENASTMKQTYATPAHVGTNARSVTQSRFGAGAVNSRFTRSGCRAAVGS
+GRVVFTRFDLVAPLIPAARMSRPV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..226b167419be537e3ff18c781d1b79817cb13f07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003054.fa
@@ -0,0 +1,6 @@
+>4_1494
+MLTLGSFALFRSGERNKFGPLTMLSAQFVSHNLTVQVMQYAHIHDEINEQLFSSRHLGEL
+LLETLGFSYEDFCAVREAIVRVHGEKFFAIRDFIGEMFEQRDEKKNDLAFEKDARSALMS
+MLELPGEGATLTVQEIVEASGVPADRTQAILDRFGLSFNDAEDALAVVTKFLSGDNPFRS
+ASLVKDADGNYILTGKPIGTDCFRQVVEDALKRVPAKFRRYEKRRMLVVVGHEVLDIRTG
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..647396c5dceb329d1faed293c106ed76c28ef2f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003058.fa
@@ -0,0 +1,2 @@
+>4_1969
+MAHHWRAVTEHPKGARSIQVLTMPLPELVRTLDAHELDHPQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b9e652e68ff34cb5eede38414c72eeaaf3ce48f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003066.fa
@@ -0,0 +1,4 @@
+>4_2150
+MNVPERGEARMRDAIHHAMALPQTALGTHCFVWGEVTTVNHTSAEPPHWFLNVRSGTDRL
+FAFHMSAATAKAVVEAMNHQRGLRWQSLFDAVDAQFMVFGYLKVAKNGVPMVSVKELSHL
+SLRVP